1
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Ciprut S, Berberich A, Knoll M, Pusch S, Hoffmann D, Furkel J, Ward Gahlawat A, Kahlert-Konzelamnn L, Sahm F, Warnken U, Winter M, Schnölzer M, Pusch S, von Deimling A, Abdollahi A, Wick W, Lemke D. AAMP is a binding partner of costimulatory human B7-H3. Neurooncol Adv 2022; 4:vdac098. [PMID: 35919070 PMCID: PMC9341442 DOI: 10.1093/noajnl/vdac098] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 11/18/2022] Open
Abstract
Background Targeted immunotherapies are of growing interest in the treatment of various cancers. B7 homolog 3 protein (B7-H3), a member of the co-stimulatory/-inhibitory B7-family, exerts immunosuppressive and pro-tumorigenic functions in various cancer types and is under evaluation in ongoing clinical trials. Unfortunately, interaction partner(s) remain unknown which restricts the druggability. Methods Aiming to identify potential binding partner(s) of B7-H3, a yeast two-hybrid and a mass spectrometry screen were performed. Potential candidates were evaluated by bimolecular fluorescence complementation (BiFC) assay, co-immunoprecipitation (co-IP), and functionally in a 3H-thymidine proliferation assay of Jurkat cells, a T-cell lineage cell line. Prognostic value of angio-associated migratory cell protein (AAMP) and B7-H3 expression was evaluated in isocitrate dehydrogenase 1 wildtype (IDH1wt) glioblastoma (GBM) patients from The Cancer Genome Atlas (TCGA)-GBM cohort. Results Of the screening candidates, CD164, AAMP, PTPRA, and SLAMF7 could be substantiated via BiFC. AAMP binding could be further confirmed via co-IP and on a functional level. AAMP was ubiquitously expressed in glioma cells, immune cells, and glioma tissue, but did not correlate with glioma grade. Finally, an interaction between AAMP and B7-H3 could be observed on expression level, hinting toward a combined synergistic effect. Conclusions AAMP was identified as a novel interaction partner of B7-H3, opening new possibilities to create a targeted therapy against the pro-tumorigenic costimulatory protein B7-H3.
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Affiliation(s)
- Sara Ciprut
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Department of Neurology, University of Heidelberg Medical School and National Center for Tumor Diseases (NCT) , Heidelberg , Germany
| | - Anne Berberich
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Department of Neurology, University of Heidelberg Medical School and National Center for Tumor Diseases (NCT) , Heidelberg , Germany
| | - Maximilian Knoll
- Clinical Cooperation Unit Translational Radiation Oncology, German Cancer Consortium (DKTK) Core Center Heidelberg, German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Division of Molecular and Translational Radiation Oncology, Department of Radiation Oncology, Heidelberg Faculty of Medicine (MFHD) and Heidelberg University Hospital (UKHD), Heidelberg Ion-Beam Therapy Center (HIT), National Center for Tumor Diseases (NCT) , Heidelberg , Germany
| | - Stefan Pusch
- German Consortium of Translational Cancer Research (DKTK), Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-University Heidelberg , Heidelberg , Germany
| | - Dirk Hoffmann
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Department of Neurology, University of Heidelberg Medical School and National Center for Tumor Diseases (NCT) , Heidelberg , Germany
- Faculty of Biosciences, Heidelberg University , Heidelberg , Germany
| | - Jennifer Furkel
- Clinical Cooperation Unit Translational Radiation Oncology, German Cancer Consortium (DKTK) Core Center Heidelberg, German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Division of Molecular and Translational Radiation Oncology, Department of Radiation Oncology, Heidelberg Faculty of Medicine (MFHD) and Heidelberg University Hospital (UKHD), Heidelberg Ion-Beam Therapy Center (HIT), National Center for Tumor Diseases (NCT) , Heidelberg , Germany
| | - Aoife Ward Gahlawat
- Clinical Cooperation Unit Translational Radiation Oncology, German Cancer Consortium (DKTK) Core Center Heidelberg, German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Division of Molecular and Translational Radiation Oncology, Department of Radiation Oncology, Heidelberg Faculty of Medicine (MFHD) and Heidelberg University Hospital (UKHD), Heidelberg Ion-Beam Therapy Center (HIT), National Center for Tumor Diseases (NCT) , Heidelberg , Germany
| | - Lena Kahlert-Konzelamnn
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Department of Neurology, University of Heidelberg Medical School and National Center for Tumor Diseases (NCT) , Heidelberg , Germany
| | - Felix Sahm
- German Consortium of Translational Cancer Research (DKTK), Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-University Heidelberg , Heidelberg , Germany
| | - Uwe Warnken
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Department of Neurology, University of Heidelberg Medical School and National Center for Tumor Diseases (NCT) , Heidelberg , Germany
| | - Martin Winter
- Department of Functional Proteome Analysis, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Martina Schnölzer
- Department of Functional Proteome Analysis, German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Sonja Pusch
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Department of Neurology, University of Heidelberg Medical School and National Center for Tumor Diseases (NCT) , Heidelberg , Germany
| | - Andreas von Deimling
- German Consortium of Translational Cancer Research (DKTK), Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Department of Neuropathology, Institute of Pathology, Ruprecht-Karls-University Heidelberg , Heidelberg , Germany
| | - Amir Abdollahi
- Clinical Cooperation Unit Translational Radiation Oncology, German Cancer Consortium (DKTK) Core Center Heidelberg, German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Division of Molecular and Translational Radiation Oncology, Department of Radiation Oncology, Heidelberg Faculty of Medicine (MFHD) and Heidelberg University Hospital (UKHD), Heidelberg Ion-Beam Therapy Center (HIT), National Center for Tumor Diseases (NCT) , Heidelberg , Germany
| | - Wolfgang Wick
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Department of Neurology, University of Heidelberg Medical School and National Center for Tumor Diseases (NCT) , Heidelberg , Germany
| | - Dieter Lemke
- Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Department of Neurology, University of Heidelberg Medical School and National Center for Tumor Diseases (NCT) , Heidelberg , Germany
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2
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Ziegler B, Yiallouros I, Trageser B, Kumar S, Mercker M, Kling S, Fath M, Warnken U, Schnölzer M, Holstein TW, Hartl M, Marciniak-Czochra A, Stetefeld J, Stöcker W, Özbek S. The Wnt-specific astacin proteinase HAS-7 restricts head organizer formation in Hydra. BMC Biol 2021; 19:120. [PMID: 34107975 PMCID: PMC8191133 DOI: 10.1186/s12915-021-01046-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 08/19/2020] [Accepted: 05/06/2021] [Indexed: 12/14/2022] Open
Abstract
Background The Hydra head organizer acts as a signaling center that initiates and maintains the primary body axis in steady state polyps and during budding or regeneration. Wnt/beta-Catenin signaling functions as a primary cue controlling this process, but how Wnt ligand activity is locally restricted at the protein level is poorly understood. Here we report a proteomic analysis of Hydra head tissue leading to the identification of an astacin family proteinase as a Wnt processing factor. Results Hydra astacin-7 (HAS-7) is expressed from gland cells as an apical-distal gradient in the body column, peaking close beneath the tentacle zone. HAS-7 siRNA knockdown abrogates HyWnt3 proteolysis in the head tissue and induces a robust double axis phenotype, which is rescued by simultaneous HyWnt3 knockdown. Accordingly, double axes are also observed in conditions of increased Wnt activity as in transgenic actin::HyWnt3 and HyDkk1/2/4 siRNA treated animals. HyWnt3-induced double axes in Xenopus embryos could be rescued by coinjection of HAS-7 mRNA. Mathematical modelling combined with experimental promotor analysis indicate an indirect regulation of HAS-7 by beta-Catenin, expanding the classical Turing-type activator-inhibitor model. Conclusions We show the astacin family protease HAS-7 maintains a single head organizer through proteolysis of HyWnt3. Our data suggest a negative regulatory function of Wnt processing astacin proteinases in the global patterning of the oral-aboral axis in Hydra. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01046-9.
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Affiliation(s)
- Berenice Ziegler
- Centre for Organismal Studies, Department of Molecular Evolution and Genomics, University of Heidelberg, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Irene Yiallouros
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg University Mainz, 55099, Mainz, Germany
| | - Benjamin Trageser
- Centre for Organismal Studies, Department of Molecular Evolution and Genomics, University of Heidelberg, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Sumit Kumar
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Moritz Mercker
- Institute for Applied Mathematics, Interdisciplinary Center for Scientific Computing, Heidelberg University, Im Neuenheimer Feld 205, 69120, Heidelberg, Germany
| | - Svenja Kling
- Centre for Organismal Studies, Department of Molecular Evolution and Genomics, University of Heidelberg, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Maike Fath
- Centre for Organismal Studies, Department of Molecular Evolution and Genomics, University of Heidelberg, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Uwe Warnken
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martina Schnölzer
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas W Holstein
- Centre for Organismal Studies, Department of Molecular Evolution and Genomics, University of Heidelberg, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany
| | - Markus Hartl
- Institute of Biochemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, A-6020, Innsbruck, Austria
| | - Anna Marciniak-Czochra
- Institute for Applied Mathematics, Interdisciplinary Center for Scientific Computing, Heidelberg University, Im Neuenheimer Feld 205, 69120, Heidelberg, Germany
| | - Jörg Stetefeld
- Department of Chemistry, University of Manitoba, 144 Dysart Road, Winnipeg, Manitoba, R3T 2 N2, Canada
| | - Walter Stöcker
- Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg University Mainz, 55099, Mainz, Germany
| | - Suat Özbek
- Centre for Organismal Studies, Department of Molecular Evolution and Genomics, University of Heidelberg, Im Neuenheimer Feld 230, 69120, Heidelberg, Germany.
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3
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Kyuno D, Bauer N, Schnölzer M, Provaznik J, Ryschich E, Hackert T, Zöller M. Distinct Origin of Claudin7 in Early Tumor Endosomes Affects Exosome Assembly. Int J Biol Sci 2019; 15:2224-2239. [PMID: 31592143 PMCID: PMC6775303 DOI: 10.7150/ijbs.35347] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 03/30/2019] [Accepted: 07/11/2019] [Indexed: 12/28/2022] Open
Abstract
Microvesicles are the body's most powerful intercellular communication system and cancer-initiating cell microvesicles (CIC-TEX) reprogram Non-CIC towards fortified malignancy. Claudin7, a CIC-biomarker in gastrointestinal tumors, is recovered in TEX. Recent evidence suggesting individual cells delivering distinct microvesicles became of particular interest for claudin7, which is part of tight junctions (TJ) and glycolipid-enriched membrane domains (GEM), GEM-located claudin7 is palmitoylated. This offered the unique possibility of exploring the contribution of a CIC marker and its origin from distinct membrane domains on CIC-TEX biogenesis and activities. Proteome and miRNA analysis of wild-type, claudin7-knockdown and a rescue with claudin7 harboring a mutated palmitoylation site (mP) of a rat pancreatic and a human colon cancer line uncovered significant, only partly overlapping contributions of palmitoylated and non-palmitoylated claudin7 to TEX composition. Palmitoylated claudin7 facilitates GEM-integrated plasma membrane and associated signaling molecule recruitment; non-palmitoylated claudin7 supports recruitment of trafficking components, proteins engaged in fatty acid metabolism and TJ proteins into TEX. Claudin7mP also assists TEX recovery of selected miRNA. Thus, distinctly located claudin7 affects CIC-TEX composition and TJ-derived cld7 might play a unique role in equipping CIC-TEX with transporters and lipid metabolism-regulating molecules, awareness of distinct TEX populations being crucial facing therapeutic translation.
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Affiliation(s)
- Daisuke Kyuno
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Germany.,Department of Surgery, Surgical Oncology and Science, Sapporo Medical University, Sapporo, Japan
| | - Nathalie Bauer
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Germany
| | | | | | - Eduard Ryschich
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Germany
| | - Thilo Hackert
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Germany
| | - Margot Zöller
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Germany
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4
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Kyuno D, Zhao K, Schnölzer M, Provaznik J, Hackert T, Zöller M. Claudin7-dependent exosome-promoted reprogramming of nonmetastasizing tumor cells. Int J Cancer 2019; 145:2182-2200. [PMID: 30945750 DOI: 10.1002/ijc.32312] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 10/02/2018] [Revised: 03/10/2019] [Accepted: 03/27/2019] [Indexed: 12/17/2022]
Abstract
Claudin7 (cld7) is a cancer-initiating cell (CIC) marker in gastrointestinal tumors, a cld7-knockdown (kd) being accompanied by loss of tumor progression. Tumor exosomes (TEX) restoring CIC activities, we explored the contribution of cld7. This became particularly interesting, as tight junction (TJ)- and glycolipid-enriched membrane domain (GEM)-derived cld7 is recruited into distinct TEX. TEXs were derived from CIC or cld7kd cells of a rat pancreatic and a human colon cancer line. TEX derived from pancreatic cancer cld7kd cells rescued with palmitoylation site-deficient cld7 (cld7mP) allowed selectively evaluating the contribution of GEM-derived TEX, only palmitoylated cld7 being integrated into GEM. Cld7 CIC-TEX promoted tumor cell dissemination and metastatic growth without a major impact on proliferation, apoptosis resistance and epithelial-mesenchymal transition. Instead, migration, invasion and (lymph)angiogenesis were strongly supported, only migration being selectively fostered by GEM-derived cld7 TEX. CIC-TEX coculture of cld7kd cells uncovered significant changes in the cld7kd cell protein and miRNA profiles. However, changes did not correspond to the CIC-TEX profile, CIC-TEX rather initiating integrin, protease and RTK, particularly lymphangiogenic receptor activation. CIC-TEX preferentially rescuing cld7kd-associated defects in signal transduction was backed up by an RTK inhibitor neutralizing the impact of CIC-TEX on tumor progression. In conclusion, cld7 contributes to selective steps of the metastatic cascade. Defects of cld7kd and cld7mP cells in migration, invasion and (lymph)angiogenesis are effaced by CIC-TEX that act by signaling cascade activation. Accordingly, RTK inhibitors are an efficient therapeutic defeating CIC-TEX.
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Affiliation(s)
- Daisuke Kyuno
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany.,Department of Surgery, Surgical Oncology and Science, Sapporo Medical University, Sapporo, Japan
| | - Kun Zhao
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Martina Schnölzer
- Functional Proteome Analysis, German Cancer Research Center, Heidelberg, Germany
| | | | - Thilo Hackert
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Margot Zöller
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
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5
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Katzenmaier EM, Fuchs V, Warnken U, Schnölzer M, Gebert J, Kopitz J. Deciphering the galectin-12 protein interactome reveals a major impact of galectin-12 on glutamine anaplerosis in colon cancer cells. Exp Cell Res 2019; 379:129-139. [PMID: 30935948 DOI: 10.1016/j.yexcr.2019.03.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 03/04/2019] [Revised: 03/22/2019] [Accepted: 03/23/2019] [Indexed: 12/12/2022]
Abstract
Galectins are β-galactoside binding proteins which possess a variety of functions including modulation of apoptosis, growth and differentiation. Hence, alterations in the expression profile have been associated with loss of cellular homeostasis contributing to tumor growth and progression. Though galectin-12 is significantly downregulated in several tumor entities, including colon cancer, its impact on cellular homeostasis as well as galectin-12 specific binding partners have not been identified so far. We therefore established an experimental strategy which is based on reversible cross-link immunoprecipitation to capture the galectin-12 protein interactome in colon cancer cells. By applying this approach, we identified 10 novel candidates of galectin-12 interacting proteins including the neutral amino acid exchanger SLC1A5. Remarkably, we uncovered that binding of galectin-12 to SLC1A5 significantly reduced glutamine uptake in our model cell line. Consequently, utilization of glutamine carbon for biomass synthesis was profoundly affected, suggesting galectin-12 as a novel inhibitor of glutamine anaplerosis in colon cancer cells. More detailed analysis revealed that colon cancer cells can counteract galectin-12 mediated glutamine deprivation by induction of compensatory mechanisms which facilitate adaption to low-glutamine conditions and thus survival.
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Affiliation(s)
- Eva-Maria Katzenmaier
- Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Germany; Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Vera Fuchs
- Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Germany; Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Uwe Warnken
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Martina Schnölzer
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Johannes Gebert
- Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Germany; Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jürgen Kopitz
- Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Germany; Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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6
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Weidmann J, Schnölzer M, Dawson PE, Hoheisel JD. Copying Life: Synthesis of an Enzymatically Active Mirror-Image DNA-Ligase Made of D-Amino Acids. Cell Chem Biol 2019; 26:645-651.e3. [PMID: 30880154 DOI: 10.1016/j.chembiol.2019.02.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 11/27/2018] [Accepted: 02/07/2019] [Indexed: 11/17/2022]
Abstract
Our objective is the creation of a mirror-image synthetic biology: that is, to mimic, entirely independent of Nature, a biological system and to re-create it from artificial component parts. Utilizing enantiomeric L-nucleotides and D-amino acids rather than the natural components, we use chemical synthesis toward a basic, self-replicating mirror-image biological system. Here, we report the synthesis of a functional DNA-ligase in the D-enantiomeric conformation, which is an exact mirror-image of the natural enzyme, exhibiting DNA ligation activity on chirally inverted nucleic acids in L-conformation, but not acting on natural substrates and with natural co-factors. Starting from the known structure of the Paramecium bursaria chlorella virus 1 DNA-ligase and the homologous but shorter DNA-ligase of Haemophilus influenza, we designed and synthesized chemically peptides, which could then be assembled into a full-length molecule yielding a functional protein. The structure and the activity of the mirror-image ligase were characterized, documenting its enantiospecific functionality.
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Affiliation(s)
- Joachim Weidmann
- Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany; Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Martina Schnölzer
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120 Heidelberg, Germany
| | - Philip E Dawson
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Jörg D Hoheisel
- Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany.
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7
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Winter M, Mayer R, Warnken U, Debus J, Abdollahi A, Schnölzer M. Synthetic phosphopeptides: From spike-in standards to affinity tools for protein-protein interaction studies. Anal Biochem 2019; 568:73-77. [PMID: 30597127 DOI: 10.1016/j.ab.2018.12.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 10/17/2017] [Revised: 12/04/2018] [Accepted: 12/21/2018] [Indexed: 11/27/2022]
Abstract
Synthetic isotope labeled phosphopeptides are valuable tools for the quantification and validation of phosphoproteome data. Here, we report that the same set of phosphopeptides, which are used as spike-in standards, can be successfully applied for identification of stimulus specific protein-protein interactions mediated by the respective phosphorylation sites. As a proof-of-concept, binding of two γH2AX (pS139) phosphosite specific interaction partners, MDC1 and 53BP1, was confirmed and elevated binding affinity was revealed in response to ionizing radiation. Our strategy is generally applicable and enables multiplexed validation and functional analysis of phosphorylation sites offering great potential for the follow-up of phosphoproteome studies.
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Affiliation(s)
- Martin Winter
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120, Heidelberg, Germany; Translational Radiation Oncology, National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 460, D-69120, Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Ramona Mayer
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120, Heidelberg, Germany
| | - Uwe Warnken
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120, Heidelberg, Germany
| | - Jürgen Debus
- Translational Radiation Oncology, National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 460, D-69120, Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany; Heidelberg Ion Beam Therapy Center (HIT), Department of Radiation Oncology, University of Heidelberg Medical School, Im Neuenheimer Feld 450, D-69120, Heidelberg, Germany; Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), Heidelberg, Germany
| | - Amir Abdollahi
- Translational Radiation Oncology, National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 460, D-69120, Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany; Heidelberg Ion Beam Therapy Center (HIT), Department of Radiation Oncology, University of Heidelberg Medical School, Im Neuenheimer Feld 450, D-69120, Heidelberg, Germany; Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), Heidelberg, Germany
| | - Martina Schnölzer
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120, Heidelberg, Germany.
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8
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Zhou C, Moustafa MR, Cao L, Kriegsmann M, Winter M, Schwager C, Jones B, Wang S, Bäuerle T, Zhou PK, Schnölzer M, Weichert W, Debus J, Abdollahi A. Modeling and multiscale characterization of the quantitative imaging based fibrosis index reveals pathophysiological, transcriptome and proteomic correlates of lung fibrosis induced by fractionated irradiation. Int J Cancer 2019; 144:3160-3173. [PMID: 30536712 PMCID: PMC6590477 DOI: 10.1002/ijc.32059] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 12/29/2017] [Revised: 11/15/2018] [Accepted: 11/21/2018] [Indexed: 12/24/2022]
Abstract
Pulmonary fibrosis represents a leading cause of morbidity and mortality worldwide. Therapy induced lung fibrosis constitutes a pivotal dose‐limiting side effect of radiotherapy and other anticancer agents. We aimed to develop objective criteria for assessment of fibrosis and discover pathophysiological and molecular correlates of lung fibrosis as a function of fractionated whole thoracic irradiation. Dose–response series of fractionated irradiation was utilized to develop a non‐invasive and quantitative measure for the degree of fibrosis – the fibrosis index (FI). The correlation of FI with histopathology, blood‐gas, transcriptome and proteome responses of the lung tissue was analyzed. Macrophages infiltration and polarization was assessed by immunohistochemistry. Fibrosis development followed a slow kinetic with maximum lung fibrosis levels detected at 24‐week post radiation insult. FI favorably correlated with radiation dose and surrogates of lung fibrosis i.e., enhanced pro‐inflammatory response, tissue remodeling and extracellular matrix deposition. The loss of lung architecture correlated with decreased epithelial marker, loss of microvascular integrity with decreased endothelial and elevated mesenchymal markers. Lung fibrosis was further attributed to a switch of the inflammatory state toward a macrophage/T‐helper cell type 2‐like (M2/Th2) polarized phenotype. Together, the multiscale characterization of FI in radiation‐induced lung fibrosis (RILF) model identified pathophysiological, transcriptional and proteomic correlates of fibrosis. Pathological immune response and endothelial/epithelial to mesenchymal transition were discovered as critical events governing lung tissue remodeling. FI will be instrumental for deciphering the molecular mechanisms governing lung fibrosis and discovery of novel targets for treatment of this devastating disease with an unmet medical need. What's new? The development of fibrosis scar tissue in the lungs is a dose‐limiting effect of radiotherapy for thoracic malignancies. Molecular mechanisms driving radiation‐induced lung fibrosis (RILF), however, remain unclear. In this study, a fibrosis index (FI) was devised to quantitatively detect spatial and temporal kinetics of lung fibrosis development. Multi‐scale characterization of FI uncovered mechanisms governing lung fibrosis, including perturbation of immune balance and microvascular integrity. Radiation dose and FI were correlated with an inflammatory switch toward a macrophage/T‐helper cell type 2‐like polarized phenotype. The findings open the way for further mechanistic study and the discovery of therapeutic targets for RILF.
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Affiliation(s)
- Cheng Zhou
- Translational Radiation Oncology, German Cancer Consortium (DKTK), National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Heidelberg Ion-Beam Therapy Centre (HIT), Department of Radiation Oncology, Heidelberg University Hospital (UKHD), Heidelberg, Germany.,Division of Molecular and Translational Radiation Oncology, Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation research in Oncology (NCRO), Heidelberg, Germany.,Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Mahmoud R Moustafa
- Translational Radiation Oncology, German Cancer Consortium (DKTK), National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Heidelberg Ion-Beam Therapy Centre (HIT), Department of Radiation Oncology, Heidelberg University Hospital (UKHD), Heidelberg, Germany.,Division of Molecular and Translational Radiation Oncology, Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation research in Oncology (NCRO), Heidelberg, Germany.,Department of Clinical Pathology, Suez Canal University, Ismailia, Egypt
| | - Liji Cao
- Division of Medical Physics in Radiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mark Kriegsmann
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Martin Winter
- Division of Molecular and Translational Radiation Oncology, Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation research in Oncology (NCRO), Heidelberg, Germany.,Department of Functional Proteome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christian Schwager
- Translational Radiation Oncology, German Cancer Consortium (DKTK), National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Heidelberg Ion-Beam Therapy Centre (HIT), Department of Radiation Oncology, Heidelberg University Hospital (UKHD), Heidelberg, Germany.,Division of Molecular and Translational Radiation Oncology, Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation research in Oncology (NCRO), Heidelberg, Germany
| | - Bleddyn Jones
- Gray Laboratory, CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, United Kingdom
| | - Shijun Wang
- Department of Pediatric Nephrology, Gastroenterology & Metabolic Diseases, Hannover Medical School, Hannover, Germany
| | - Tobias Bäuerle
- Institute of Radiology, University Hospital Erlangen, Erlangen, Germany
| | - Ping-Kun Zhou
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, China
| | - Martina Schnölzer
- Division of Molecular and Translational Radiation Oncology, Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation research in Oncology (NCRO), Heidelberg, Germany.,Department of Functional Proteome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Wilko Weichert
- Institute of Pathology, Technical University of Munich (TUM), Munich, Germany
| | - Juergen Debus
- Translational Radiation Oncology, German Cancer Consortium (DKTK), National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Heidelberg Ion-Beam Therapy Centre (HIT), Department of Radiation Oncology, Heidelberg University Hospital (UKHD), Heidelberg, Germany.,Division of Molecular and Translational Radiation Oncology, Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation research in Oncology (NCRO), Heidelberg, Germany
| | - Amir Abdollahi
- Translational Radiation Oncology, German Cancer Consortium (DKTK), National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Heidelberg Ion-Beam Therapy Centre (HIT), Department of Radiation Oncology, Heidelberg University Hospital (UKHD), Heidelberg, Germany.,Division of Molecular and Translational Radiation Oncology, Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation research in Oncology (NCRO), Heidelberg, Germany
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9
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Schenk C, Meyrath M, Warnken U, Schnölzer M, Mier W, Harak C, Lohmann V. Characterization of a Threonine-Rich Cluster in Hepatitis C Virus Nonstructural Protein 5A and Its Contribution to Hyperphosphorylation. J Virol 2018; 92:JVI.00737-18. [PMID: 30258001 PMCID: PMC6258934 DOI: 10.1128/jvi.00737-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 04/30/2018] [Accepted: 09/20/2018] [Indexed: 12/13/2022] Open
Abstract
Hepatitis C virus (HCV) nonstructural protein 5A (NS5A) is a phosphoprotein with key functions in regulating viral RNA replication and assembly. Two phosphoisoforms are discriminated by their different apparent molecular weights: a basally phosphorylated (p56) and a hyperphosphorylated (p58) variant. The precise mechanisms governing p58 synthesis and specific functions of the isoforms are poorly understood. Our study aimed at a deeper understanding of determinants involved in p58 synthesis. We analyzed two variants of p56 and p58 of isolate JFH-1 separately by mass spectrometry using an expression model and thereby identified a threonine-rich phosphopeptide exclusively found in the hyperphosphorylated variant. Individual exchange of possible phosphoacceptor sites to phosphoablatant or -mimetic residues had little impact on HCV replication or assembly in cell culture. A phosphospecific antibody recognizing pT242 revealed that this position was indeed phosphorylated only in p58 and depended on casein kinase Iα. Importantly, phosphoablative mutations at positions T244 and S247 abrogated pT242 detection without substantial effects on global p58 levels, whereas mutations in the preceding serine-rich cluster dramatically reduced total p58 levels but had minor impact on pT242 levels, suggesting the existence of distinct subspecies of hyperphosphorylated NS5A. Mass spectrometry analyses of different genotypes showed variable phosphorylation patterns across NS5A and suggested that the threonine-rich region is also phosphorylated at T242 in gt4a and at S249 in gt1a, gt1b, and gt4a. Our data therefore indicate that p58 is not a single homogenously phosphorylated protein species but rather a population of various phosphoisoforms, with high variability between genotypes.IMPORTANCE Hepatitis C virus infections affect 71 million people worldwide and cause severe chronic liver disease. Recently, efficient antiviral therapies have been established, with inhibitors of nonstructural protein NS5A as a cornerstone. NS5A is a central regulator of HCV replication and assembly but is still enigmatic in its molecular functions. It exists in two phosphoisoforms, p56 and p58. We identified a phosphopeptide exclusively found in p58 and analyzed the determinants involved in phosphorylation of this region. We found evidence for very different phosphorylation patterns resulting in p58. These results challenge the concept of p58 being a homogenous species of NS5A molecules phosphorylated at the same positions and argues for at least two independently phosphorylated variants showing the same electrophoretic mobility, likely serving different functions.
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Affiliation(s)
- Christian Schenk
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Max Meyrath
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Uwe Warnken
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martina Schnölzer
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Walter Mier
- Department of Nuclear Medicine, Heidelberg University Hospital, Heidelberg, Germany
| | - Christian Harak
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
| | - Volker Lohmann
- Department of Infectious Diseases, Molecular Virology, University of Heidelberg, Heidelberg, Germany
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10
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Michalak M, Warnken U, Schnölzer M, Gabius HJ, Kopitz J. Detection of malignancy-associated phosphoproteome changes in human colorectal cancer induced by cell surface binding of growth-inhibitory galectin-4. IUBMB Life 2018; 71:364-375. [PMID: 30550624 DOI: 10.1002/iub.1987] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [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: 10/19/2018] [Revised: 11/21/2018] [Accepted: 11/21/2018] [Indexed: 01/28/2023]
Abstract
Emerging evidence on efficient tumor growth regulation by endogenous lectins directs interest to determine on a proof-of-principle level the range of information on alterations provided by full-scale analysis using phosphoproteomics. In our pilot study, we tested galectin-4 (gal-4) that is a growth inhibitor for colon cancer cells (CRC), here working with the LS 180 line. In order to cover monitoring of short- and long-term effects stable isotope labeling by amino acids in cell culture-based quantitative phosphoproteomic analyses were conducted on LS 180 cell preparations collected 1 and 72 h after adding gal-4 to the culture medium. After short-term treatment, 981 phosphosites, all of them S/T based, were detected by phosphoproteomics. Changes higher than 1.5-fold were seen for eight sites in seven proteins. Most affected were the BET1 homolog (BET1), whose level of phosphorylation at S50 was about threefold reduced, and centromere protein F (CENPF), extent of phosphorylation at S3119 doubling in gal-4-treated cells. Phosphoproteome analysis after 72 h of treatment revealed marked changes at 33 S/T-based phosphosites from 29 proteins. Prominent increase of phosphorylation was observed for cofilin-1 at position S3. Extent of phosphorylation of the glutamine transporter SLC1A5 at position S503 was decreased by a factor of 3. Altered phosphorylation of BET1, CENPF, and cofilin-1 as well as a significant effect of gal-4 treatment on glutamine uptake by cells were substantiated by independent methods in the Vaco 432, Colo 205, CX 1, and HCT 116 cell lines. With the example of gal-4 which functions as a tumor suppressor in CRC cells, we were able to prove that cell surface binding of the lectin not only markedly influences the cell proteome, but also has a bearing on malignancy-associated intracellular protein phosphorylation. These results underscore the potential of this approach to give further work on elucidating the details of signaling underlying galectin-triggered growth inhibition a clear direction. © 2018 IUBMB Life, 71(3):364-375, 2019.
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Affiliation(s)
- Malwina Michalak
- Department of Applied Tumor Biology, Institute of Pathology, Medical School of the Ruprecht-Karls-University, Heidelberg, Germany.,Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Uwe Warnken
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martina Schnölzer
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hans-Joachim Gabius
- Faculty of Veterinary Medicine, Institute of Physiological Chemistry, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Jürgen Kopitz
- Department of Applied Tumor Biology, Institute of Pathology, Medical School of the Ruprecht-Karls-University, Heidelberg, Germany.,Clinical Cooperation Unit Applied Tumor Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany
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11
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Canet-Pons J, Schubert R, Duecker RP, Schrewe R, Wölke S, Kieslich M, Schnölzer M, Chiocchetti A, Auburger G, Zielen S, Warnken U. Ataxia telangiectasia alters the ApoB and reelin pathway. Neurogenetics 2018; 19:237-255. [DOI: 10.1007/s10048-018-0557-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 10/09/2018] [Indexed: 02/07/2023]
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12
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Phillips EL, Bethke F, Balss J, Pusch S, Christen S, Schnölzer M, Habel A, Capper D, Deimling AV, Fendt SM, Lichter P, Goidts V. Abstract 1906: PFKFB4, much more than just a glycolytic gene. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-1906] [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
Glioblastoma is one of the most aggressive primary brain tumors in adults, with a dismal median overall survival of only 14 months after diagnosis. Glioblastoma stem-like cells (GSCs) are particularly resistant to current therapies, capable of self-renewal and tumour initiation and are hence thought to be major contributors to patient relapse. A kinome and phosphatome wide screen revealed glycolysis gene 6-Phosphofructo-2-Kinase/Fructose-2,6-Biphosphatase 4 (PFKFB4) as an important candidate gene for GSC survival. Notably, silencing PFKFB4 in an orthotopic xenograft mouse model of glioblastoma completely rid the mice of the tumor. Here we show a brand new function of PFKFB4, independent of its role in glycolysis - namely in the regulation of HIF1α, which is upregulated in GSCs. Gene expression profiling revealed a downregulation in HIF1α target genes in PFKFB4-silenced GSCs, and HIF1α protein levels are also dramatically reduced upon silencing. Mass spectrometric analysis of immunoprecipitated PFKFB4 protein revealed a novel interaction partner, F-box only protein 28 (FBXO28), an E3 ubiqutin ligase. Co-immunoprecipation assays show that FBXO28 forms an SCF multi-protein ubiquitin ligase complex with CUL1 and SKP1. Ubiquitylation studies of HIF1α show that PFKFB4 stabilizes this crucial protein in GSCs by preventing its targeting by FBXO28 for proteasomal degradation. These new findings, coupled with its cancer specific expression in a variety of tumor entities, makes PFKFB4 a compelling target.
Citation Format: Emma L. Phillips, Frederic Bethke, Jörg Balss, Stefan Pusch, Stefan Christen, Martina Schnölzer, Antje Habel, David Capper, Andreas Von Deimling, Sarah-Maria Fendt, Peter Lichter, Violaine Goidts. PFKFB4, much more than just a glycolytic gene [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 1906.
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13
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Ecker J, Thatikonda V, Oehme I, Valinciute G, Selt F, Buhl JL, Usta D, Tilburg CMV, Herold-Mende C, Schnölzer M, Warnken U, Kool M, Jäger N, Pfister SM, Witt O, Milde T. MBRS-12. INTERFERENCE WITH THE FUNCTION OF MYC IN GROUP 3 MEDULLOBLASTOMA. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy059.457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Jonas Ecker
- Clinical Cooperation Unit Pediatric Oncology, Pre-Clinical Program, Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- KiTZ Clinical Trial Unit (ZIPO), Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
| | - Venu Thatikonda
- Division of Pediatric Neurooncology, Pre-Clinical Program, Hopp Children’s Cancer Center at the NCT (KiTZ), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Ina Oehme
- Clinical Cooperation Unit Pediatric Oncology, Pre-Clinical Program, Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Gintvile Valinciute
- Clinical Cooperation Unit Pediatric Oncology, Pre-Clinical Program, Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Florian Selt
- Clinical Cooperation Unit Pediatric Oncology, Pre-Clinical Program, Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- KiTZ Clinical Trial Unit (ZIPO), Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
| | - Juliane L Buhl
- Clinical Cooperation Unit Pediatric Oncology, Pre-Clinical Program, Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Diren Usta
- Clinical Cooperation Unit Pediatric Oncology, Pre-Clinical Program, Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Cornelis M van Tilburg
- KiTZ Clinical Trial Unit (ZIPO), Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
| | | | - Martina Schnölzer
- Functional Proteome Analysis (B100), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Uwe Warnken
- Functional Proteome Analysis (B100), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marcel Kool
- Division of Pediatric Neurooncology, Pre-Clinical Program, Hopp Children’s Cancer Center at the NCT (KiTZ), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Natalie Jäger
- Division of Pediatric Neurooncology, Pre-Clinical Program, Hopp Children’s Cancer Center at the NCT (KiTZ), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Stefan M Pfister
- KiTZ Clinical Trial Unit (ZIPO), Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, Pre-Clinical Program, Hopp Children’s Cancer Center at the NCT (KiTZ), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Olaf Witt
- Clinical Cooperation Unit Pediatric Oncology, Pre-Clinical Program, Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- KiTZ Clinical Trial Unit (ZIPO), Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
| | - Till Milde
- Clinical Cooperation Unit Pediatric Oncology, Pre-Clinical Program, Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
- KiTZ Clinical Trial Unit (ZIPO), Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Hopp Children’s Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
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14
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Zöller M, Zhao K, Kutlu N, Bauer N, Provaznik J, Hackert T, Schnölzer M. Immunoregulatory Effects of Myeloid-Derived Suppressor Cell Exosomes in Mouse Model of Autoimmune Alopecia Areata. Front Immunol 2018; 9:1279. [PMID: 29951053 PMCID: PMC6008552 DOI: 10.3389/fimmu.2018.01279] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Accepted: 05/22/2018] [Indexed: 01/28/2023] Open
Abstract
The treatment of autoimmune diseases still poses a major challenge, frequently relying on non-specific immunosuppressive drugs. Current efforts aim at reestablishing self tolerance using immune cells with suppressive activity like the regulatory T cells (Treg) or the myeloid-derived suppressor cells (MDSC). We have demonstrated therapeutic efficacy of MDSC in mouse Alopecia Areata (AA). In the same AA model, we now asked whether MDSC exosomes (MDSC-Exo) can replace MDSC. MDSC-Exo from bone marrow cells (BMC) cultures of healthy donors could substantially facilitate treatment. With knowledge on MDSC-Exo being limited, their suitability needs to be verified in advance. Protein marker profiles suggest comparability of BMC- to ex vivo collected inflammatory MDSC/MDSC-Exo in mice with a chronic contact dermatitis, which is a therapeutic option in AA. Proteome analyses substantiated a large overlap of function-relevant molecules in MDSC and MDSC-Exo. Furthermore, MDSC-Exo are taken up by T cells, macrophages, NK, and most avidly by Treg and MDSC-Exo uptake exceeds binding of MDSC themselves. In AA mice, MDSC-Exo preferentially target skin-draining lymph nodes and cells in the vicinity of remnant hair follicles. MDSC-Exo uptake is accompanied by a strong increase in Treg, reduced T helper proliferation, mitigated cytotoxic activity, and a slight increase in lymphocyte apoptosis. Repeated MDSC-Exo application in florid AA prevented progression and sufficed for partial hair regrowth. Deep sequencing of lymphocyte mRNA from these mice revealed a significant increase in immunoregulatory mRNA, including FoxP3 and arginase 1. Downregulated mRNA was preferentially engaged in prohibiting T cell hyperreactivity. Taken together, proteome analysis provided important insights into potential MDSC-Exo activities, these Exo preferentially homing into AA-affected organs. Most importantly, changes in leukocyte mRNA seen after treatment of AA mice with MDSC-Exo sustainably supports the strong impact on the adaptive and the non-adaptive immune system, with Treg expansion being a dominant feature. Thus, MDSC-Exo could potentially serve as therapeutic agents in treating AA and other autoimmune diseases.
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Affiliation(s)
- Margot Zöller
- Tumor Cell Biology, Department of Surgery, University Hospital of Heidelberg, Heidelberg, Germany
| | - Kun Zhao
- Tumor Cell Biology, Department of Surgery, University Hospital of Heidelberg, Heidelberg, Germany
| | - Natalia Kutlu
- Tumor Cell Biology, Department of Surgery, University Hospital of Heidelberg, Heidelberg, Germany
| | - Nathalie Bauer
- Tumor Cell Biology, Department of Surgery, University Hospital of Heidelberg, Heidelberg, Germany
| | - Jan Provaznik
- Gene Core Unit, EMBL Heidelberg, Heidelberg, Germany
| | - Thilo Hackert
- Pancreas Section, Department of Surgery, University Hospital of Heidelberg, Heidelberg, Germany
| | - Martina Schnölzer
- Functional Proteome Analysis, German Cancer Research Center, Heidelberg, Germany
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15
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Hashani M, Witzel HR, Pawella LM, Lehmann-Koch J, Schumacher J, Mechtersheimer G, Schnölzer M, Schirmacher P, Roth W, Straub BK. Widespread expression of perilipin 5 in normal human tissues and in diseases is restricted to distinct lipid droplet subpopulations. Cell Tissue Res 2018; 374:121-136. [PMID: 29752569 DOI: 10.1007/s00441-018-2845-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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: 12/04/2017] [Accepted: 04/18/2018] [Indexed: 12/18/2022]
Abstract
Diseases associated with the accumulation of lipid droplets are increasing in western countries. Lipid droplet biogenesis, structure and degradation are regulated by proteins of the perilipin family. Perilipin 5 has been shown to regulate basal lipolysis in oxidative tissues. We examine perilipin 5 in normal human tissues and in diseases using protein biochemical and microscopic techniques. Perilipin 5 was constitutively located at small lipid droplets in skeletal myocytes, cardiomyocytes and brown adipocytes. In addition, perilipin 5 was detected in the epithelia of the gastrointestinal and urogenital tract, especially in hepatocytes, the mitochondria-rich parietal cells of the stomach, tubular kidney cells and ductal cells of the salivary gland and pancreas. Granular cytoplasmic expression, without a lipid droplet-bound localization was detected elsewhere. In cardiomyopathies, in skeletal muscle diseases and during hepatocyte steatogenesis, perilipin 5 was upregulated and localized to larger and more numerous lipid droplets. In steatotic human hepatocytes, perilipin 5 was moderately increased and colocalized with perilipins 1 and 2 but not with perilipin 3 at lipid droplets. In liver diseases implicated in alterations of mitochondria, such as mitochondriopathies, alcoholic liver disease, Wilson's disease and acute liver injury, perilipin 5 was frequently localized to small lipid droplets and less in the cytoplasm. In tumorigenesis, perilipin 5 was especially upregulated in lipo-, leio- and rhabdomyosarcoma and hepatocellular and renal cell carcinoma. In summary, our study provides evidence that perilipin 5 is not restricted to certain cell types but localizes to distinct lipid droplet subpopulations reflecting a possible function in oxidative energy supply in normal tissues and in diseases.
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Affiliation(s)
- Merita Hashani
- Department of General Pathology, Institute of Pathology, University Hospital, Heidelberg, Germany.,Institute of Pathology, University Hospital of Prishtina, Prishtina, Kosovo
| | - Hagen Roland Witzel
- Institute of Pathology, University Medicine, Johannes Gutenberg-University Mainz, Langenbeckstr. 1, 55131, Mainz, Germany
| | - Lena Maria Pawella
- Department of General Pathology, Institute of Pathology, University Hospital, Heidelberg, Germany
| | - Judith Lehmann-Koch
- Department of General Pathology, Institute of Pathology, University Hospital, Heidelberg, Germany
| | - Jens Schumacher
- Department of Internal Medicine III, Division of Translational and Experimental Oncology, University Hospital Mainz, Mainz, Germany
| | - Gunhild Mechtersheimer
- Department of General Pathology, Institute of Pathology, University Hospital, Heidelberg, Germany
| | - Martina Schnölzer
- Functional Proteome Analysis, German Cancer Research Center Heidelberg (DKFZ), INF 580, Heidelberg, Germany
| | - Peter Schirmacher
- Department of General Pathology, Institute of Pathology, University Hospital, Heidelberg, Germany
| | - Wilfried Roth
- Institute of Pathology, University Medicine, Johannes Gutenberg-University Mainz, Langenbeckstr. 1, 55131, Mainz, Germany
| | - Beate Katharina Straub
- Department of General Pathology, Institute of Pathology, University Hospital, Heidelberg, Germany. .,Institute of Pathology, University Medicine, Johannes Gutenberg-University Mainz, Langenbeckstr. 1, 55131, Mainz, Germany.
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16
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Dettling S, Stamova S, Warta R, Schnölzer M, Rapp C, Rathinasamy A, Reuss D, Pocha K, Roesch S, Jungk C, Warnken U, Eckstein V, Grabe N, Schramm C, Weigand MA, von Deimling A, Unterberg A, Beckhove P, Herold-Mende C. Identification of CRKII, CFL1, CNTN1, NME2, and TKT as Novel and Frequent T-Cell Targets in Human IDH-Mutant Glioma. Clin Cancer Res 2018; 24:2951-2962. [PMID: 29563135 DOI: 10.1158/1078-0432.ccr-17-1839] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 11/23/2017] [Accepted: 03/15/2018] [Indexed: 11/16/2022]
Abstract
Purpose: Successful immunotherapies for IDHmut gliomas require better knowledge of T-cell target antigens. Here, we elucidated their antigen repertoire recognized by spontaneous T-cell responses using an unbiased proteomic approach.Experimental Design: Protein fractionations of tissue lysates from IDHmut gliomas (n = 4) were performed. Fractions were tested by IFNγ ELISpot assay for recognition through patients' T cells. Proteins of immunogenic fractions were identified by mass spectrometry and validated by in silico-predicted synthetic long peptides in patients of origin, additional IDHmut glioma patients (n = 16), and healthy donors (n = 13). mRNA and protein expression of immunogenic antigens was analyzed in tumor tissues and IDHmut glioma stem-like cells (GSC). HLA-A*02-restricted T-cell epitopes were functionally determined by short peptides and numbers of antigen-specific T cells by HLA-peptide tetramer analysis.Results: A total of 2,897 proteins were identified in immunogenic tumor fractions. Based on a thorough filter process, 79 proteins were selected as potential T-cell antigens. Twenty-six of these were recognized by the patients' T cells, and five of them (CRKII, CFL1, CNTN1, NME2, and TKT) in up to 56% unrelated IDHmut glioma patients. Most immunogenic tumor-associated antigens (TAA) were expressed in IDHmut gliomas and GSCs, while being almost absent in normal brain tissues. Finally, we identified HLA-A*02-restricted epitopes for CRKII, NME2, and TKT that were recognized by up to 2.82% of antigen-specific peripheral cytotoxic T cells in IDHmut glioma patients.Conclusions: By analyzing the repertoire of T-cell target antigens in IDHmut glioma patients, we identified five novel immunogenic TAAs and confirmed their expression on IDHmut tumors and GSCs. Clin Cancer Res; 24(12); 2951-62. ©2018 AACR.
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Affiliation(s)
- Steffen Dettling
- Division of Experimental Neurosurgery, Department of Neurosurgery, University Hospital of Heidelberg, Heidelberg, Germany
| | - Slava Stamova
- Regensburg Center for Interventional Immunology (RCI) and University Medical Center of Regensburg, Regensburg, Germany
| | - Rolf Warta
- Division of Experimental Neurosurgery, Department of Neurosurgery, University Hospital of Heidelberg, Heidelberg, Germany
| | - Martina Schnölzer
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carmen Rapp
- Division of Experimental Neurosurgery, Department of Neurosurgery, University Hospital of Heidelberg, Heidelberg, Germany
| | - Anchana Rathinasamy
- Regensburg Center for Interventional Immunology (RCI) and University Medical Center of Regensburg, Regensburg, Germany
| | - David Reuss
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,German Cancer Consortium (DKTK), CCU Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kolja Pocha
- Division of Experimental Neurosurgery, Department of Neurosurgery, University Hospital of Heidelberg, Heidelberg, Germany
| | - Saskia Roesch
- Division of Experimental Neurosurgery, Department of Neurosurgery, University Hospital of Heidelberg, Heidelberg, Germany
| | - Christine Jungk
- Division of Experimental Neurosurgery, Department of Neurosurgery, University Hospital of Heidelberg, Heidelberg, Germany
| | - Uwe Warnken
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Volker Eckstein
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Niels Grabe
- Hamamatsu Tissue Imaging and Analysis Center (TIGA), BIOQUANT, University of Heidelberg, Heidelberg, Germany
| | - Christoph Schramm
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Markus A Weigand
- Department of Anesthesiology, Heidelberg University Hospital, Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany.,German Cancer Consortium (DKTK), CCU Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andreas Unterberg
- Division of Experimental Neurosurgery, Department of Neurosurgery, University Hospital of Heidelberg, Heidelberg, Germany
| | - Philipp Beckhove
- Regensburg Center for Interventional Immunology (RCI) and University Medical Center of Regensburg, Regensburg, Germany
| | - Christel Herold-Mende
- Division of Experimental Neurosurgery, Department of Neurosurgery, University Hospital of Heidelberg, Heidelberg, Germany.
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17
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Wang Z, von Au A, Schnölzer M, Hackert T, Zöller M. CD44v6-competent tumor exosomes promote motility, invasion and cancer-initiating cell marker expression in pancreatic and colorectal cancer cells. Oncotarget 2018; 7:55409-55436. [PMID: 27419629 PMCID: PMC5342426 DOI: 10.18632/oncotarget.10580] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [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: 05/14/2016] [Accepted: 07/01/2016] [Indexed: 12/21/2022] Open
Abstract
Cancer-initiating cells (CIC) account for metastatic spread, which may rely mostly on CIC exosomes (TEX) that affect host cells and can transfer CIC features into Non-CIC. The CIC marker CD44 variant isoform v6 (CD44v6) being known for metastasis-promotion, we elaborated in cells its contribution to migration and invasion and in TEX the tranfer of migratory and invasive capacity to Non-CIC, using a CD44v6 knockdown (CD44v6kd) as Non-CIC model.A CD44v6kd in human pancreatic and colorectal cancer (PaCa, CoCa) lines led to loss of CIC characteristics including downregulation of additional CIC markers, particularly Tspan8. This aggravated the loss of CD44v6-promoted motility and invasion. Loss of motility relies on the distorted cooperation of CD44v6 and Tspan8 with associated integrins and loss of invasiveness on reduced protease expression. These deficits, transferred into TEX, severely altered the CD44v6kd-TEX composition. As a consequence, unlike the CIC-TEX, CD44v6kd TEX were not taken up by CD44v6kd cells and CIC. The uptake of CIC-TEX was accompanied by partial correction of CIC marker and protease expression in CD44v6kd cells, which regained migratory, invasive and metastatic competence. CIC-TEX also fostered angiogenesis and expansion of myeloid cells, likely due to a direct impact of CIC-TEX on the host, which could be supported by reprogrammed CD44v6kd cells.Taken together, the striking loss of tumor progression by a CD44v6kd relies on the capacity of CD44v6 to cooperate with associating integrins and proteases and its promotion of additional CIC marker expression. The defects by a CD44v6kd are efficiently corrected upon CIC-TEX uptake.
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Affiliation(s)
- Zhe Wang
- Tumor Cell Biology, University Hospital of Surgery, Heidelberg, Germany
| | - Anja von Au
- Tumor Cell Biology, University Hospital of Surgery, Heidelberg, Germany
| | - Martina Schnölzer
- Proteome Analysis Department, German Cancer Research Center, Heidelberg, Germany
| | - Thilo Hackert
- Section Pancreas Research, University Hospital of Surgery, Heidelberg, Germany
| | - Margot Zöller
- Tumor Cell Biology, University Hospital of Surgery, Heidelberg, Germany
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18
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Thuma F, Heiler S, Schnölzer M, Zöller M. Palmitoylated claudin7 captured in glycolipid-enriched membrane microdomains promotes metastasis via associated transmembrane and cytosolic molecules. Oncotarget 2017; 7:30659-77. [PMID: 27120791 PMCID: PMC5058708 DOI: 10.18632/oncotarget.8928] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [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: 11/26/2015] [Accepted: 03/31/2016] [Indexed: 12/13/2022] Open
Abstract
In epithelial cells claudin7 (cld7) is a major component of tight junctions, but is also recovered from glycolipid-enriched membrane microdomains (GEM). In tumor cells, too, cld7 exists in two stages. Only GEM-located cld7, which is palmitoylated, promotes metastasis. Searching for the underlying mechanism(s) revealed the following.The metastatic capacity of the rat pancreatic adenocarcinoma cell line ASML is lost by a knockdown (kd) of cld7 and is not regained by rescuing cld7 with a mutated palmitoylation site (cld7mPalm). ASML-cld7kd and ASML-cld7mPalm cells show reduced motility and invasiveness. This is due to cld7, but not cld7mPalm associating with α6β4, ezrin, uPAR and MMP14, which jointly support motility and invasion. Palmitoylated cld7 also is engaged in drug resistance by repressing Pten, allowing activation of the antiapoptotic PI3K/Akt pathway. An association of cld7mPalm with the major Pten phosphorylating kinases does not restore apoptosis resistance as phosphorylated Pten is not guided towards GEM to compete with non-phosphorylated Pten. The pathway whereby palmitoylated cld7 supports expression of several EMT genes and nuclear translocation of EMT transcription factors remains to be unraveled. An association with Notch, reduced in ASML-cld7mPalm cells, might be the starting point. Finally, GEM-located, palmitoylated cld7 associates with several components of vesicle transport machineries engaged in exosome biogenesis.Taken together, prerequisites for cld7 acting as a cancer-initiating cell marker are GEM location and palmitoylation, which support a multitude of associations and integration into exosomes. The latter suggests palmitoylated cld7 contributing to message transfer via exosomes.
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Affiliation(s)
- Florian Thuma
- Department of Tumor Cell Biology, University Hospital of Surgery, Heidelberg, Germany
| | - Sarah Heiler
- Department of Tumor Cell Biology, University Hospital of Surgery, Heidelberg, Germany
| | - Martina Schnölzer
- Department of Functional Proteome Analysis, German Cancer Research Center, Heidelberg, Germany
| | - Margot Zöller
- Department of Tumor Cell Biology, University Hospital of Surgery, Heidelberg, Germany
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19
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Sciuto MR, Warnken U, Schnölzer M, Valvo C, Brunetto L, Boe A, Biffoni M, Krammer PH, De Maria R, Haas TL. Two-Step Coimmunoprecipitation (TIP) Enables Efficient and Highly Selective Isolation of Native Protein Complexes. Mol Cell Proteomics 2017; 17:993-1009. [PMID: 29217617 DOI: 10.1074/mcp.o116.065920] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 11/22/2017] [Indexed: 11/06/2022] Open
Abstract
Coimmunoprecipitation (co-IP) is one of the most frequently used techniques to study protein-protein (PPIs) or protein-nucleic acid interactions (PNIs). However, the presence of coprecipitated contaminants is a well-recognized issue associated with single-step co-IPs. To overcome this limitation, we developed the two-step co-IP (TIP) strategy that enables sequential coimmunoprecipitations of endogenous protein complexes. TIP can be performed with a broad range of mono- and polyclonal antibodies targeting a single protein or different components of a given complex. TIP results in a highly selective enrichment of protein complexes and thus outperforms single-step co-IPs for downstream applications such as mass spectrometry for the identification of PPIs and quantitative PCR for the analysis of PNIs. We benchmarked TIP for the identification of CD95/FAS-interacting proteins in primary human CD4+ T cells, which recapitulated all major known interactors, but also enabled the proteomics discovery of PPM1G and IPO7 as new interaction partners. For its feasibility and high performance, we propose TIP as an advanced tool for the isolation of highly purified protein-protein and protein-nucleic acid complexes under native expression conditions.
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Affiliation(s)
- Maria Rita Sciuto
- From the ‡Department of Hematology and Oncology, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy;
| | - Uwe Warnken
- §Functional Proteome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Martina Schnölzer
- §Functional Proteome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Cecilia Valvo
- From the ‡Department of Hematology and Oncology, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy.,¶Institute of General Pathology, Catholic University and Gemelli Polyclinic, Largo F. Vito 1, 00168, Rome, Italy
| | - Lidia Brunetto
- From the ‡Department of Hematology and Oncology, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Alessandra Boe
- From the ‡Department of Hematology and Oncology, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Mauro Biffoni
- From the ‡Department of Hematology and Oncology, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Peter H Krammer
- ‖Department of Tumor Immunology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Ruggero De Maria
- ¶Institute of General Pathology, Catholic University and Gemelli Polyclinic, Largo F. Vito 1, 00168, Rome, Italy
| | - Tobias L Haas
- From the ‡Department of Hematology and Oncology, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy; .,¶Institute of General Pathology, Catholic University and Gemelli Polyclinic, Largo F. Vito 1, 00168, Rome, Italy
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20
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Blank MF, Chen S, Poetz F, Schnölzer M, Voit R, Grummt I. SIRT7-dependent deacetylation of CDK9 activates RNA polymerase II transcription. Nucleic Acids Res 2017; 45:2675-2686. [PMID: 28426094 PMCID: PMC5389538 DOI: 10.1093/nar/gkx053] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [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] [Received: 10/18/2016] [Accepted: 01/20/2017] [Indexed: 01/08/2023] Open
Abstract
SIRT7 is an NAD+-dependent protein deacetylase that regulates cell growth and proliferation. Previous studies have shown that SIRT7 is required for RNA polymerase I (Pol I) transcription and pre-rRNA processing. Here, we took a proteomic approach to identify novel molecular targets and characterize the role of SIRT7 in non-nucleolar processes. We show that SIRT7 interacts with numerous proteins involved in transcriptional regulation and RNA metabolism, the majority of interactions requiring ongoing transcription. In addition to its role in Pol I transcription, we found that SIRT7 also regulates transcription of snoRNAs and mRNAs. Mechanistically, SIRT7 promotes the release of P-TEFb from the inactive 7SK snRNP complex and deacetylates CDK9, a subunit of the elongation factor P-TEFb, which activates transcription by phosphorylating serine 2 within the C-terminal domain (CTD) of Pol II. SIRT7 counteracts GCN5-directed acetylation of lysine 48 within the catalytic domain of CDK9, deacetylation promoting CTD phosphorylation and transcription elongation.
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Affiliation(s)
- Maximilian F Blank
- Molecular Biology of the Cell II, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Sifan Chen
- Molecular Biology of the Cell II, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Fabian Poetz
- Molecular Biology of the Cell II, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Martina Schnölzer
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Renate Voit
- Molecular Biology of the Cell II, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Ingrid Grummt
- Molecular Biology of the Cell II, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
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21
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Haas TL, Sciuto MR, Brunetto L, Valvo C, Signore M, Fiori ME, di Martino S, Giannetti S, Morgante L, Boe A, Patrizii M, Warnken U, Schnölzer M, Ciolfi A, Di Stefano C, Biffoni M, Ricci-Vitiani L, Pallini R, De Maria R. Integrin α7 Is a Functional Marker and Potential Therapeutic Target in Glioblastoma. Cell Stem Cell 2017; 21:35-50.e9. [DOI: 10.1016/j.stem.2017.04.009] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 02/16/2017] [Accepted: 04/20/2017] [Indexed: 12/26/2022]
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22
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Ecker J, Oehme I, Selt F, Kool M, Chavez L, Hohloch J, Valinciute G, van Tilburg CM, Schnölzer M, Warnken U, Wechsler-Reya R, Pfister SM, Witt O, Milde T. MEDU-20. TARGETING OF MYC BY HDAC INHIBITION IN MYC AMPLIFIED GROUP 3 MEDULLOBLASTOMA. Neuro Oncol 2017. [DOI: 10.1093/neuonc/nox083.170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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23
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Worst TS, von Hardenberg J, Gross JC, Erben P, Schnölzer M, Hausser I, Bugert P, Michel MS, Boutros M. Database-augmented Mass Spectrometry Analysis of Exosomes Identifies Claudin 3 as a Putative Prostate Cancer Biomarker. Mol Cell Proteomics 2017; 16:998-1008. [PMID: 28396511 DOI: 10.1074/mcp.m117.068577] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/23/2017] [Indexed: 01/01/2023] Open
Abstract
In prostate cancer and other malignancies sensitive and robust biomarkers are lacking or have relevant limitations. Prostate specific antigen (PSA), the only biomarker widely used in prostate cancer, is suffering from low specificity. Exosomes offer new perspectives in the discovery of blood-based biomarkers. Here we present a proof-of principle study for a proteomics-based identification pipeline, implementing existing data sources, to exemplarily identify exosome-based biomarker candidates in prostate cancer.Exosomes from malignant PC3 and benign PNT1A cells and from FBS-containing medium were isolated using sequential ultracentrifugation. Exosome and control samples were analyzed on an LTQ-Orbitrap XL mass spectrometer. Proteomic data is available via ProteomeXchange with identifier PXD003651. We developed a scoring scheme to rank 64 proteins exclusively found in PC3 exosomes, integrating data from four public databases and published mass spectrometry data sets. Among the top candidates, we focused on the tight junction protein claudin 3. Retests under serum-free conditions using immunoblotting and immunogold labeling confirmed the presence of claudin 3 on PC3 exosomes. Claudin 3 levels were determined in the blood plasma of patients with localized (n = 58; 42 with Gleason score 6-7, 16 with Gleason score ≥8) and metastatic prostate cancer (n = 11) compared with patients with benign prostatic hyperplasia (n = 15) and healthy individuals (n = 15) using ELISA, without prior laborious exosome isolation. ANOVA showed different CLDN3 plasma levels in these groups (p = 0.004). CLDN3 levels were higher in patients with Gleason ≥8 tumors compared with patients with benign prostatic hyperplasia (p = 0.012) and Gleason 6-7 tumors (p = 0.029). In patients with localized tumors CLDN3 levels predicted a Gleason score ≥ 8 (AUC = 0.705; p = 0.016) and did not correlate with serum PSA.By using the described workflow claudin 3 was identified and validated as a potential blood-based biomarker in prostate cancer. Furthermore this workflow could serve as a template to be used in other cancer entities.
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Affiliation(s)
- Thomas Stefan Worst
- From the ‡Department of Urology, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany; .,§Department of Signaling and Functional Genomics, German Cancer Research Center, Heidelberg, Germany
| | - Jost von Hardenberg
- From the ‡Department of Urology, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany.,§Department of Signaling and Functional Genomics, German Cancer Research Center, Heidelberg, Germany
| | - Julia Christina Gross
- §Department of Signaling and Functional Genomics, German Cancer Research Center, Heidelberg, Germany.,¶Haematology and Oncology and Developmental Biochemistry, University Medical Center, Göttingen, Germany
| | - Philipp Erben
- From the ‡Department of Urology, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Martina Schnölzer
- ‖Genomics and Proteomics Core Facility, German Cancer Research Center, Heidelberg, Germany
| | - Ingrid Hausser
- **Institute of Pathology IPH, University Clinic Heidelberg and Electron Microscopy Core Facility, University of Heidelberg, Germany
| | - Peter Bugert
- ‡‡Institute of Transfusion Medicine and Immunology, Heidelberg University, Medical Faculty Mannheim, German Red Cross Blood Service Baden-Württemberg-Hessen, Mannheim, Germany
| | - Maurice Stephan Michel
- From the ‡Department of Urology, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Michael Boutros
- §Department of Signaling and Functional Genomics, German Cancer Research Center, Heidelberg, Germany
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24
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Fricke F, Lee J, Michalak M, Warnken U, Hausser I, Suarez-Carmona M, Halama N, Schnölzer M, Kopitz J, Gebert J. TGFBR2-dependent alterations of exosomal cargo and functions in DNA mismatch repair-deficient HCT116 colorectal cancer cells. Cell Commun Signal 2017; 15:14. [PMID: 28376875 PMCID: PMC5379773 DOI: 10.1186/s12964-017-0169-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 03/21/2017] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Colorectal cancers (CRCs) that lack DNA mismatch repair function exhibit the microsatellite unstable (MSI) phenotype and are characterized by the accumulation of frameshift mutations at short repetitive DNA sequences (microsatellites). These tumors recurrently show inactivating frameshift mutations in the tumor suppressor Transforming Growth Factor Beta Receptor Type 2 (TGFBR2) thereby abrogating downstream signaling. How altered TGFBR2 signaling affects exosome-mediated communication between MSI tumor cells and their environment has not been resolved. Here, we report on molecular alterations of exosomes shed by MSI cells and the biological response evoked in recipient cells. METHODS Exosomes were isolated and characterized by electron microscopy, nanoparticle tracking, and western blot analysis. TGFBR2-dependent effects on the cargo and functions of exosomes were studied in a MSI CRC model cell line enabling reconstituted and inducible TGFBR2 expression and signaling. Microsatellite frameshift mutations in exosomal and cellular DNA were examined by PCR-based DNA fragment analysis and exosomal protein profiles were identified by mass spectrometry. Uptake of fluorescent-labeled exosomes by hepatoma recipient cells was monitored by confocal microscopy. TGFBR2-dependent exosomal effects on secreted cytokine levels of recipient cells were analyzed by Luminex technology and ELISA. RESULTS Frameshift mutation patterns in microsatellite stretches of TGFBR2 and other MSI target genes were found to be reflected in the cargo of MSI CRC-derived exosomes. At the proteome level, reconstituted TGFBR2 expression and signaling uncovered two protein subsets exclusively occurring in exosomes derived from TGFBR2-deficient (14 proteins) or TGFBR2-proficient (five proteins) MSI donor cells. Uptake of these exosomes by recipient cells caused increased secretion (2-6 fold) of specific cytokines (Interleukin-4, Stem Cell Factor, Platelet-derived Growth Factor-B), depending on the TGFBR2 expression status of the tumor cell. CONCLUSION Our results indicate that the coding MSI phenotype of DNA mismatch repair-deficient CRC cells is maintained in their exosomal DNA. Moreover, we uncovered that a recurrent MSI tumor driver mutation like TGFBR2 can reprogram the protein content of MSI cell-derived exosomes and in turn modulate the cytokine secretion profile of recipient cells. Apart from its diagnostic potential, these TGFBR2-dependent exosomal molecular and proteomic signatures might help to understand the signaling routes used by MSI tumors. Fricke et al. uncovered coding microsatellite instability-associated mutations of colorectal tumor driver genes like TGFBR2 in MSI tumor cellderived exosomes. Depending on the TGFBR2 expression status of their donor cells, shed exosomes show distinct proteomic signatures and promote altered cytokine secretion profiles in recipient cells.
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Affiliation(s)
- Fabia Fricke
- Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
- Department of Cancer Early Detection, German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
| | - Jennifer Lee
- Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
- Department of Cancer Early Detection, German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
- Present address: Tissue Genesis, Suite 1000, Tissue Genesis Tower, 810 Richards Street, Honolulu, HI 96813 USA
| | - Malwina Michalak
- Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
- Department of Cancer Early Detection, German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
| | - Uwe Warnken
- Functional Proteome Analysis and Core Facility Protein Analysis (B100), German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Ingrid Hausser
- Department of General Pathology, Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
| | - Meggy Suarez-Carmona
- Department of Medical Oncology, National Center for Tumor diseases (NCT), Tissue Imaging and Analysis Center, Bioquant, University Hospital Heidelberg, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Niels Halama
- Department of Medical Oncology, National Center for Tumor diseases (NCT), Tissue Imaging and Analysis Center, Bioquant, University Hospital Heidelberg, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Martina Schnölzer
- Functional Proteome Analysis and Core Facility Protein Analysis (B100), German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Jürgen Kopitz
- Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
- Department of Cancer Early Detection, German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
| | - Johannes Gebert
- Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
- Department of Cancer Early Detection, German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
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25
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Winter M, Dokic I, Schlegel J, Warnken U, Debus J, Abdollahi A, Schnölzer M. Deciphering the Acute Cellular Phosphoproteome Response to Irradiation with X-rays, Protons and Carbon Ions. Mol Cell Proteomics 2017; 16:855-872. [PMID: 28302921 DOI: 10.1074/mcp.m116.066597] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 03/15/2017] [Indexed: 12/15/2022] Open
Abstract
Radiotherapy is a cornerstone of cancer therapy. The recently established particle therapy with raster-scanning protons and carbon ions landmarks a new era in the field of high-precision cancer medicine. However, molecular mechanisms governing radiation induced intracellular signaling remain elusive. Here, we present the first comprehensive proteomic and phosphoproteomic study applying stable isotope labeling by amino acids in cell culture (SILAC) in combination with high-resolution mass spectrometry to decipher cellular response to irradiation with X-rays, protons and carbon ions. At protein expression level limited alterations were observed 2 h post irradiation of human lung adenocarcinoma cells. In contrast, 181 phosphorylation sites were found to be differentially regulated out of which 151 sites were not hitherto attributed to radiation response as revealed by crosscheck with the PhosphoSitePlus database.Radiation-induced phosphorylation of the p(S/T)Q motif was the prevailing regulation pattern affecting proteins involved in DNA damage response signaling. Because radiation doses were selected to produce same level of cell kill and DNA double-strand breakage for each radiation quality, DNA damage responsive phosphorylation sites were regulated to same extent. However, differential phosphorylation between radiation qualities was observed for 55 phosphorylation sites indicating the existence of distinct signaling circuitries induced by X-ray versus particle (proton/carbon) irradiation beyond the canonical DNA damage response. This unexpected finding was confirmed in targeted spike-in experiments using synthetic isotope labeled phosphopeptides. Herewith, we successfully validated uniform DNA damage response signaling coexisting with altered signaling involved in apoptosis and metabolic processes induced by X-ray and particle based treatments.In summary, the comprehensive insight into the radiation-induced phosphoproteome landscape is instructive for the design of functional studies aiming to decipher cellular signaling processes in response to radiotherapy, space radiation or ionizing radiation per se Further, our data will have a significant impact on the ongoing debate about patient treatment modalities.
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Affiliation(s)
- Martin Winter
- From the ‡Functional Proteome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany.,§Translational Radiation Oncology, National Center for Tumor diseases (NCT), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 460, D-69120 Heidelberg, Germany.,¶German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Ivana Dokic
- §Translational Radiation Oncology, National Center for Tumor diseases (NCT), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 460, D-69120 Heidelberg, Germany.,¶German Cancer Consortium (DKTK), Heidelberg, Germany.,‖Heidelberg Ion Beam Therapy Center (HIT), Department of Radiation Oncology, University of Heidelberg Medical School, Im Neuenheimer Feld 450, D-69120 Heidelberg, Germany.,**Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), Heidelberg, Germany
| | - Julian Schlegel
- §Translational Radiation Oncology, National Center for Tumor diseases (NCT), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 460, D-69120 Heidelberg, Germany.,¶German Cancer Consortium (DKTK), Heidelberg, Germany.,‖Heidelberg Ion Beam Therapy Center (HIT), Department of Radiation Oncology, University of Heidelberg Medical School, Im Neuenheimer Feld 450, D-69120 Heidelberg, Germany.,**Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), Heidelberg, Germany
| | - Uwe Warnken
- From the ‡Functional Proteome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| | - Jürgen Debus
- §Translational Radiation Oncology, National Center for Tumor diseases (NCT), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 460, D-69120 Heidelberg, Germany.,¶German Cancer Consortium (DKTK), Heidelberg, Germany.,‖Heidelberg Ion Beam Therapy Center (HIT), Department of Radiation Oncology, University of Heidelberg Medical School, Im Neuenheimer Feld 450, D-69120 Heidelberg, Germany.,**Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), Heidelberg, Germany
| | - Amir Abdollahi
- §Translational Radiation Oncology, National Center for Tumor diseases (NCT), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 460, D-69120 Heidelberg, Germany.,¶German Cancer Consortium (DKTK), Heidelberg, Germany.,‖Heidelberg Ion Beam Therapy Center (HIT), Department of Radiation Oncology, University of Heidelberg Medical School, Im Neuenheimer Feld 450, D-69120 Heidelberg, Germany.,**Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), Heidelberg, Germany
| | - Martina Schnölzer
- From the ‡Functional Proteome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany;
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26
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Abstract
Inactivating mutations in single genes can trigger, prevent, promote, or alleviate diseases. Identifying such disease-related genes is a main pillar of medical research. Since proteins play a crucial role in mediating these effects, their impact on the diseased cells' proteome including posttranslational modifications has to be elucidated for a detailed understanding of the role of these genes in the disease process. In complex disorders, like cancer, several genes contribute to the disease process, thereby hampering the assignment of a proteomic change to the corresponding causative gene. To enable comprehensive screening for the impact of inactivation of a gene, e.g., loss of a tumor suppressor in cancer, on the cellular proteome, we present a strategy based on combination of three technologies that is recombinase-mediated cassette exchange, click chemistry, and mass spectrometry. The methodology is exemplified by the analysis of the proteomic changes induced by the loss of a tumor suppressor gene in colorectal cancer cells. To demonstrate the applicability to screen for posttranslational modification changes, we also describe the analysis of protein glycosylation changes caused by the tumor suppressor inactivation. In principle, this strategy can be applied to analyze the effects of any gene of interest on protein expression as well as posttranslational modification by glycosylation. Moreover adaptation of the strategy to an appropriate cell culture model has the potential for application on a broad range of diseases where the disease-promoting mutations have been identified.
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Affiliation(s)
- J Gebert
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany; Cancer Early Detection, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - M Schnölzer
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - U Warnken
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - J Kopitz
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany; Cancer Early Detection, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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Michalak M, Warnken U, André S, Schnölzer M, Gabius HJ, Kopitz J. Detection of Proteome Changes in Human Colon Cancer Induced by Cell Surface Binding of Growth-Inhibitory Human Galectin-4 Using Quantitative SILAC-Based Proteomics. J Proteome Res 2016; 15:4412-4422. [DOI: 10.1021/acs.jproteome.6b00473] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Malwina Michalak
- Department
of Applied Tumor Biology, Institute of Pathology, Medical School of the Ruprecht-Karls-University, 69120 Heidelberg, Germany
- Cancer
Early Detection, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Uwe Warnken
- Functional
Proteome Analysis, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Sabine André
- Institute
of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinärstraße 13, 80539 Munich, Germany
| | - Martina Schnölzer
- Functional
Proteome Analysis, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Hans-Joachim Gabius
- Institute
of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinärstraße 13, 80539 Munich, Germany
| | - Juergen Kopitz
- Department
of Applied Tumor Biology, Institute of Pathology, Medical School of the Ruprecht-Karls-University, 69120 Heidelberg, Germany
- Cancer
Early Detection, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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Ecker J, Oehme I, Selt F, Kool M, Schnölzer M, Warnken U, Brabetz S, Wechsler-Reya R, Kulozik AE, Pfister SM, Witt O, Milde T. Targeting the interaction of HDAC2 and MYC in Group 3 medulloblastoma. Klin Padiatr 2016. [DOI: 10.1055/s-0036-1593553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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García Caballero G, Kaltner H, Michalak M, Shilova N, Yegres M, André S, Ludwig AK, Manning JC, Schmidt S, Schnölzer M, Bovin NV, Reusch D, Kopitz J, Gabius HJ. Chicken GRIFIN: A homodimeric member of the galectin network with canonical properties and a unique expression profile. Biochimie 2016; 128-129:34-47. [PMID: 27296808 DOI: 10.1016/j.biochi.2016.06.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [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: 05/06/2016] [Accepted: 06/03/2016] [Indexed: 12/12/2022]
Abstract
Occurrence of the adhesion/growth-regulatory galectins as family sets the challenge to achieve a complete network analysis. Along this route taken for a well-suited model organism (chicken), we fill the remaining gap to characterize its seventh member known from rat as galectin-related inter-fiber protein (GRIFIN) in the lens. Its single-copy gene is common to vertebrates, with one or more deviations from the so-called signature sequence for ligand (lactose) contact. The chicken protein is a homodimeric agglutinin with capacity to bind β-galactosides, especially the histo-blood group B tetrasaccharide, shown by solid-phase/cell assays and a glycan microarray. Mass spectrometric identification of two lactose-binding peptides after tryptic on-bead fragmentation suggests an interaction at the canonical region despite a sequence change from Arg to Val at the site, which impairs reactivity of human galectin-1. RT-PCR and Western blot analyses of specimen from adult chicken organs reveal restriction of expression to the lens, here immunohistochemically throughout its main body. This report sets the stage for detailed structure-activity studies to define factors relevant for affinity beyond the signature sequence and to perform the first complete network analysis of the galectin family in developing and adult organs of a vertebrate.
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Affiliation(s)
- Gabriel García Caballero
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinärstr. 13, 80539 Munich, Germany
| | - Herbert Kaltner
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinärstr. 13, 80539 Munich, Germany
| | - Malwina Michalak
- Department of Applied Tumor Biology, Institute of Pathology, Medical School of the Ruprecht-Karls-University, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
| | - Nadezhda Shilova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, Moscow, Russia
| | - Michelle Yegres
- Pharma Biotech Development Penzberg, Roche Diagnostics GmbH, 82377 Penzberg, Germany
| | - Sabine André
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinärstr. 13, 80539 Munich, Germany
| | - Anna-Kristin Ludwig
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinärstr. 13, 80539 Munich, Germany
| | - Joachim C Manning
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinärstr. 13, 80539 Munich, Germany
| | - Sebastian Schmidt
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinärstr. 13, 80539 Munich, Germany
| | - Martina Schnölzer
- Genomics and Proteomics Core Facility, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Nicolai V Bovin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya, Moscow, Russia
| | - Dietmar Reusch
- Pharma Biotech Development Penzberg, Roche Diagnostics GmbH, 82377 Penzberg, Germany
| | - Jürgen Kopitz
- Department of Applied Tumor Biology, Institute of Pathology, Medical School of the Ruprecht-Karls-University, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
| | - Hans-Joachim Gabius
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinärstr. 13, 80539 Munich, Germany.
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Ecker J, Oehme I, Selt F, Kool M, Schnölzer M, Warnken U, Brabetz S, Wechsler-Reya R, Kulozik AE, Pfister SM, Witt O, Milde T. MB-57INTERACTION OF HDAC2 AND MYC IN GROUP 3 MEDULLOBLASTOMA - A NOVEL THERAPEUTIC TARGET. Neuro Oncol 2016. [DOI: 10.1093/neuonc/now076.54] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Petersen HO, Höger SK, Looso M, Lengfeld T, Kuhn A, Warnken U, Nishimiya-Fujisawa C, Schnölzer M, Krüger M, Özbek S, Simakov O, Holstein TW. A Comprehensive Transcriptomic and Proteomic Analysis of Hydra Head Regeneration. Mol Biol Evol 2015; 32:1928-47. [PMID: 25841488 PMCID: PMC4833066 DOI: 10.1093/molbev/msv079] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The cnidarian freshwater polyp Hydra sp. exhibits an unparalleled regeneration capacity in the animal kingdom. Using an integrative transcriptomic and stable isotope labeling by amino acids in cell culture proteomic/phosphoproteomic approach, we studied stem cell-based regeneration in Hydra polyps. As major contributors to head regeneration, we identified diverse signaling pathways adopted for the regeneration response as well as enriched novel genes. Our global analysis reveals two distinct molecular cascades: an early injury response and a subsequent, signaling driven patterning of the regenerating tissue. A key factor of the initial injury response is a general stabilization of proteins and a net upregulation of transcripts, which is followed by a subsequent activation cascade of signaling molecules including Wnts and transforming growth factor (TGF) beta-related factors. We observed moderate overlap between the factors contributing to proteomic and transcriptomic responses suggesting a decoupled regulation between the transcriptional and translational levels. Our data also indicate that interstitial stem cells and their derivatives (e.g., neurons) have no major role in Hydra head regeneration. Remarkably, we found an enrichment of evolutionarily more recent genes in the early regeneration response, whereas conserved genes are more enriched in the late phase. In addition, genes specific to the early injury response were enriched in transposon insertions. Genetic dynamicity and taxon-specific factors might therefore play a hitherto underestimated role in Hydra regeneration.
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Affiliation(s)
- Hendrik O Petersen
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Stefanie K Höger
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Mario Looso
- Max Planck Institute (MPI) for Heart and Lung Research, Bad Nauheim, Germany
| | - Tobias Lengfeld
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Anne Kuhn
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Uwe Warnken
- Functional Proteome Analysis Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Chiemi Nishimiya-Fujisawa
- Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, Myodaiji, Okazaki, Japan
| | - Martina Schnölzer
- Functional Proteome Analysis Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marcus Krüger
- Max Planck Institute (MPI) for Heart and Lung Research, Bad Nauheim, Germany CECAD, University of Cologne, Germany
| | - Suat Özbek
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Oleg Simakov
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany Molecular Genetics Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Thomas W Holstein
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
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Lee J, Warnken U, Schnölzer M, Gebert J, Kopitz J. A new method for detection of tumor driver-dependent changes of protein sialylation in a colon cancer cell line reveals nectin-3 as TGFBR2 target. Protein Sci 2015; 24:1686-94. [PMID: 26177744 DOI: 10.1002/pro.2741] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [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: 05/28/2015] [Accepted: 06/25/2015] [Indexed: 02/03/2023]
Abstract
Protein-linked glycans play key roles in cell differentiation, cell-cell interactions, cell growth, adhesion and immune response. Aberrant glycosylation is a characteristic feature of tumor cells and is involved in tumor growth, escape from apoptosis, metastasis formation, and resistance to therapy. It can serve as cancer biomarker and treatment target. To enable comprehensive screening for the impact of tumor driving mutations in colorectal cancer cells we present a method for specific analysis of tumor driver-induced glycome changes. The strategy is based on a combination of three technologies, that is recombinase-mediated cassette exchange (RMCE), Click-It chemistry and mass spectrometry. The new method is exemplified by the analysis of the impact of inactivating mutations of the TGF-ß-receptor type II (TGFBR2) on sialic acid incorporation into protein-linked glycans of the colon cancer cell line HCT116. Overall, 70 proteins were found to show de novo sialic acid incorporation exclusively upon TGFBR2 expression whereas 7 proteins lost sialylation upon TGFBR2 reconstitution. Validation of detected candidate glycoproteins is demonstrated with the cell surface glycoprotein nectin-3 known to be involved in metastasis, invasion and prognosis of various cancers. Altogether, our new approach can help to systematically puzzle out the influence of tumor-specific mutations in a major signaling pathway, as exemplified by the TGFBR2 tumor suppressor, on the tumor glycome. It facilitates the identification of glycan-based tumor markers that could be used for diagnostic and therapeutic applications. In principle the outlined strategy can be adapted to any cancer cell line, tumor driver mutation and several glycan-building blocks.
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Affiliation(s)
- Jennifer Lee
- Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Department of Cancer Early Detection, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Uwe Warnken
- Department of Functional Proteome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martina Schnölzer
- Department of Functional Proteome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Johannes Gebert
- Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Department of Cancer Early Detection, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jürgen Kopitz
- Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Department of Cancer Early Detection, German Cancer Research Center (DKFZ), Heidelberg, Germany
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Lee J, Fricke F, Warnken U, Schnölzer M, Kopitz J, Gebert J. Reconstitution of TGFBR2-Mediated Signaling Causes Upregulation of GDF-15 in HCT116 Colorectal Cancer Cells. PLoS One 2015; 10:e0131506. [PMID: 26114631 PMCID: PMC4484253 DOI: 10.1371/journal.pone.0131506] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [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: 02/25/2015] [Accepted: 06/03/2015] [Indexed: 12/21/2022] Open
Abstract
Although inactivating frameshift mutations in the Transforming growth factor beta receptor type 2 (TGFBR2) gene are considered as drivers of microsatellite unstable (MSI) colorectal tumorigenesis, consequential alterations of the downstream target proteome are not resolved completely. Applying a click-it chemistry protein labeling approach combined with mass spectrometry in a MSI colorectal cancer model cell line, we identified 21 de novo synthesized proteins differentially expressed upon reconstituted TGFBR2 expression. One candidate gene, the TGF-ß family member Growth differentiation factor-15 (GDF-15), exhibited TGFBR2-dependent transcriptional upregulation causing increased intracellular and extracellular protein levels. As a new TGFBR2 target gene it may provide a link between the TGF-ß branch and the BMP/GDF branch of SMAD-mediated signaling.
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Affiliation(s)
- Jennifer Lee
- Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Cancer Early Detection, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Fabia Fricke
- Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Cancer Early Detection, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Uwe Warnken
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martina Schnölzer
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jürgen Kopitz
- Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Cancer Early Detection, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Johannes Gebert
- Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
- Cancer Early Detection, German Cancer Research Center (DKFZ), Heidelberg, Germany
- * E-mail:
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Lim HW, Kang SG, Ryu JK, Schilling B, Fei M, Lee IS, Kehasse A, Shirakawa K, Yokoyama M, Schnölzer M, Kasler HG, Kwon HS, Gibson BW, Sato H, Akassoglou K, Xiao C, Littman DR, Ott M, Verdin E. SIRT1 deacetylates RORγt and enhances Th17 cell generation. ACTA ACUST UNITED AC 2015; 212:973. [PMID: 25987725 PMCID: PMC4451124 DOI: 10.1084/jem.2013237805062015c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Lim HW, Kang SG, Ryu JK, Schilling B, Fei M, Lee IS, Kehasse A, Shirakawa K, Yokoyama M, Schnölzer M, Kasler HG, Kwon HS, Gibson BW, Sato H, Akassoglou K, Xiao C, Littman DR, Ott M, Verdin E. SIRT1 deacetylates RORγt and enhances Th17 cell generation. ACTA ACUST UNITED AC 2015; 212:607-17. [PMID: 25918343 PMCID: PMC4419343 DOI: 10.1084/jem.20132378] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [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] [Received: 11/15/2013] [Accepted: 04/03/2015] [Indexed: 01/30/2023]
Abstract
Lim et al. demonstrate that protein deacetylase, Sirtuin 1, promotes autoimmunity by deacetylating RORγt increasing its transcriptional activity and promoting Th17 differentiation and function. Blockade or loss of Sirtuin 1 results in protection from multiple sclerosis-like disease in mice. The balance of effector and regulatory T cell function, dependent on multiple signals and epigenetic regulators, is critical to immune self-tolerance. Dysregulation of T helper 17 (Th17) effector cells is associated with multiple autoimmune diseases, including multiple sclerosis. Here, we report that Sirtuin 1 (SIRT1), a protein deacetylase previously reported to have an antiinflammatory function, in fact promotes autoimmunity by deacetylating RORγt, the signature transcription factor of Th17 cells. SIRT1 increases RORγt transcriptional activity, enhancing Th17 cell generation and function. Both T cell–specific Sirt1 deletion and treatment with pharmacologic SIRT1 inhibitors suppress Th17 differentiation and are protective in a mouse model of multiple sclerosis. Moreover, analysis of infiltrating cell populations during disease induction in mixed hematopoietic chimeras shows a marked bias against Sirt1-deficient Th17 cells. These findings reveal an unexpected proinflammatory role of SIRT1 and, importantly, support the possible therapeutic use of SIRT1 inhibitors against autoimmunity.
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Affiliation(s)
- Hyung W Lim
- Gladstone Institute of Virology and Immunology, Gladstone Institute of Neurological Disease, School of Medecine, Department of Neurology, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158 Gladstone Institute of Virology and Immunology, Gladstone Institute of Neurological Disease, School of Medecine, Department of Neurology, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158
| | - Seung Goo Kang
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037
| | - Jae Kyu Ryu
- Gladstone Institute of Virology and Immunology, Gladstone Institute of Neurological Disease, School of Medecine, Department of Neurology, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158
| | | | - Mingjian Fei
- Gladstone Institute of Virology and Immunology, Gladstone Institute of Neurological Disease, School of Medecine, Department of Neurology, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158 Gladstone Institute of Virology and Immunology, Gladstone Institute of Neurological Disease, School of Medecine, Department of Neurology, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158
| | - Intelly S Lee
- Gladstone Institute of Virology and Immunology, Gladstone Institute of Neurological Disease, School of Medecine, Department of Neurology, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158 Gladstone Institute of Virology and Immunology, Gladstone Institute of Neurological Disease, School of Medecine, Department of Neurology, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158
| | | | - Kotaro Shirakawa
- Gladstone Institute of Virology and Immunology, Gladstone Institute of Neurological Disease, School of Medecine, Department of Neurology, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158 Gladstone Institute of Virology and Immunology, Gladstone Institute of Neurological Disease, School of Medecine, Department of Neurology, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158
| | - Masaru Yokoyama
- Laboratory of Viral Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo 208-0011, Japan
| | | | - Herbert G Kasler
- Gladstone Institute of Virology and Immunology, Gladstone Institute of Neurological Disease, School of Medecine, Department of Neurology, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158 Gladstone Institute of Virology and Immunology, Gladstone Institute of Neurological Disease, School of Medecine, Department of Neurology, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158
| | - Hye-Sook Kwon
- Gladstone Institute of Virology and Immunology, Gladstone Institute of Neurological Disease, School of Medecine, Department of Neurology, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158 Gladstone Institute of Virology and Immunology, Gladstone Institute of Neurological Disease, School of Medecine, Department of Neurology, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158
| | - Bradford W Gibson
- Gladstone Institute of Virology and Immunology, Gladstone Institute of Neurological Disease, School of Medecine, Department of Neurology, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158 Buck Institute for Research on Aging, Novato, CA 94945
| | - Hironori Sato
- Laboratory of Viral Genomics, Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo 208-0011, Japan
| | - Katerina Akassoglou
- Gladstone Institute of Virology and Immunology, Gladstone Institute of Neurological Disease, School of Medecine, Department of Neurology, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158 Gladstone Institute of Virology and Immunology, Gladstone Institute of Neurological Disease, School of Medecine, Department of Neurology, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158
| | - Changchun Xiao
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037
| | - Dan R Littman
- Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, The Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016 Molecular Pathogenesis Program, The Kimmel Center for Biology and Medicine of the Skirball Institute, The Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016
| | - Melanie Ott
- Gladstone Institute of Virology and Immunology, Gladstone Institute of Neurological Disease, School of Medecine, Department of Neurology, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158 Gladstone Institute of Virology and Immunology, Gladstone Institute of Neurological Disease, School of Medecine, Department of Neurology, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158
| | - Eric Verdin
- Gladstone Institute of Virology and Immunology, Gladstone Institute of Neurological Disease, School of Medecine, Department of Neurology, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158 Gladstone Institute of Virology and Immunology, Gladstone Institute of Neurological Disease, School of Medecine, Department of Neurology, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158
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Vértesy S, Michalak M, Miller MC, Schnölzer M, André S, Kopitz J, Mayo KH, Gabius HJ. Structural significance of galectin design: impairment of homodimer stability by linker insertion and partial reversion by ligand presence. Protein Eng Des Sel 2015; 28:199-210. [PMID: 25796447 DOI: 10.1093/protein/gzv014] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [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: 12/19/2014] [Accepted: 02/11/2015] [Indexed: 11/13/2022] Open
Abstract
Lectins translate information encoded in glycan chains of cellular glycoconjugates into bioeffects. The topological presentation of contact sites for cognate sugar binding is a crucial factor toward this end. To dissect the significance of such phylogenetically conserved properties, the design and engineering of non-natural variants are attractive approaches. Here, a homodimeric human lectin, i.e. adhesion/growth-regulatory galectin-1, is converted into a tandem-repeat display by introducing the 33-amino-acid linker of another family member (i.e. galectin-8). The yield of variant was reduced by about a third. This protein had ∼10-fold higher activity in hemagglutination. Nearly complete sequence determination by mass-spectrometric in-source decay and fingerprinting excluded the presence of any modifications. When (1)H-(15)N heteronuclear single-quantum coherence data on the (15)N-labeled variant and wild-type protein were compared, changes in chemical shifts, signal intensities and resonance multiplicities revealed reduction of stability of interfacial contacts between the lectin domains and an increase in inter-domain flexibility. When both binding sites in the variant were loaded with ligand, association of the two carbohydrate recognition domains was enhanced, corroborated by gel filtration. Dynamic changes in the spatial presentation of the two lectin domains in the context of a tandem-repeat display can alter counterreceptor targeting relative to the fixed positions found in the proto-type galectin homodimer.
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Affiliation(s)
- Sabine Vértesy
- Institut für Physiologische Chemie, Tierärztliche Fakultät, Ludwig-Maximilians Universität, Veterinär-straße 13, 80539 München, Germany
| | - Malwina Michalak
- Abteilung für Angewandte Tumorbiologie, Pathologisches Institut, Klinikum der Ruprecht-Karls-Universität, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
| | - Michelle C Miller
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Health Sciences Center, 6-155 Jackson Hall, 321 Church Str., Minneapolis, MN 55455, USA
| | - Martina Schnölzer
- Funktionelle Proteomanalyse, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Sabine André
- Institut für Physiologische Chemie, Tierärztliche Fakultät, Ludwig-Maximilians Universität, Veterinär-straße 13, 80539 München, Germany
| | - Jürgen Kopitz
- Abteilung für Angewandte Tumorbiologie, Pathologisches Institut, Klinikum der Ruprecht-Karls-Universität, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany
| | - Kevin H Mayo
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Health Sciences Center, 6-155 Jackson Hall, 321 Church Str., Minneapolis, MN 55455, USA
| | - Hans-Joachim Gabius
- Institut für Physiologische Chemie, Tierärztliche Fakultät, Ludwig-Maximilians Universität, Veterinär-straße 13, 80539 München, Germany
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Klein-Scory S, Tehrani MM, Eilert-Micus C, Adamczyk KA, Wojtalewicz N, Schnölzer M, Hahn SA, Schmiegel W, Schwarte-Waldhoff I. New insights in the composition of extracellular vesicles from pancreatic cancer cells: implications for biomarkers and functions. Proteome Sci 2014; 12:50. [PMID: 25469109 PMCID: PMC4251850 DOI: 10.1186/s12953-014-0050-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [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: 04/30/2014] [Accepted: 09/16/2014] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Pancreatic cancer development is associated with characteristic alterations like desmoplastic reaction and immune escape which are mediated by the cell-cell communication mechanism and by the microenvironment of the cells. The whole of released components are important determinants in these processes. Especially the extracellular vesicles released by pancreatic cancer cells play a role in cell communication and modulate cell growth and immune responses. RESULTS Here, we present the proteomic description of affinity purified extracellular vesicles from pancreatic tumour cells, compared to the secretome, defined as the whole of the proteins released by pancreatic cancer cells. The proteomic data provide comprehensive catalogues of hundreds of proteins, and the comparison reveals a special proteomic composition of pancreatic cancer cell derived extracellular vesicles. The functional analysis of the protein composition displayed that membrane proteins, glycoproteins, small GTP binding proteins and a further, heterogeneous group of proteins are enriched in vesicles, whereas proteins derived from proteasomes and ribosomes, as well as metabolic enzymes, are not components of the vesicles. Furthermore proteins playing a role in carcinogenesis and modulators of the extracellular matrix (ECM) or cell-cell interactions are components of affinity purified extracellular vesicles. CONCLUSION The data deepen the knowledge of extracellular vesicle composition by hundreds of proteins that have not been previously described as vesicle components released by pancreatic cancer cells. Extracellular vesicles derived from pancreatic cancer cells show common proteins shared with other vesicles as well as cell type specific proteins indicating biomarker candidates and suggesting functional roles in cancer cell stroma interactions.
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Affiliation(s)
- Susanne Klein-Scory
- />IMBL, Medical Clinic Knappschaftskrankenhaus Bochum GmbH, Ruhr-University Bochum, In der Schornau 23-25, 44892 Bochum, Germany
| | - Mahnaz Moradian Tehrani
- />Functional Proteome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Christina Eilert-Micus
- />IMBL, Medical Clinic Knappschaftskrankenhaus Bochum GmbH, Ruhr-University Bochum, In der Schornau 23-25, 44892 Bochum, Germany
| | - Kamila A Adamczyk
- />IMBL, Medical Clinic Knappschaftskrankenhaus Bochum GmbH, Ruhr-University Bochum, In der Schornau 23-25, 44892 Bochum, Germany
| | - Nathalie Wojtalewicz
- />IMBL, Medical Clinic Knappschaftskrankenhaus Bochum GmbH, Ruhr-University Bochum, In der Schornau 23-25, 44892 Bochum, Germany
| | - Martina Schnölzer
- />Functional Proteome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Stephan A Hahn
- />Molecular Gastrointestinal Oncology MGO, Ruhr-University Bochum, Universitätsstraße 150, 44780 Bochum, Germany
| | - Wolff Schmiegel
- />IMBL, Medical Clinic Knappschaftskrankenhaus Bochum GmbH, Ruhr-University Bochum, In der Schornau 23-25, 44892 Bochum, Germany
- />Medical Department, Medical Clinic Knappschaftskrankenhaus Bochum GmbH, Ruhr-University Bochum, In der Schornau 23-25, 44892 Bochum, Germany
| | - Irmgard Schwarte-Waldhoff
- />IMBL, Medical Clinic Knappschaftskrankenhaus Bochum GmbH, Ruhr-University Bochum, In der Schornau 23-25, 44892 Bochum, Germany
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Ballikaya S, Lee J, Warnken U, Schnölzer M, Gebert J, Kopitz J. De Novo proteome analysis of genetically modified tumor cells by a metabolic labeling/azide-alkyne cycloaddition approach. Mol Cell Proteomics 2014; 13:3446-56. [PMID: 25225355 DOI: 10.1074/mcp.m113.036665] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Activin receptor type II (ACVR2) is a member of the transforming growth factor type II receptor family and controls cell growth and differentiation, thereby acting as a tumor suppressor. ACVR2 inactivation is known to drive colorectal tumorigenesis. We used an ACVR2-deficient microsatellite unstable colon cancer cell line (HCT116) to set up a novel experimental design for comprehensive analysis of proteomic changes associated with such functional loss of a tumor suppressor. To this end we combined two existing technologies. First, the ACVR2 gene was reconstituted in an ACVR2-deficient colorectal cancer (CRC) cell line by means of recombinase-mediated cassette exchange, resulting in the generation of an inducible expression system that allowed the regulation of ACVR2 gene expression in a doxycycline-dependent manner. Functional expression in the induced cells was explicitly proven. Second, we used the methionine analog azidohomoalanine for metabolic labeling of newly synthesized proteins in our cell line model. Labeled proteins were tagged with biotin via a Click-iT chemistry approach enabling specific extraction of labeled proteins by streptavidin-coated beads. Tryptic on-bead digestion of captured proteins and subsequent ultra-high-performance LC coupled to LTQ Orbitrap XL mass spectrometry identified 513 proteins, with 25 of them differentially expressed between ACVR2-deficient and -proficient cells. Among these, several candidates that had already been linked to colorectal cancer or were known to play a key role in cell growth or apoptosis control were identified, proving the utility of the presented experimental approach. In principle, this strategy can be adapted to analyze any gene of interest and its effect on the cellular de novo proteome.
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Affiliation(s)
- Seda Ballikaya
- From the ‡Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, INF 224, 69120 Heidelberg, Germany; §Cancer Early Detection, German Cancer Research Center (DKFZ), INF 280, 69120 Heidelberg, Germany
| | - Jennifer Lee
- From the ‡Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, INF 224, 69120 Heidelberg, Germany; §Cancer Early Detection, German Cancer Research Center (DKFZ), INF 280, 69120 Heidelberg, Germany
| | - Uwe Warnken
- ‖Functional Proteome Analysis, German Cancer Research Center (DKFZ), INF 280, 69120 Heidelberg, Germany
| | - Martina Schnölzer
- ‖Functional Proteome Analysis, German Cancer Research Center (DKFZ), INF 280, 69120 Heidelberg, Germany
| | - Johannes Gebert
- From the ‡Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, INF 224, 69120 Heidelberg, Germany; §Cancer Early Detection, German Cancer Research Center (DKFZ), INF 280, 69120 Heidelberg, Germany
| | - Jürgen Kopitz
- From the ‡Department of Applied Tumor Biology, Institute of Pathology, University Hospital Heidelberg, INF 224, 69120 Heidelberg, Germany; §Cancer Early Detection, German Cancer Research Center (DKFZ), INF 280, 69120 Heidelberg, Germany;
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Kopitz J, Vértesy S, André S, Fiedler S, Schnölzer M, Gabius HJ. Human chimera-type galectin-3: defining the critical tail length for high-affinity glycoprotein/cell surface binding and functional competition with galectin-1 in neuroblastoma cell growth regulation. Biochimie 2014; 104:90-9. [PMID: 24909114 DOI: 10.1016/j.biochi.2014.05.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [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: 04/15/2014] [Accepted: 05/26/2014] [Indexed: 11/16/2022]
Abstract
Many human proteins have a modular design with receptor and structural domains. Using adhesion/growth-regulatory galectin-3 as model, we describe an interdisciplinary strategy to define the functional significance of its tail established by nine non-triple helical collagen-like repeats (I-IX) and the N-terminal peptide. Genetic engineering with sophisticated mass spectrometric product analysis provided the tools for biotesting, i.e. eight protein variants with different degrees of tail truncation. Evidently,various aspects of galectin-3 activity (cis binding and cell bridging) are affected by tail shortening in a different manner. Thus, this combined approach reveals an unsuspected complexity of structure-function relationship, encouraging further application beyond this chimera-type galectin.
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Affiliation(s)
- Jürgen Kopitz
- Abteilung für Angewandte Tumorbiologie, Zentrum Pathologie, Klinikum der Ruprecht-Karls-Universität, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany.
| | - Sabine Vértesy
- Institut für Physiologische Chemie, Tierärztliche Fakultät, Ludwig-Maximilians-Universität, Veterinärstraße 13, 80539 München, Germany
| | - Sabine André
- Institut für Physiologische Chemie, Tierärztliche Fakultät, Ludwig-Maximilians-Universität, Veterinärstraße 13, 80539 München, Germany
| | - Sabine Fiedler
- Funktionelle Proteomanalyse, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Martina Schnölzer
- Funktionelle Proteomanalyse, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Hans-Joachim Gabius
- Institut für Physiologische Chemie, Tierärztliche Fakultät, Ludwig-Maximilians-Universität, Veterinärstraße 13, 80539 München, Germany
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Klaus C, Kaemmerer E, Reinartz A, Schneider U, Plum P, Jeon MK, Hose J, Hartmann F, Schnölzer M, Wagner N, Kopitz J, Gassler N. TP53 status regulates ACSL5-induced expression of mitochondrial mortalin in enterocytes and colorectal adenocarcinomas. Cell Tissue Res 2014; 357:267-78. [PMID: 24770931 DOI: 10.1007/s00441-014-1826-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 01/23/2014] [Indexed: 12/25/2022]
Abstract
Acyl-CoA synthetase 5 (ACSL5), a mitochondrially localized enzyme, catalyzes the synthesis of long-chain fatty acid thioesters and is physiologically involved in pro-apoptotic sensing of enterocytes. The aim of the present study is to identify an ACSL5-dependent regulation of mitochondrially expressed proteins and the characterization of related pathways in normal and diseased human intestinal mucosa. Proteomics of isolated mitochondria from ACSL5 transfectants and CaCo2 controls were performed. ACSL5-dependent protein synthesis was verified with quantitative reverse transcription plus the polymerase chain reaction, Western blotting, short-interfering-RNA-mediated gene silencing and additional cell culture experiments. Lipid changes were analyzed with tandem mass spectrometry. ACSL5-related pathways were characterized in normal mucosa and sporadic adenocarcinomas of the human intestine. In CaCo2 cells transfected with ACSL5, mortalin (HSPA9) was about two-fold increased in mitochondria, whereas cytoplasmic mortalin levels were unchanged. Disturbance of acyl-CoA/sphingolipid metabolism, induced by ACSL5 over-expression, was characterized as crucial. ACSL5-related over-expression of mitochondrial mortalin was found in HEK293 and Lovo (wild-type TP53 [tumor protein p53]) and CaCo2 (p53-negative; TP53 mutated) cells but not in Colo320DM cells (mutated TP53). In normal human intestinal mucosa, an increasing gradient of both ACSL5 and mortalin from bottom to top was observed, whereas p53 (wild-type TP53) decreased. In sporadic intestinal adenocarcinomas with strong p53 immunostaining (mutated TP53), ACSL5-related mortalin expression was heterogeneous. ACSL5-induced mitochondrial mortalin expression is assumed to be a stress response to ACSL5-related changes in lipid metabolism and is regulated by the TP53 status. Uncoupling of ACSL5 and mitochondrial mortalin by mutated TP53 could be important in colorectal carcinogenesis.
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Affiliation(s)
- Christina Klaus
- Institute of Pathology, RWTH Aachen University, Pauwelsstrasse 30, 52074, Aachen, Germany
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Wojtalewicz N, Sadeqzadeh E, Weiß JV, Tehrani MM, Klein-Scory S, Hahn S, Schmiegel W, Warnken U, Schnölzer M, de Bock CE, Thorne RF, Schwarte-Waldhoff I. A soluble form of the giant cadherin Fat1 is released from pancreatic cancer cells by ADAM10 mediated ectodomain shedding. PLoS One 2014; 9:e90461. [PMID: 24625754 PMCID: PMC3953070 DOI: 10.1371/journal.pone.0090461] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [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: 10/11/2013] [Accepted: 01/28/2014] [Indexed: 01/14/2023] Open
Abstract
In pancreatic cancer, there is a clear unmet need to identify new serum markers for either early diagnosis, therapeutic stratification or patient monitoring. Proteomic analysis of tumor cell secretomes is a promising approach to indicate proteins released from tumor cells in vitro. Ectodomain shedding of transmembrane proteins has previously been shown to contribute significant fractions the tumor cell secretomes and to generate valuable serum biomarkers. Here we introduce a soluble form of the giant cadherin Fat1 as a novel biomarker candidate. Fat1 expression and proteolytic processing was analyzed by mass spectrometry and Western blotting using pancreatic cancer cell lines as compared to human pancreatic ductal epithelial cells. RNA expression in cancer tissues was assessed by in silico analysis of publically available microarray data. Involvement of ADAM10 (A Disintegrin and metalloproteinase domain-containing protein 10) in Fat1 ectodomain shedding was analyzed by chemical inhibition and knockdown experiments. A sandwich ELISA was developed to determine levels of soluble Fat1 in serum samples. In the present report we describe the release of high levels of the ectodomain of Fat1 cadherin into the secretomes of human pancreatic cancer cells in vitro, a process that is mediated by ADAM10. We confirm the full-length and processed heterodimeric form of Fat1 expressed on the plasma membrane and also show the p60 C-terminal transmembrane remnant fragment corresponding to the shed ectodomain. Fat1 and its sheddase ADAM10 are overexpressed in pancreatic adenocarcinomas and ectodomain shedding is also recapitulated in vivo leading to increased Fat1 serum levels in some pancreatic cancer patients. We suggest that soluble Fat1 may find an application as a marker for patient monitoring complementing carbohydrate antigen 19-9 (CA19-9). In addition, detailed analysis of the diverse processed protein isoforms of the candidate tumor suppressor Fat1 can also contribute to our understanding of cell biology and tumor behavior.
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Affiliation(s)
- Nathalie Wojtalewicz
- Department of Internal Medicine, IMBL, Knappschaftskrankenhaus, Ruhr-University Bochum, Bochum, Germany
| | - Elham Sadeqzadeh
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, Australia
| | - Jakob V. Weiß
- Department of Internal Medicine, IMBL, Knappschaftskrankenhaus, Ruhr-University Bochum, Bochum, Germany
| | | | - Susanne Klein-Scory
- Department of Internal Medicine, IMBL, Knappschaftskrankenhaus, Ruhr-University Bochum, Bochum, Germany
| | - Stephan Hahn
- Department of Molecular Gastrointestinal Oncology, Ruhr-University Bochum, Bochum, Germany
| | - Wolff Schmiegel
- Department of Internal Medicine, Knappschaftskrankenhaus, Ruhr-University Bochum, Bochum, Germany
| | - Uwe Warnken
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martina Schnölzer
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Charles E. de Bock
- Center for the Biology of Disease, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
| | - Rick F. Thorne
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, Australia
| | - Irmgard Schwarte-Waldhoff
- Department of Internal Medicine, IMBL, Knappschaftskrankenhaus, Ruhr-University Bochum, Bochum, Germany
- * E-mail:
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Haderk F, Hanna B, Richter K, Schnölzer M, Zenz T, Stilgenbauer S, Lichter P, Seiffert M. Extracellular vesicles in chronic lymphocytic leukemia. Leuk Lymphoma 2014; 54:1826-30. [PMID: 23848063 DOI: 10.3109/10428194.2013.796052] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Extracellular vesicles (EVs) are membrane-enclosed nanoparticles 30 to 1000 nm in size and represent a novel mechanism of cell communication. By transferring RNA and protein from their cell of origin, they can reprogram target cells and thus are involved in changes within the cellular microenvironment - a key player in CLL pathogenesis. In the current study, we were able to isolate EVs of 20 to 300 nm from blood plasma of CLL patients as well as from supernatant of primary CLL cells in culture. Further, proteomic profiling by Coomassie staining of SDS-PAGE gels and by mass spectrometry revealed an EV-specific protein profile. These findings suggest that EVs represent an important mean of CLL cells to interact with other cells, which might contribute to the establishment of a pro-survival microenvironment for CLL cells.
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Affiliation(s)
- Franziska Haderk
- Department of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
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Schröder S, Herker E, Itzen F, He D, Thomas S, Gilchrist DA, Kaehlcke K, Cho S, Pollard KS, Capra JA, Schnölzer M, Cole PA, Geyer M, Bruneau BG, Adelman K, Ott M. Acetylation of RNA polymerase II regulates growth-factor-induced gene transcription in mammalian cells. Mol Cell 2014; 52:314-24. [PMID: 24207025 DOI: 10.1016/j.molcel.2013.10.009] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 08/26/2013] [Accepted: 09/27/2013] [Indexed: 11/17/2022]
Abstract
Lysine acetylation regulates transcription by targeting histones and nonhistone proteins. Here we report that the central regulator of transcription, RNA polymerase II, is subject to acetylation in mammalian cells. Acetylation occurs at eight lysines within the C-terminal domain (CTD) of the largest polymerase subunit and is mediated by p300/KAT3B. CTD acetylation is specifically enriched downstream of the transcription start sites of polymerase-occupied genes genome-wide, indicating a role in early stages of transcription initiation or elongation. Mutation of lysines or p300 inhibitor treatment causes the loss of epidermal growth-factor-induced expression of c-Fos and Egr2, immediate-early genes with promoter-proximally paused polymerases, but does not affect expression or polymerase occupancy at housekeeping genes. Our studies identify acetylation as a new modification of the mammalian RNA polymerase II required for the induction of growth factor response genes.
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Affiliation(s)
- Sebastian Schröder
- Gladstone Institutes, San Francisco, CA 94158, USA; University of California, San Francisco, San Francisco, CA 94143, USA
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Weiler M, Blaes J, Pusch S, Sahm F, Czabanka M, Luger S, Bunse L, Solecki G, Eichwald V, Jugold M, Hodecker S, Osswald M, Meisner C, Hielscher T, Rübmann P, Pfenning PN, Ronellenfitsch M, Kempf T, Schnölzer M, Abdollahi A, Lang F, Bendszus M, von Deimling A, Winkler F, Weller M, Vajkoczy P, Platten M, Wick W. mTOR target NDRG1 confers MGMT-dependent resistance to alkylating chemotherapy. Proc Natl Acad Sci U S A 2014; 111:409-14. [PMID: 24367102 PMCID: PMC3890826 DOI: 10.1073/pnas.1314469111] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A hypoxic microenvironment induces resistance to alkylating agents by activating targets in the mammalian target of rapamycin (mTOR) pathway. The molecular mechanisms involved in this mTOR-mediated hypoxia-induced chemoresistance, however, are unclear. Here we identify the mTOR target N-myc downstream regulated gene 1 (NDRG1) as a key determinant of resistance toward alkylating chemotherapy, driven by hypoxia but also by therapeutic measures such as irradiation, corticosteroids, and chronic exposure to alkylating agents via distinct molecular routes involving hypoxia-inducible factor (HIF)-1alpha, p53, and the mTOR complex 2 (mTORC2)/serum glucocorticoid-induced protein kinase 1 (SGK1) pathway. Resistance toward alkylating chemotherapy but not radiotherapy was dependent on NDRG1 expression and activity. In posttreatment tumor tissue of patients with malignant gliomas, NDRG1 was induced and predictive of poor response to alkylating chemotherapy. On a molecular level, NDRG1 bound and stabilized methyltransferases, chiefly O(6)-methylguanine-DNA methyltransferase (MGMT), a key enzyme for resistance to alkylating agents in glioblastoma patients. In patients with glioblastoma, MGMT promoter methylation in tumor tissue was not more predictive for response to alkylating chemotherapy in patients who received concomitant corticosteroids.
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Affiliation(s)
- Markus Weiler
- German Cancer Consortium, Clinical Cooperation Units Neurooncology and Neuropathology, Helmholtz Group Experimental Neuroimmunology, Small Animal Imaging Facility, Biostatistics, and Functional Proteome Analysis, German Cancer Research Center, D-69120 Heidelberg, Germany
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Benbahouche NEH, Iliopoulos I, Török I, Marhold J, Henri J, Kajava AV, Farkaš R, Kempf T, Schnölzer M, Meyer P, Kiss I, Bertrand E, Mechler BM, Pradet-Balade B. Drosophila Spag is the homolog of RNA polymerase II-associated protein 3 (RPAP3) and recruits the heat shock proteins 70 and 90 (Hsp70 and Hsp90) during the assembly of cellular machineries. J Biol Chem 2014; 289:6236-47. [PMID: 24394412 DOI: 10.1074/jbc.m113.499608] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The R2TP is a recently identified Hsp90 co-chaperone, composed of four proteins as follows: Pih1D1, RPAP3, and the AAA(+)-ATPases RUVBL1 and RUVBL2. In mammals, the R2TP is involved in the biogenesis of cellular machineries such as RNA polymerases, small nucleolar ribonucleoparticles and phosphatidylinositol 3-kinase-related kinases. Here, we characterize the spaghetti (spag) gene of Drosophila, the homolog of human RPAP3. This gene plays an essential function during Drosophila development. We show that Spag protein binds Drosophila orthologs of R2TP components and Hsp90, like its yeast counterpart. Unexpectedly, Spag also interacts and stimulates the chaperone activity of Hsp70. Using null mutants and flies with inducible RNAi, we show that spaghetti is necessary for the stabilization of snoRNP core proteins and target of rapamycin activity and likely the assembly of RNA polymerase II. This work highlights the strong conservation of both the HSP90/R2TP system and its clients and further shows that Spag, unlike Saccharomyces cerevisiae Tah1, performs essential functions in metazoans. Interaction of Spag with both Hsp70 and Hsp90 suggests a model whereby R2TP would accompany clients from Hsp70 to Hsp90 to facilitate their assembly into macromolecular complexes.
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Affiliation(s)
- Nour El Houda Benbahouche
- From the Equipe Labellisée Ligue Contre le Cancer, Institut de Génétique Moléculaire de Montpellier, UMR 5535 CNRS, 1919 Route de Mende, 34293 Montpellier Cedex 5, France
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Felix K, Hauck O, Fritz S, Hinz U, Schnölzer M, Kempf T, Warnken U, Michel A, Pawlita M, Werner J. Serum protein signatures differentiating autoimmune pancreatitis versus pancreatic cancer. PLoS One 2013; 8:e82755. [PMID: 24349355 PMCID: PMC3857261 DOI: 10.1371/journal.pone.0082755] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 11/04/2013] [Indexed: 12/24/2022] Open
Abstract
Autoimmune pancreatitis (AIP) is defined by characteristic lymphoplasmacytic infiltrate, ductal strictures and a pancreatic enlargement or mass that can mimic pancreatic cancer (PaCa). The distinction between this benign disease and pancreatic cancer can be challenging. However, an accurate diagnosis may pre-empt the misdiagnosis of cancer, allowing the appropriate medical treatment of AIP and, consequently, decreasing the number of unnecessary pancreatic resections. Mass spectrometry (MS) and two-dimensional differential gel electrophoresis (2D-DIGE) have been applied to analyse serum protein alterations associated with AIP and PaCa, and to identify protein signatures indicative of the diseases. Patients' sera were immunodepleted from the 20 most prominent serum proteins prior to further 2D-DIGE and image analysis. The identity of the most-discriminatory proteins detected, was performed by MS and ELISAs were applied to confirm their expression. Serum profiling data analysis with 2D-DIGE revealed 39 protein peaks able to discriminate between AIP and PaCa. Proteins were purified and further analysed by MALDI-TOF-MS. Peptide mass fingerprinting led to identification of eleven proteins. Among them apolipoprotein A-I, apolipoprotein A-II, transthyretin, and tetranectin were identified and found as 3.0-, 3.5-, 2-, and 1.6-fold decreased in PaCa sera, respectively, whereas haptoglobin and apolipoprotein E were found to be 3.8- and 1.6-fold elevated in PaCa sera. With the exception of haptoglobin the ELISA results of the identified proteins confirmed the 2D-DIGE image analysis characteristics. Integration of the identified serum proteins as AIP markers may have considerable potential to provide additional information for the diagnosis of AIP to choose the appropriate treatment.
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Affiliation(s)
- Klaus Felix
- Department of General Surgery, University of Heidelberg, INF 110, Heidelberg, Germany
- * E-mail: (KF)
| | - Oliver Hauck
- Department of General Surgery, University of Heidelberg, INF 110, Heidelberg, Germany
| | - Stefan Fritz
- Department of General Surgery, University of Heidelberg, INF 110, Heidelberg, Germany
| | - Ulf Hinz
- Department of General Surgery, University of Heidelberg, INF 110, Heidelberg, Germany
| | - Martina Schnölzer
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), INF 580, Heidelberg, Germany
| | - Tore Kempf
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), INF 580, Heidelberg, Germany
| | - Uwe Warnken
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), INF 580, Heidelberg, Germany
| | - Angelika Michel
- Infection and Cancer Program, German Cancer Research Center (DKFZ), INF 260, Heidelberg, Germany
| | - Michael Pawlita
- Infection and Cancer Program, German Cancer Research Center (DKFZ), INF 260, Heidelberg, Germany
| | - Jens Werner
- Department of General Surgery, University of Heidelberg, INF 110, Heidelberg, Germany
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Li J, Bonifati S, Hristov G, Marttila T, Valmary-Degano S, Stanzel S, Schnölzer M, Mougin C, Aprahamian M, Grekova SP, Raykov Z, Rommelaere J, Marchini A. Synergistic combination of valproic acid and oncolytic parvovirus H-1PV as a potential therapy against cervical and pancreatic carcinomas. EMBO Mol Med 2013; 5:1537-55. [PMID: 24092664 PMCID: PMC3799578 DOI: 10.1002/emmm.201302796] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [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: 03/25/2013] [Revised: 08/05/2013] [Accepted: 08/07/2013] [Indexed: 11/24/2022] Open
Abstract
The rat parvovirus H-1PV has oncolytic and tumour-suppressive properties potentially exploitable in cancer therapy. This possibility is being explored and results are encouraging, but it is necessary to improve the oncotoxicity of the virus. Here we show that this can be achieved by co-treating cancer cells with H-1PV and histone deacetylase inhibitors (HDACIs) such as valproic acid (VPA). We demonstrate that these agents act synergistically to kill a range of human cervical carcinoma and pancreatic carcinoma cell lines by inducing oxidative stress, DNA damage and apoptosis. Strikingly, in rat and mouse xenograft models, H-1PV/VPA co-treatment strongly inhibits tumour growth promoting complete tumour remission in all co-treated animals. At the molecular level, we found acetylation of the parvovirus nonstructural protein NS1 at residues K85 and K257 to modulate NS1-mediated transcription and cytotoxicity, both of which are enhanced by VPA treatment. These results warrant clinical evaluation of H-1PV/VPA co-treatment against cervical and pancreatic ductal carcinomas.
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Affiliation(s)
- Junwei Li
- Infection and Cancer Program, Tumor Virology Division (F010), German Cancer Research Center (DKFZ), Heidelberg, Germany
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Djuika CF, Fiedler S, Schnölzer M, Sanchez C, Lanzer M, Deponte M. Plasmodium falciparum antioxidant protein as a model enzyme for a special class of glutaredoxin/glutathione-dependent peroxiredoxins. Biochim Biophys Acta Gen Subj 2013; 1830:4073-90. [DOI: 10.1016/j.bbagen.2013.04.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 04/15/2013] [Accepted: 04/16/2013] [Indexed: 01/06/2023]
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Aretz S, Krohne TU, Kammerer K, Warnken U, Hotz-Wagenblatt A, Bergmann M, Stanzel BV, Kempf T, Holz FG, Schnölzer M, Kopitz J. In-depth mass spectrometric mapping of the human vitreous proteome. Proteome Sci 2013; 11:22. [PMID: 23688336 PMCID: PMC3689628 DOI: 10.1186/1477-5956-11-22] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [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] [Received: 01/15/2013] [Accepted: 04/26/2013] [Indexed: 01/31/2023] Open
Abstract
Mapping of proteins involved in normal eye functions is a prerequisite to identify pathological changes during eye disease processes. We therefore analysed the proteome of human vitreous by applying in-depth proteomic screening technologies. For ethical reasons human vitreous samples were obtained by vitrectomy from “surrogate normal patients” with epiretinal gliosis that is considered to constitute only negligible pathological vitreoretinal changes. We applied different protein prefractionation strategies including liquid phase isoelectric focussing, 1D SDS gel electrophoresis and a combination of both and compared the number of identified proteins obtained by the respective method. Liquid phase isoelectric focussing followed by SDS gel electrophoresis increased the number of identified proteins by a factor of five compared to the analysis of crude unseparated human vitreous. Depending on the prefractionation method proteins were subjected to trypsin digestion either in-gel or in solution and the resulting peptides were analysed on a UPLC system coupled online to an LTQ Orbitrap XL mass spectrometer. The obtained mass spectra were searched against the SwissProt database using the Mascot search engine. Bioinformatics tools were used to annotate known biological functions to the detected proteins. Following this strategy we examined the vitreous proteomes of three individuals and identified 1111 unique proteins. Besides structural, transport and binding proteins, we detected 261 proteins with known enzymatic activity, 51 proteases, 35 protease inhibitors, 35 members of complement and coagulation cascades, 15 peptide hormones, 5 growth factors, 11 cytokines, 47 receptors, 30 proteins of visual perception, 91 proteins involved in apoptosis regulation and 265 proteins with signalling activity. This highly complex mixture strikingly differs from the human plasma proteome. Thus human vitreous fluid seems to be a unique body fluid. 262 unique proteins were detected which are present in all three patient samples indicating that these might represent the constitutive protein pattern of human vitreous. The presented catalogue of human vitreous proteins will enhance our understanding of physiological processes in the eye and provides the groundwork for future studies on pathological vitreous proteome changes.
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Affiliation(s)
- Sebastian Aretz
- Institute of Pathology, University of Heidelberg, Im Neuenheimer Feld 220, Heidelberg, D-69120, Germany.
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Mier W, Krämer S, Zitzmann S, Altmann A, Leotta K, Schierbaum U, Schnölzer M, Eisenhut M, Haberkorn U. PEGylation enables the specific tumor accumulation of a peptide identified by phage display. Org Biomol Chem 2013; 11:2706-11. [DOI: 10.1039/c3ob27475f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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