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Bley H, Krisp C, Schöbel A, Hehner J, Schneider L, Becker M, Stegmann C, Heidenfels E, Nguyen-Dinh V, Schlüter H, Gerold G, Herker E. Proximity labeling of host factor ANXA3 in HCV infection reveals a novel LARP1 function in viral entry. J Biol Chem 2024:107286. [PMID: 38636657 DOI: 10.1016/j.jbc.2024.107286] [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: 12/20/2023] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 04/20/2024] Open
Abstract
Hepatitis C virus (HCV) infection is tightly connected to the lipid metabolism with lipid droplets (LDs) serving as assembly sites for progeny virions. A previous LD proteome analysis identified annexin A3 (ANXA3) as an important HCV host factor that is enriched at LDs in infected cells and required for HCV morphogenesis. To further characterize ANXA3 function in HCV, we performed proximity labeling using ANXA3-BioID2 as bait in HCV-infected cells. Two of the top proteins identified proximal to ANXA3 during HCV infection were the La-related protein 1 (LARP1) and the ADP ribosylation factor-like protein 8B (ARL8B), both of which have been previously described to act in HCV particle production. In follow-up experiments ARL8B functioned as a pro-viral HCV host factor without localizing to LDs and thus likely independent of ANXA3. In contrast, LARP1 interacts with HCV core protein in an RNA-dependent manner and is translocated to LDs by core protein. Knockdown of LARP1 decreased HCV spreading without altering HCV RNA replication or viral titers. Unexpectedly, entry of HCV particles and E1/E2-pseudotyped lentiviral particles was reduced by LARP1 depletion, whereas particle production was not altered. Using a recombinant vesicular stomatitis virus (VSV)ΔG entry assay, we showed that LARP1 depletion also decreased entry of VSV with VSV, MERS, and CHIKV glycoproteins. Therefore, our data expand the role of LARP1 as an HCV host factor that is most prominently involved in the early steps of infection, likely contributing to endocytosis of viral particles through the pleiotropic effect LARP1 has on the cellular translatome.
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Affiliation(s)
- Hanna Bley
- Institute of Virology, Philipps-University Marburg, Marburg, Germany
| | - Christoph Krisp
- Section Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Anja Schöbel
- Institute of Virology, Philipps-University Marburg, Marburg, Germany
| | - Julia Hehner
- Institute of Virology, Philipps-University Marburg, Marburg, Germany
| | - Laura Schneider
- Institute of Virology, Philipps-University Marburg, Marburg, Germany
| | - Miriam Becker
- Institute for Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hanover, Hanover, Germany
| | - Cora Stegmann
- Institute for Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hanover, Hanover, Germany
| | - Elisa Heidenfels
- Institute of Virology, Philipps-University Marburg, Marburg, Germany
| | - Van Nguyen-Dinh
- Institute of Virology, Philipps-University Marburg, Marburg, Germany
| | - Hartmut Schlüter
- Section Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Gisa Gerold
- Institute for Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hanover, Hanover, Germany; Department of Clinical Microbiology, Virology, Umeå University, Umeå, Sweden; Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden
| | - Eva Herker
- Institute of Virology, Philipps-University Marburg, Marburg, Germany,.
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2
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Henis M, Rücker T, Scharrenberg R, Richter M, Baltussen L, Hong S, Meka DP, Schwanke B, Neelagandan N, Daaboul D, Murtaza N, Krisp C, Harder S, Schlüter H, Kneussel M, Hermans-Borgmeyer I, de Wit J, Singh KK, Duncan KE, de Anda FC. The autism susceptibility kinase, TAOK2, phosphorylates eEF2 and modulates translation. Sci Adv 2024; 10:eadf7001. [PMID: 38608030 PMCID: PMC11014455 DOI: 10.1126/sciadv.adf7001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 03/12/2024] [Indexed: 04/14/2024]
Abstract
Genes implicated in translation control have been associated with autism spectrum disorders (ASDs). However, some important genetic causes of autism, including the 16p11.2 microdeletion, bear no obvious connection to translation. Here, we use proteomics, genetics, and translation assays in cultured cells and mouse brain to reveal altered translation mediated by loss of the kinase TAOK2 in 16p11.2 deletion models. We show that TAOK2 associates with the translational machinery and functions as a translational brake by phosphorylating eukaryotic elongation factor 2 (eEF2). Previously, all signal-mediated regulation of translation elongation via eEF2 phosphorylation was believed to be mediated by a single kinase, eEF2K. However, we show that TAOK2 can directly phosphorylate eEF2 on the same regulatory site, but functions independently of eEF2K signaling. Collectively, our results reveal an eEF2K-independent signaling pathway for control of translation elongation and suggest altered translation as a molecular component in the etiology of some forms of ASD.
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Affiliation(s)
- Melad Henis
- Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
- Department of Anatomy and Embryology, Faculty of Veterinary Medicine, New Valley University, 72511 El-Kharga, Egypt
| | - Tabitha Rücker
- Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Robin Scharrenberg
- Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Melanie Richter
- Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Lucas Baltussen
- VIB Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium
- KU Leuven Department of Neurosciences, Leuven Brain Institute, Herestraat 49, 3000 Leuven, Belgium
| | - Shuai Hong
- Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Durga Praveen Meka
- Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Birgit Schwanke
- Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Nagammal Neelagandan
- Neuronal Translational Control Group, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), Falkenried 94, 20251 Hamburg, Germany
- Institute of Bioengineering (IBI), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Danie Daaboul
- VIB Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium
- KU Leuven Department of Neurosciences, Leuven Brain Institute, Herestraat 49, 3000 Leuven, Belgium
| | - Nadeem Murtaza
- Krembil Research Institute, Donald K. Johnson Eye Institute, University Health Network, 60 Leonard Ave, Toronto, Ontario M5T 0S8, Canada
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster University, Hamilton, Ontario L8S 4A9, Canada
| | - Christoph Krisp
- Institute for Clinical Chemistry and Laboratory Medicine, Mass Spectrometric Proteomics Group, Campus Forschung, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany
| | - Sönke Harder
- Institute for Clinical Chemistry and Laboratory Medicine, Mass Spectrometric Proteomics Group, Campus Forschung, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany
| | - Hartmut Schlüter
- Institute for Clinical Chemistry and Laboratory Medicine, Mass Spectrometric Proteomics Group, Campus Forschung, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany
| | - Matthias Kneussel
- Institute of Neurogenetics, Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf (UKE), 20251 Hamburg, Germany
| | - Irm Hermans-Borgmeyer
- Transgenic Service Group, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), Falkenried 94, 20251 Hamburg, Germany
| | - Joris de Wit
- VIB Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium
- KU Leuven Department of Neurosciences, Leuven Brain Institute, Herestraat 49, 3000 Leuven, Belgium
| | - Karun K. Singh
- Krembil Research Institute, Donald K. Johnson Eye Institute, University Health Network, 60 Leonard Ave, Toronto, Ontario M5T 0S8, Canada
- Faculty of Medicine, University of Toronto, Medical Sciences Building, 1 King's College Cir, Toronto, Ontario M5S 1 A8, Canada
| | - Kent E. Duncan
- Neuronal Translational Control Group, Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf (UKE), Falkenried 94, 20251 Hamburg, Germany
- Evotec SE, Manfred Eigen Campus, Essener Bogen 7, 22419 Hamburg, Germany
| | - Froylan Calderón de Anda
- Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
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3
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Schneegans S, Löptien J, Mojzisch A, Loreth D, Kretz O, Raschdorf C, Hanssen A, Gocke A, Siebels B, Gunasekaran K, Ding Y, Oliveira-Ferrer L, Brylka L, Schinke T, Schlüter H, Paatero I, Voß H, Werner S, Pantel K, Wikman H. HERC5 downregulation in non-small cell lung cancer is associated with altered energy metabolism and metastasis. J Exp Clin Cancer Res 2024; 43:110. [PMID: 38605423 PMCID: PMC11008035 DOI: 10.1186/s13046-024-03020-z] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/20/2024] [Indexed: 04/13/2024] Open
Abstract
BACKGROUND Metastasis is the leading cause of cancer-related death in non-small cell lung cancer (NSCLC) patients. We previously showed that low HERC5 expression predicts early tumor dissemination and a dismal prognosis in NSCLC patients. Here, we performed functional studies to unravel the mechanism underlying the "metastasis-suppressor" effect of HERC5, with a focus on mitochondrial metabolism pathways. METHODS We assessed cell proliferation, colony formation potential, anchorage-independent growth, migration, and wound healing in NSCLC cell line models with HERC5 overexpression (OE) or knockout (KO). To study early tumor cell dissemination, we used these cell line models in zebrafish experiments and performed intracardial injections in nude mice. Mass spectrometry (MS) was used to analyze protein changes in whole-cell extracts. Furthermore, electron microscopy (EM) imaging, cellular respiration, glycolytic activity, and lactate production were used to investigate the relationships with mitochondrial energy metabolism pathways. RESULTS Using different in vitro NSCLC cell line models, we showed that NSCLC cells with low HERC5 expression had increased malignant and invasive properties. Furthermore, two different in vivo models in zebrafish and a xenograft mouse model showed increased dissemination and metastasis formation (in particular in the brain). Functional enrichment clustering of MS data revealed an increase in mitochondrial proteins in vitro when HERC5 levels were high. Loss of HERC5 leads to an increased Warburg effect, leading to improved adaptation and survival under prolonged inhibition of oxidative phosphorylation. CONCLUSIONS Taken together, these results indicate that low HERC5 expression increases the metastatic potential of NSCLC in vitro and in vivo. Furthermore, HERC5-induced proteomic changes influence mitochondrial pathways, ultimately leading to alterations in energy metabolism and demonstrating its role as a new potential metastasis suppressor gene.
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Affiliation(s)
- Svenja Schneegans
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Jana Löptien
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Angelika Mojzisch
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Desirée Loreth
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Oliver Kretz
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christoph Raschdorf
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Annkathrin Hanssen
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Antonia Gocke
- Section Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg- Eppendorf, Hamburg, Germany
| | - Bente Siebels
- Section Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Karthikeyan Gunasekaran
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Yi Ding
- Department of Gynecology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Laura Brylka
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thorsten Schinke
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hartmut Schlüter
- Section Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ilkka Paatero
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Hannah Voß
- Section Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Werner
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Klaus Pantel
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Harriet Wikman
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany.
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Rezasoltani S, Looha MA, Aghdaei HA, Jasemi S, Sechi LA, Gazouli M, Sadeghi A, Torkashvand S, Baniali R, Schlüter H, Zali MR, Feizabadi MM. Correction to: 16 S rRNA sequencing analysis of the oral and fecal microbiota in colorectal cancer positives versus colorectal cancer negatives in Iranian population. Gut Pathog 2024; 16:15. [PMID: 38504333 PMCID: PMC10949609 DOI: 10.1186/s13099-024-00607-x] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/21/2024] Open
Affiliation(s)
- Sama Rezasoltani
- Section Mass Spectrometric Proteomics, Diagnostic Center, University Medical Center Hamburg-Eppendorf (UKE), 20246, Hamburg, Germany
- Division of Oral Microbiology and Immunology, Department of Operative Dentistry, Periodontology and Preventive Dentistry, RWTH University Hospital, Pauwelsstrasse 30, 52057, Aachen, Germany
| | - Mehdi Azizmohammad Looha
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, 19835-178, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, 19835-178, Iran
| | - Seyedesomayeh Jasemi
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43b, Sassari, 07100, Italy
| | - Leonardo Antonio Sechi
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43b, Sassari, 07100, Italy.
- Struttura Complessa Microbiologia e Virologia, Azienda Ospedaliera Universitaria, Sassari, 07100, Italy.
| | - Maria Gazouli
- Department of Basic Medical Sciences, Laboratory of Biology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Amir Sadeghi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, 19835-178, Iran
| | - Shirin Torkashvand
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, 19835-178, Iran
| | - Reyhaneh Baniali
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, 19835-178, Iran
| | - Hartmut Schlüter
- Section Mass Spectrometric Proteomics, Diagnostic Center, University Medical Center Hamburg-Eppendorf (UKE), 20246, Hamburg, Germany
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, 19835-178, Iran
| | - Mohammad Mehdi Feizabadi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, 19835-178, Iran.
- Thoracic Research Center, Imam Khomeini Hospital Complex, Tehran University of medical Sciences, Tehran, Iran.
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5
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Meka DP, Richter M, Rücker T, Voss H, Rissiek A, Krisp C, Kumar NH, Schwanke B, Fornasiero EF, Schlüter H, Calderon de Anda F. Protocol for differential multi-omic analyses of distinct cell types in the mouse cerebral cortex. STAR Protoc 2024; 5:102793. [PMID: 38157295 PMCID: PMC10792265 DOI: 10.1016/j.xpro.2023.102793] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/05/2023] [Accepted: 12/06/2023] [Indexed: 01/03/2024] Open
Abstract
Here, we present a protocol for differential multi-omic analyses of distinct cell types in the developing mouse cerebral cortex. We describe steps for in utero electroporation, subsequent flow-cytometry-based isolation of developing mouse cortical cells, bulk RNA sequencing or quantitative liquid chromatography-tandem mass spectrometry, and bioinformatic analyses. This protocol can be applied to compare the proteomes and transcriptomes of developing mouse cortical cell populations after various manipulations (e.g., epigenetic). For complete details on the use and execution of this protocol, please refer to Meka et al. (2022).1.
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Affiliation(s)
- Durga Praveen Meka
- RG Neuronal Development, Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Melanie Richter
- RG Neuronal Development, Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Tabitha Rücker
- RG Neuronal Development, Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany.
| | - Hannah Voss
- Institute for Clinical Chemistry and Laboratory Medicine, Mass Spectrometric Proteomics Group, Campus Forschung, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Anne Rissiek
- Cytometry und Cell Sorting Core Unit, Department of Stem Cell Transplantation, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Christoph Krisp
- Institute for Clinical Chemistry and Laboratory Medicine, Mass Spectrometric Proteomics Group, Campus Forschung, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Nisha Hemandhar Kumar
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Birgit Schwanke
- RG Neuronal Development, Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Eugenio F Fornasiero
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany; Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Hartmut Schlüter
- Diagnostic Center, Section Mass Spectrometric Proteomics Group, Campus Forschung, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany.
| | - Froylan Calderon de Anda
- RG Neuronal Development, Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany.
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6
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Rezasoltani S, Azizmohammad Looha M, Asadzadeh Aghdaei H, Jasemi S, Sechi LA, Gazouli M, Sadeghi A, Torkashvand S, Baniali R, Schlüter H, Zali MR, Feizabadi MM. 16S rRNA sequencing analysis of the oral and fecal microbiota in colorectal cancer positives versus colorectal cancer negatives in Iranian population. Gut Pathog 2024; 16:9. [PMID: 38378690 PMCID: PMC10880352 DOI: 10.1186/s13099-024-00604-0] [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] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 02/06/2024] [Indexed: 02/22/2024] Open
Abstract
BACKGROUND Colorectal cancer (CRC) poses a significant healthcare challenge, accounting for nearly 6.1% of global cancer cases. Early detection, facilitated by population screening utilizing innovative biomarkers, is pivotal for mitigating CRC incidence. This study aims to scrutinize the fecal and salivary microbiomes of CRC-positive individuals (CPs) in comparison to CRC-negative counterparts (CNs) to enhance early CRC diagnosis through microbial biomarkers. MATERIAL AND METHODS A total of 80 oral and stool samples were collected from Taleghani Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran, encompassing both CPs and CNs undergoing screening. Microbial profiling was conducted using 16S rRNA sequencing assays, employing the Nextera XT Index Kit on an Illumina NovaSeq platform. RESULTS Distinct microbial profiles were observed in saliva and stool samples of CPs, diverging significantly from those of CNs at various taxonomic levels, including phylum, family, and species. Saliva samples from CPs exhibited abundance of Calothrix parietina, Granulicatella adiacens, Rothia dentocariosa, and Rothia mucilaginosa, absent in CNs. Additionally, Lachnospiraceae and Prevotellaceae were markedly higher in CPs' feces, while the Fusobacteria phylum was significantly elevated in CPs' saliva. Conversely, the non-pathogenic bacterium Akkermansia muciniphila exhibited a significant decrease in CPs' fecal samples compared to CNs. CONCLUSION Through meticulous selection of saliva and stool microbes based on Mean Decrease GINI values and employing logistic regression for saliva and support vector machine models for stool, we successfully developed a microbiota test with heightened sensitivity and specificity for early CRC detection.
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Grants
- RIGLD1065 Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- RIGLD1065 Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Regione Autonoma della Sardegna, legge regionale 12 dicembre 2022, n. 22 UNISS FAR fondi ricercar 2021, 2022 and Fondazione di Sardegna 2017
- Regione Autonoma della Sardegna, legge regionale 12 dicembre 2022, n. 22 UNISS FAR fondi ricercar 2021, 2022 and Fondazione di Sardegna 2017
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Affiliation(s)
- Sama Rezasoltani
- Section Mass Spectrometric Proteomics, Diagnostic Center, University Medical Center Hamburg-Eppendorf (UKE), 20246, Hamburg, Germany
- Division of Oral Microbiology and Immunology, Department of Operative Dentistry, Periodontology and Preventive Dentistry, RWTH University Hospital, 52057 Aachen, Germany
| | - Mehdi Azizmohammad Looha
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, 19835-178, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, 19835-178, Iran
| | - Seyedesomayeh Jasemi
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43b, 07100, Sassari, Italy
| | - Leonardo Antonio Sechi
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43b, 07100, Sassari, Italy.
- Struttura Complessa Microbiologia e Virologia, Azienda Ospedaliera Universitaria, 07100 Sassari, Italy.
| | - Maria Gazouli
- Department of Basic Medical Sciences, Laboratory of Biology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Amir Sadeghi
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, 19835-178, Iran
| | - Shirin Torkashvand
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, 19835-178, Iran
| | - Reyhaneh Baniali
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, 19835-178, Iran
| | - Hartmut Schlüter
- Section Mass Spectrometric Proteomics, Diagnostic Center, University Medical Center Hamburg-Eppendorf (UKE), 20246, Hamburg, Germany
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, 19835-178, Iran
| | - Mohammad Mehdi Feizabadi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, 19835-178, Iran.
- Thoracic Research Center, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran.
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7
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Laskou A, Znalesniak EB, Harder S, Schlüter H, Jechorek D, Langer K, Strecker C, Matthes C, Tchaikovski SN, Hoffmann W. Different Forms of TFF3 in the Human Endocervix, including a Complex with IgG Fc Binding Protein (FCGBP), and Further Aspects of the Cervico-Vaginal Innate Immune Barrier. Int J Mol Sci 2024; 25:2287. [PMID: 38396964 PMCID: PMC10888570 DOI: 10.3390/ijms25042287] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/05/2024] [Accepted: 02/10/2024] [Indexed: 02/25/2024] Open
Abstract
TFF3 is a typical secretory poplypeptide of mucous epithelia belonging to the trefoil factor family (TFF) of lectins. In the intestine, respiratory tract, and saliva, TFF3 mainly exists as a high-molecular-mass complex with IgG Fc binding protein (FCGBP), which is indicative of a role in mucosal innate immunity. For the first time, we identified different forms of TFF3 in the endocervix, i.e., monomeric and homodimeric TFF3, as well as a high-molecular-mass TFF3-FCGBP complex; the latter also exists in a hardly soluble form. Immunohistochemistry co-localized TFF3 and FCGBP. Expression analyses of endocervical and post-menopausal vaginal specimens revealed a lack of mucin and TFF3 transcripts in the vaginal specimens. In contrast, genes encoding other typical components of the innate immune defense were expressed in both the endocervix and vagina. Of note, FCGBP is possibly fucosylated. Endocervical specimens from transgender individuals after hormonal therapy showed diminished expression, particularly of FCGBP. Furthermore, mucus swabs from the endocervix and vagina were analyzed concerning TFF3, FCGBP, and lysozyme. It was the aim of this study to illuminate several aspects of the cervico-vaginal innate immune barrier, which is clinically relevant as bacterial and viral infections are also linked to infertility, pre-term birth and cervical cancer.
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Affiliation(s)
- Aikaterini Laskou
- Institute of Molecular Biology and Medicinal Chemistry, Otto-von-Guericke University Magdeburg, Leipziger Str. 44, 39120 Magdeburg, Germany
| | - Eva B. Znalesniak
- Institute of Molecular Biology and Medicinal Chemistry, Otto-von-Guericke University Magdeburg, Leipziger Str. 44, 39120 Magdeburg, Germany
| | - Sönke Harder
- Section Mass Spectrometric Proteomics, Diagnostic Center, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Hartmut Schlüter
- Section Mass Spectrometric Proteomics, Diagnostic Center, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Dörthe Jechorek
- Institute of Pathology, Otto-von-Guericke University Magdeburg, Leipziger Str. 44, 39120 Magdeburg, Germany
| | - Kathrin Langer
- Institute of Pathology, Otto-von-Guericke University Magdeburg, Leipziger Str. 44, 39120 Magdeburg, Germany
| | - Carina Strecker
- Department of Gynecology and Obstetrics, Otto-von-Guericke University Magdeburg, Gerhart-Hauptmann-Str. 35, 39108 Magdeburg, Germany
| | - Claudia Matthes
- Department of Gynecology and Obstetrics, Otto-von-Guericke University Magdeburg, Gerhart-Hauptmann-Str. 35, 39108 Magdeburg, Germany
| | - Svetlana N. Tchaikovski
- Department of Gynecology and Obstetrics, Otto-von-Guericke University Magdeburg, Gerhart-Hauptmann-Str. 35, 39108 Magdeburg, Germany
| | - Werner Hoffmann
- Institute of Molecular Biology and Medicinal Chemistry, Otto-von-Guericke University Magdeburg, Leipziger Str. 44, 39120 Magdeburg, Germany
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8
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Pietsch N, Chen CY, Kupsch S, Bacmeister L, Geertz B, Herera-Rivero M, Voß H, Krämer E, Braren I, Westermann D, Schlüter H, Mearini G, Schlossarek S, van der Velden J, Caporizzo MA, Lindner D, Prosser BL, Carrier L. Chronic activation of tubulin tyrosination in HCM mice and human iPSC-engineered heart tissues improves heart function. bioRxiv 2024:2023.05.25.542365. [PMID: 37292763 PMCID: PMC10245930 DOI: 10.1101/2023.05.25.542365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Rationale: Hypertrophic cardiomyopathy (HCM) is the most common cardiac genetic disorder caused by sarcomeric gene variants and associated with left ventricular (LV) hypertrophy and diastolic dysfunction. The role of the microtubule network has recently gained interest with the findings that -α-tubulin detyrosination (dTyr-tub) is markedly elevated in heart failure. Acute reduction of dTyr-tub by inhibition of the detyrosinase (VASH/SVBP complex) or activation of the tyrosinase (tubulin tyrosine ligase, TTL) markedly improved contractility and reduced stiffness in human failing cardiomyocytes, and thus poses a new perspective for HCM treatment. Objective: In this study, we tested the impact of chronic tubulin tyrosination in a HCM mouse model ( Mybpc3 -knock-in; KI), in human HCM cardiomyocytes and in SVBP-deficient human engineered heart tissues (EHTs). Methods and Results: AAV9-mediated TTL transfer was applied in neonatal wild-type (WT) rodents and 3-week-old KI mice and in HCM human induced pluripotent stem cell (hiPSC)-derived cardiomyocytes. We show that i) TTL for 6 weeks dose-dependently reduced dTyr-tub and improved contractility without affecting cytosolic calcium transients in WT cardiomyocytes; ii) TTL for 12 weeks improved diastolic filling, cardiac output and stroke volume and reduced stiffness in KI mice; iii) TTL for 10 days normalized cell hypertrophy in HCM hiPSC-cardiomyocytes; iv) TTL induced a marked transcription and translation of several tubulins and modulated mRNA or protein levels of components of mitochondria, Z-disc, ribosome, intercalated disc, lysosome and cytoskeleton in KI mice; v) SVBP-deficient EHTs exhibited reduced dTyr-tub levels, higher force and faster relaxation than TTL-deficient and WT EHTs. RNA-seq and mass spectrometry analysis revealed distinct enrichment of cardiomyocyte components and pathways in SVBP-KO vs. TTL-KO EHTs. Conclusion: This study provides the first proof-of-concept that chronic activation of tubulin tyrosination in HCM mice and in human EHTs improves heart function and holds promise for targeting the non-sarcomeric cytoskeleton in heart disease.
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9
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Tholey A, Schlüter H. Top-down proteomics and proteoforms - special issue. Proteomics 2024; 24:e2200375. [PMID: 38351467 DOI: 10.1002/pmic.202200375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 11/09/2023] [Indexed: 02/16/2024]
Affiliation(s)
- Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Hartmut Schlüter
- Institute of Clinical Chemistry and Laboratory Medicine, Section Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
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10
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Hidayah SN, Biabani A, Gaikwad M, Nissen P, Voß H, Riedner M, Schlüter H, Siebels B. Application of sample displacement batch chromatography for fractionation of proteoforms. Proteomics 2024; 24:e2200424. [PMID: 37750450 DOI: 10.1002/pmic.202200424] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/27/2023]
Abstract
Fractionation of proteoforms is currently the most challenging topic in the field of proteoform analysis. The need for considering the existence of proteoforms in experimental approaches is not only important in Life Science research in general but especially in the manufacturing of therapeutic proteins (TPs) like recombinant therapeutic antibodies (mAbs). Some of the proteoforms of TPs have significantly decreased actions or even cause side effects. The identification and removal of proteoforms differing from the main species, having the desired action, is challenging because the difference in the composition of atoms is often very small and their concentration in comparison to the main proteoform can be low. In this study, we demonstrate that sample displacement batch chromatography (SDBC) is an easy-to-handle, economical, and efficient method for fractionating proteoforms. As a model sample a commercial ovalbumin fraction was used, containing many ovalbumin proteoforms. The most promising parameters for the SDBC were determined by a screening approach and applied for a 10-segment fractionation of ovalbumin with cation exchange chromatography resins. Mass spectrometry of intact proteoforms was used for characterizing the SDBC fractionation process. By SDBC, a significant separation of different proteoforms was obtained.
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Affiliation(s)
- Siti Nurul Hidayah
- Section Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Universitas Gadjah Mada, Sleman, Yogyakarta, Indonesia
| | - Ali Biabani
- Section Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Manasi Gaikwad
- Section Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Paula Nissen
- Section Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hannah Voß
- Section Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maria Riedner
- Technology Platform Mass Spectrometry, University of Hamburg, Hamburg, Germany
| | - Hartmut Schlüter
- Section Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Bente Siebels
- Section Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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11
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Worthmann A, Ridder J, Piel SYL, Evangelakos I, Musfeldt M, Voß H, O'Farrell M, Fischer AW, Adak S, Sundd M, Siffeti H, Haumann F, Kloth K, Bierhals T, Heine M, Pertzborn P, Pauly M, Scholz JJ, Kundu S, Fuh MM, Neu A, Tödter K, Hempel M, Knippschild U, Semenkovich CF, Schlüter H, Heeren J, Scheja L, Kubisch C, Schlein C. Fatty acid synthesis suppresses dietary polyunsaturated fatty acid use. Nat Commun 2024; 15:45. [PMID: 38167725 PMCID: PMC10762034 DOI: 10.1038/s41467-023-44364-y] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
Dietary polyunsaturated fatty acids (PUFA) are increasingly recognized for their health benefits, whereas a high production of endogenous fatty acids - a process called de novo lipogenesis (DNL) - is closely linked to metabolic diseases. Determinants of PUFA incorporation into complex lipids are insufficiently understood and may influence the onset and progression of metabolic diseases. Here we show that fatty acid synthase (FASN), the key enzyme of DNL, critically determines the use of dietary PUFA in mice and humans. Moreover, the combination of FASN inhibition and PUFA-supplementation decreases liver triacylglycerols (TAG) in mice fed with high-fat diet. Mechanistically, FASN inhibition causes higher PUFA uptake via the lysophosphatidylcholine transporter MFSD2A, and a diacylglycerol O-acyltransferase 2 (DGAT2)-dependent incorporation of PUFA into TAG. Overall, the outcome of PUFA supplementation may depend on the degree of endogenous DNL and combining PUFA supplementation and FASN inhibition might be a promising approach to target metabolic disease.
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Affiliation(s)
- Anna Worthmann
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julius Ridder
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sharlaine Y L Piel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ioannis Evangelakos
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Melina Musfeldt
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hannah Voß
- Section / Core Facility Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marie O'Farrell
- Sagimet Biosciences Inc., 155 Bovet Rd., San Mateo, CA, 94402, USA
| | - Alexander W Fischer
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Sangeeta Adak
- Division of Endocrinology, Metabolism & Lipid Research, Department of Medicine, Washington University, St. Louis, MO, USA
| | - Monica Sundd
- National Institute of Immunology, New Delhi, India
| | - Hasibullah Siffeti
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Friederike Haumann
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katja Kloth
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Markus Heine
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Paul Pertzborn
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mira Pauly
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julia-Josefine Scholz
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Suman Kundu
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021 and Department of Biological Sciences, Birla Institute of Technology and Science Pilani, K K Birla Goa Campus, Goa, 403726, India
| | - Marceline M Fuh
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Axel Neu
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Klaus Tödter
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Human Genetics, University Hospital Heidelberg, Im Neuenheimer Feld 440, 69120, Heidelberg, Germany
| | - Uwe Knippschild
- Department of General and Visceral Surgery, University Hospital Ulm, Ulm, Germany
| | - Clay F Semenkovich
- Division of Endocrinology, Metabolism & Lipid Research, Department of Medicine, Washington University, St. Louis, MO, USA
| | - Hartmut Schlüter
- Section / Core Facility Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Joerg Heeren
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ludger Scheja
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christian Kubisch
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christian Schlein
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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12
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Dottermusch M, Biabani A, Lempertz T, Schumann Y, Navolic J, Godbole S, Obrecht D, Frank S, Dorostkar MM, Voß H, Schlüter H, Rutkowski S, Schüller U, Neumann JE. Integrated proteomics spotlight the proteasome as a therapeutic vulnerability in Embryonal Tumors with Multilayered Rosettes. Neuro Oncol 2023:noad265. [PMID: 38158710 DOI: 10.1093/neuonc/noad265] [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: 09/27/2023] [Indexed: 01/03/2024] Open
Abstract
BACKGROUND Embryonal tumors with multilayered rosettes (ETMR) are rare malignant embryonal brain tumors. The prognosis of ETMR is poor and novel therapeutic approaches are desperately needed. Comprehension of ETMR tumor biology is currently based on only few previous molecular studies, which mainly focused on the analyses of nucleic acids. In this study, we explored integrated ETMR proteomics. METHODS Using mass spectrometry, proteome data were acquired from 16 ETMR and the ETMR cell line BT183. Proteome data were integrated with case-matched global DNA methylation data, publicly available transcriptome data, and proteome data of further embryonal and pediatric brain tumors. RESULTS Proteome-based cluster analyses grouped ETMR samples according to histomorphology, separating neuropil-rich tumors with neuronal signatures from primitive tumors with signatures relating to stemness and chromosome organization. Integrated proteomics showcased that ETMR and BT183 cells harbor proteasome regulatory proteins in abundancy, implicating their strong dependency on the proteasome machinery to safeguard proteostasis. Indeed, in vitro assays using BT183 highlighted that ETMR tumor cells are highly vulnerable towards treatment with the CNS penetrant proteasome inhibitor Marizomib. CONCLUSIONS In summary, histomorphology stipulates the proteome signatures of ETMR, and proteasome regulatory proteins are pervasively abundant in these tumors. As validated in vitro, proteasome inhibition poses a promising therapeutic option in ETMR.
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Affiliation(s)
- Matthias Dottermusch
- Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ali Biabani
- Section of Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tasja Lempertz
- Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Yannis Schumann
- Chair for High Performance Computing, Helmut-Schmidt University, Hamburg, Germany
| | - Jelena Navolic
- Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Shweta Godbole
- Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Denise Obrecht
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stephan Frank
- Division of Neuropathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Mario M Dorostkar
- Center for Neuropathology and Prion Research, Ludwig Maximilian University, Munich, Germany
| | - Hannah Voß
- Section of Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hartmut Schlüter
- Section of Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Rutkowski
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ulrich Schüller
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Children's Cancer Research Center Hamburg, Hamburg, Germany
| | - Julia E Neumann
- Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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13
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Navolić J, Moritz M, Voß H, Schlumbohm S, Schumann Y, Schlüter H, Neumann JE, Hahn J. Direct 3D Sampling of the Embryonic Mouse Head: Layer-wise Nanosecond Infrared Laser (NIRL) Ablation from Scalp to Cortex for Spatially Resolved Proteomics. Anal Chem 2023; 95:17220-17227. [PMID: 37956982 PMCID: PMC10688223 DOI: 10.1021/acs.analchem.3c02637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 06/16/2023] [Revised: 10/06/2023] [Accepted: 10/12/2023] [Indexed: 11/21/2023]
Abstract
Common workflows in bottom-up proteomics require homogenization of tissue samples to gain access to the biomolecules within the cells. The homogenized tissue samples often contain many different cell types, thereby representing an average of the natural proteome composition, and rare cell types are not sufficiently represented. To overcome this problem, small-volume sampling and spatial resolution are needed to maintain a better representation of the sample composition and their proteome signatures. Using nanosecond infrared laser ablation, the region of interest can be targeted in a three-dimensional (3D) fashion, whereby the spatial information is maintained during the simultaneous process of sampling and homogenization. In this study, we ablated 40 μm thick consecutive layers directly from the scalp through the cortex of embryonic mouse heads and analyzed them by subsequent bottom-up proteomics. Extra- and intracranial ablated layers showed distinct proteome profiles comprising expected cell-specific proteins. Additionally, known cortex markers like SOX2, KI67, NESTIN, and MAP2 showed a layer-specific spatial protein abundance distribution. We propose potential new marker proteins for cortex layers, such as MTA1 and NMRAL1. The obtained data confirm that the new 3D tissue sampling and homogenization method is well suited for investigating the spatial proteome signature of tissue samples in a layerwise manner. Characterization of the proteome composition of embryonic skin and bone structures, meninges, and cortex lamination in situ enables a better understanding of molecular mechanisms of development during embryogenesis and disease pathogenesis.
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Affiliation(s)
- Jelena Navolić
- Research
Group Molecular Pathology in Neurooncology, Center for Molecular Neurobiology
(ZMNH), University Medical Center Hamburg−Eppendorf, Falkenried 94, 20251 Hamburg, Germany
| | - Manuela Moritz
- Section/Core
Facility Mass Spectrometry and Proteomics, Center for Diagnostics, University Medical Center Hamburg−Eppendorf, Martinistraße 52, 20251 Hamburg, Germany
| | - Hannah Voß
- Section/Core
Facility Mass Spectrometry and Proteomics, Center for Diagnostics, University Medical Center Hamburg−Eppendorf, Martinistraße 52, 20251 Hamburg, Germany
| | - Simon Schlumbohm
- High
Performance Computing, Helmut Schmidt University, Holstenhofweg 85, 22043 Hamburg, Germany
| | - Yannis Schumann
- High
Performance Computing, Helmut Schmidt University, Holstenhofweg 85, 22043 Hamburg, Germany
| | - Hartmut Schlüter
- Section/Core
Facility Mass Spectrometry and Proteomics, Center for Diagnostics, University Medical Center Hamburg−Eppendorf, Martinistraße 52, 20251 Hamburg, Germany
| | - Julia E. Neumann
- Research
Group Molecular Pathology in Neurooncology, Center for Molecular Neurobiology
(ZMNH), University Medical Center Hamburg−Eppendorf, Falkenried 94, 20251 Hamburg, Germany
- Institute
of Neuropathology, University Medical Center
Hamburg−Eppendorf, Martinistraße 52, 20251 Hamburg, Germany
| | - Jan Hahn
- Section/Core
Facility Mass Spectrometry and Proteomics, Center for Diagnostics, University Medical Center Hamburg−Eppendorf, Martinistraße 52, 20251 Hamburg, Germany
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14
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Höpfner D, Cichy A, Pogenberg V, Krisp C, Mezouar S, Bach NC, Grotheer J, Zarza SM, Martinez E, Bonazzi M, Feige MJ, Sieber SA, Schlüter H, Itzen A. The DNA-binding induced (de)AMPylation activity of a Coxiella burnetii Fic enzyme targets Histone H3. Commun Biol 2023; 6:1124. [PMID: 37932372 PMCID: PMC10628234 DOI: 10.1038/s42003-023-05494-7] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 10/20/2023] [Indexed: 11/08/2023] Open
Abstract
The intracellular bacterial pathogen Coxiella burnetii evades the host response by secreting effector proteins that aid in establishing a replication-friendly niche. Bacterial filamentation induced by cyclic AMP (Fic) enzymes can act as effectors by covalently modifying target proteins with the posttranslational AMPylation by transferring adenosine monophosphate (AMP) from adenosine triphosphate (ATP) to a hydroxyl-containing side chain. Here we identify the gene product of C. burnetii CBU_0822, termed C. burnetii Fic 2 (CbFic2), to AMPylate host cell histone H3 at serine 10 and serine 28. We show that CbFic2 acts as a bifunctional enzyme, both capable of AMPylation as well as deAMPylation, and is regulated by the binding of DNA via a C-terminal helix-turn-helix domain. We propose that CbFic2 performs AMPylation in its monomeric state, switching to a deAMPylating dimer upon DNA binding. This study unveils reversible histone modification by a specific enzyme of a pathogenic bacterium.
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Affiliation(s)
- Dorothea Höpfner
- Institute of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246, Hamburg, Germany
| | - Adam Cichy
- Center for Integrated Protein Science Munich (CIPSM), Department Chemistry, Group of Proteinchemistry, Technical University of Munich, Lichtenbergstraße 4, 85747, Garching, Germany
| | - Vivian Pogenberg
- Institute of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246, Hamburg, Germany
| | - Christoph Krisp
- Institute of Clinical Chemistry and Laboratory Medicine, Section Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246, Hamburg, Germany
| | - Soraya Mezouar
- Aix-Marseille University, Institut de Recherche pour la Développement (IRD), Assistance Publique-Hôpitaux de Marseille (APHM), Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Boulevard Jean Moulin, 13005, Marseille, France
| | - Nina C Bach
- Technical University of Munich (TUM), TUM School of Natural Sciences, Department of Biosciences, Chair of Organic Chemistry II, Center for Functional Protein Assemblies (CPA), Ernst-Otto-Fischer Straße 8, 85748, Garching, Germany
| | - Jan Grotheer
- Institute of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246, Hamburg, Germany
| | - Sandra Madariaga Zarza
- Aix-Marseille University, Institut de Recherche pour la Développement (IRD), Assistance Publique-Hôpitaux de Marseille (APHM), Microbes Evolution Phylogeny and Infections (MEPHI), Institut Hospitalo-Universitaire (IHU)-Méditerranée Infection, Boulevard Jean Moulin, 13005, Marseille, France
| | - Eric Martinez
- Cellular and Molecular Biology of Bacterial Infections, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, UMR 9004 - Centre national de la recherche scientifique (CNRS), 1919 Route de Mende, 34293, Montpellier, France
| | - Matteo Bonazzi
- Cellular and Molecular Biology of Bacterial Infections, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, UMR 9004 - Centre national de la recherche scientifique (CNRS), 1919 Route de Mende, 34293, Montpellier, France
| | - Matthias J Feige
- Center for Functional Protein Assemblies (CPA), Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Stephan A Sieber
- Technical University of Munich (TUM), TUM School of Natural Sciences, Department of Biosciences, Chair of Organic Chemistry II, Center for Functional Protein Assemblies (CPA), Ernst-Otto-Fischer Straße 8, 85748, Garching, Germany
| | - Hartmut Schlüter
- Institute of Clinical Chemistry and Laboratory Medicine, Section Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246, Hamburg, Germany
| | - Aymelt Itzen
- Institute of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246, Hamburg, Germany.
- Center for Structural Systems Biology (CSSB), University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246, Hamburg, Germany.
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15
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Siemes D, Vancamp P, Markova B, Spangenberg P, Shevchuk O, Siebels B, Schlüter H, Mayerl S, Heuer H, Engel DR. Proteome Analysis of Thyroid Hormone Transporter Mct8/Oatp1c1-Deficient Mice Reveals Novel Dysregulated Target Molecules Involved in Locomotor Function. Cells 2023; 12:2487. [PMID: 37887331 PMCID: PMC10605308 DOI: 10.3390/cells12202487] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 10/28/2023] Open
Abstract
Thyroid hormone (TH) transporter MCT8 deficiency causes severe locomotor disabilities likely due to insufficient TH transport across brain barriers and, consequently, compromised neural TH action. As an established animal model for this disease, Mct8/Oatp1c1 double knockout (DKO) mice exhibit strong central TH deprivation, locomotor impairments and similar histo-morphological features as seen in MCT8 patients. The pathways that cause these neuro-motor symptoms are poorly understood. In this paper, we performed proteome analysis of brain sections comprising cortical and striatal areas of 21-day-old WT and DKO mice. We detected over 2900 proteins by liquid chromatography mass spectrometry, 67 of which were significantly different between the genotypes. The comparison of the proteomic and published RNA-sequencing data showed a significant overlap between alterations in both datasets. In line with previous observations, DKO animals exhibited decreased myelin-associated protein expression and altered protein levels of well-established neuronal TH-regulated targets. As one intriguing new candidate, we unraveled and confirmed the reduced protein and mRNA expression of Pde10a, a striatal enzyme critically involved in dopamine receptor signaling, in DKO mice. As altered PDE10A activities are linked to dystonia, reduced basal ganglia PDE10A expression may represent a key pathogenic pathway underlying human MCT8 deficiency.
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Affiliation(s)
- Devon Siemes
- Department of Immunodynamics, Institute for Experimental Immunology and Imaging, University Duisburg-Essen, 45141 Essen, Germany; (D.S.); (P.S.); (O.S.); (D.R.E.)
| | - Pieter Vancamp
- Department of Endocrinology, Diabetes and Metabolism, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany; (P.V.); (B.M.); (S.M.)
| | - Boyka Markova
- Department of Endocrinology, Diabetes and Metabolism, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany; (P.V.); (B.M.); (S.M.)
| | - Philippa Spangenberg
- Department of Immunodynamics, Institute for Experimental Immunology and Imaging, University Duisburg-Essen, 45141 Essen, Germany; (D.S.); (P.S.); (O.S.); (D.R.E.)
| | - Olga Shevchuk
- Department of Immunodynamics, Institute for Experimental Immunology and Imaging, University Duisburg-Essen, 45141 Essen, Germany; (D.S.); (P.S.); (O.S.); (D.R.E.)
| | - Bente Siebels
- Section Mass Spectrometric Proteomics, Diagnostic Center, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (B.S.); (H.S.)
| | - Hartmut Schlüter
- Section Mass Spectrometric Proteomics, Diagnostic Center, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; (B.S.); (H.S.)
| | - Steffen Mayerl
- Department of Endocrinology, Diabetes and Metabolism, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany; (P.V.); (B.M.); (S.M.)
| | - Heike Heuer
- Department of Endocrinology, Diabetes and Metabolism, University Hospital Essen, University Duisburg-Essen, 45147 Essen, Germany; (P.V.); (B.M.); (S.M.)
| | - Daniel Robert Engel
- Department of Immunodynamics, Institute for Experimental Immunology and Imaging, University Duisburg-Essen, 45141 Essen, Germany; (D.S.); (P.S.); (O.S.); (D.R.E.)
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16
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Dyshlovoy SA, Hauschild J, Venz S, Krisp C, Kolbe K, Zapf S, Heinemann S, Fita KD, Shubina LK, Makarieva TN, Guzii AG, Rohlfing T, Kaune M, Busenbender T, Mair T, Moritz M, Poverennaya EV, Schlüter H, Serdyuk V, Stonik VA, Dierlamm J, Bokemeyer C, Mohme M, Westphal M, Lamszus K, von Amsberg G, Maire CL. Rhizochalinin Exhibits Anticancer Activity and Synergizes with EGFR Inhibitors in Glioblastoma In Vitro Models. Mol Pharm 2023; 20:4994-5005. [PMID: 37733943 DOI: 10.1021/acs.molpharmaceut.3c00217] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Abstract
Rhizochalinin (Rhiz) is a recently discovered cytotoxic sphingolipid synthesized from the marine natural compound rhizochalin. Previously, Rhiz demonstrated high in vitro and in vivo efficacy in various cancer models. Here, we report Rhiz to be highly active in human glioblastoma cell lines as well as in patient-derived glioma-stem like neurosphere models. Rhiz counteracted glioblastoma cell proliferation by inducing apoptosis, G2/M-phase cell cycle arrest, and inhibition of autophagy. Proteomic profiling followed by bioinformatic analysis suggested suppression of the Akt pathway as one of the major biological effects of Rhiz. Suppression of Akt as well as IGF-1R and MEK1/2 kinase was confirmed in Rhiz-treated GBM cells. In addition, Rhiz pretreatment resulted in a more pronounced inhibitory effect of γ-irradiation on the growth of patient-derived glioma-spheres, an effect to which the Akt inhibition may also contribute decisively. In contrast, EGFR upregulation, observed in all GBM neurospheres under Rhiz treatment, was postulated to be a possible sign of incipient resistance. In line with this, combinational therapy with EGFR-targeted tyrosine kinase inhibitors synergistically increased the efficacy of Rhiz resulting in dramatic inhibition of GBM cell viability as well as a significant reduction of neurosphere size in the case of combination with lapatinib. Preliminary in vitro data generated using a parallel artificial membrane permeability (PAMPA) assay suggested that Rhiz cannot cross the blood brain barrier and therefore alternative drug delivery methods should be used in the further in vivo studies. In conclusion, Rhiz is a promising new candidate for the treatment of human glioblastoma, which should be further developed in combination with EGFR inhibitors.
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Affiliation(s)
- Sergey A Dyshlovoy
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald Tumorzentrum - University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg 20251, Germany
- Laboratory of Biologically Active Compounds, Institute of Science-Intensive Technologies and Advanced Materials, Far Eastern Federal University, Vladivostok 690922, Russian Federation
| | - Jessica Hauschild
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald Tumorzentrum - University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg 20251, Germany
| | - Simone Venz
- Department of Medical Biochemistry and Molecular Biology, University of Greifswald, Greifswald 17489, Germany
- Interfacultary Institute of Genetics and Functional Genomics, Department of Functional Genomics, University of Greifswald, Greifswald 17489, Germany
| | - Christoph Krisp
- Section / Core Facility Mass Spectrometric Proteomics, Center of Diagnostics, University Medical Center Hamburg-Eppendorf, Hamburg 20251, Germany
| | - Katharina Kolbe
- Laboratory for Brain Tumor Research, Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg 20251, Germany
| | - Svenja Zapf
- Laboratory for Brain Tumor Research, Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg 20251, Germany
| | - Sarina Heinemann
- Laboratory for Brain Tumor Research, Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg 20251, Germany
| | - Krystian D Fita
- Laboratory for Brain Tumor Research, Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg 20251, Germany
| | - Larisa K Shubina
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-East Branch, Russian Academy of Sciences, Vladivostok 690022, Russian Federation
| | - Tatyana N Makarieva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-East Branch, Russian Academy of Sciences, Vladivostok 690022, Russian Federation
| | - Alla G Guzii
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-East Branch, Russian Academy of Sciences, Vladivostok 690022, Russian Federation
| | - Tina Rohlfing
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald Tumorzentrum - University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg 20251, Germany
| | - Moritz Kaune
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald Tumorzentrum - University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg 20251, Germany
| | - Tobias Busenbender
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald Tumorzentrum - University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg 20251, Germany
| | - Thomas Mair
- Section / Core Facility Mass Spectrometric Proteomics, Center of Diagnostics, University Medical Center Hamburg-Eppendorf, Hamburg 20251, Germany
| | - Manuela Moritz
- Section / Core Facility Mass Spectrometric Proteomics, Center of Diagnostics, University Medical Center Hamburg-Eppendorf, Hamburg 20251, Germany
| | - Ekaterina V Poverennaya
- Laboratory of Proteoform Interactomics, Institute of Biomedical Chemistry, Moscow 119121, Russian Federation
| | - Hartmut Schlüter
- Section / Core Facility Mass Spectrometric Proteomics, Center of Diagnostics, University Medical Center Hamburg-Eppendorf, Hamburg 20251, Germany
| | - Volodymyr Serdyuk
- Zentrum für Molekulare Neurobiologie (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg 20251, Germany
| | - Valentin A Stonik
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far-East Branch, Russian Academy of Sciences, Vladivostok 690022, Russian Federation
| | - Judith Dierlamm
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald Tumorzentrum - University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg 20251, Germany
| | - Carsten Bokemeyer
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald Tumorzentrum - University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg 20251, Germany
| | - Malte Mohme
- Laboratory for Brain Tumor Research, Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg 20251, Germany
| | - Manfred Westphal
- Laboratory for Brain Tumor Research, Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg 20251, Germany
| | - Katrin Lamszus
- Laboratory for Brain Tumor Research, Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg 20251, Germany
| | - Gunhild von Amsberg
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald Tumorzentrum - University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg 20251, Germany
- Martini-Klinik, Prostate Cancer Center, University Hospital Hamburg-Eppendorf, Hamburg 20251, Germany
| | - Cecile L Maire
- Laboratory for Brain Tumor Research, Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg 20251, Germany
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17
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Lassé M, El Saghir J, Berthier CC, Eddy S, Fischer M, Laufer SD, Kylies D, Hutzfeldt A, Bonin LL, Dumoulin B, Menon R, Vega-Warner V, Eichinger F, Alakwaa F, Fermin D, Billing AM, Minakawa A, McCown PJ, Rose MP, Godfrey B, Meister E, Wiech T, Noriega M, Chrysopoulou M, Brandts P, Ju W, Reinhard L, Hoxha E, Grahammer F, Lindenmeyer MT, Huber TB, Schlüter H, Thiel S, Mariani LH, Puelles VG, Braun F, Kretzler M, Demir F, Harder JL, Rinschen MM. An integrated organoid omics map extends modeling potential of kidney disease. Nat Commun 2023; 14:4903. [PMID: 37580326 PMCID: PMC10425428 DOI: 10.1038/s41467-023-39740-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 09/27/2022] [Accepted: 06/27/2023] [Indexed: 08/16/2023] Open
Abstract
Kidney organoids are a promising model to study kidney disease, but their use is constrained by limited knowledge of their functional protein expression profile. Here, we define the organoid proteome and transcriptome trajectories over culture duration and upon exposure to TNFα, a cytokine stressor. Older organoids increase deposition of extracellular matrix but decrease expression of glomerular proteins. Single cell transcriptome integration reveals that most proteome changes localize to podocytes, tubular and stromal cells. TNFα treatment of organoids results in 322 differentially expressed proteins, including cytokines and complement components. Transcript expression of these 322 proteins is significantly higher in individuals with poorer clinical outcomes in proteinuric kidney disease. Key TNFα-associated protein (C3 and VCAM1) expression is increased in both human tubular and organoid kidney cell populations, highlighting the potential for organoids to advance biomarker development. By integrating kidney organoid omic layers, incorporating a disease-relevant cytokine stressor and comparing with human data, we provide crucial evidence for the functional relevance of the kidney organoid model to human kidney disease.
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Affiliation(s)
- Moritz Lassé
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jamal El Saghir
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Celine C Berthier
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Sean Eddy
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Matthew Fischer
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Sandra D Laufer
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Dominik Kylies
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Arvid Hutzfeldt
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Bernhard Dumoulin
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Rajasree Menon
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Virginia Vega-Warner
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Felix Eichinger
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Fadhl Alakwaa
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Damian Fermin
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Anja M Billing
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Akihiro Minakawa
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Phillip J McCown
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Michael P Rose
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Bradley Godfrey
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Elisabeth Meister
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thorsten Wiech
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Pathology, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Mercedes Noriega
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Pathology, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | | | - Paul Brandts
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Wenjun Ju
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Linda Reinhard
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Elion Hoxha
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Florian Grahammer
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maja T Lindenmeyer
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tobias B Huber
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hartmut Schlüter
- Section Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Steffen Thiel
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Laura H Mariani
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
| | - Victor G Puelles
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Pathology, Aarhus University Hospital, Aarhus, Denmark
| | - Fabian Braun
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Matthias Kretzler
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Fatih Demir
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Jennifer L Harder
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, USA.
| | - Markus M Rinschen
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany.
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.
- Aarhus Institute of Advanced Studies (AIAS), Aarhus, Denmark.
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18
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Salm F, Znalesniak EB, Laskou A, Harder S, Schlüter H, Hoffmann W. Expression Profiling along the Murine Intestine: Different Mucosal Protection Systems and Alterations in Tff1-Deficient Animals. Int J Mol Sci 2023; 24:12684. [PMID: 37628863 PMCID: PMC10454331 DOI: 10.3390/ijms241612684] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/03/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
Tff1 is a typical gastric peptide secreted together with the mucin, Muc5ac. Tff1-deficient (Tff1KO) mice are well known for their prominent gastric phenotype and represent a recognized model for antral tumorigenesis. Notably, intestinal abnormalities have also been reported in the past in these animals. Here, we have compared the expression of selected genes in Tff1KO mice and their corresponding wild-type littermates (RT-PCR analyses), focusing on different mucosal protection systems along the murine intestine. As hallmarks, genes were identified with maximum expression in the proximal colon and/or the duodenum: Agr2, Muc6/A4gnt/Tff2, Tff1, Fut2, Gkn2, Gkn3, Duox2/Lpo, Nox1. This is indicative of different protection systems such as Tff2/Muc6, Tff1-Fcgbp, gastrokines, fucosylation, and reactive oxygen species (ROS) in the proximal colon and/or duodenum. Few significant transcriptional changes were observed in the intestine of Tff1KO mice when compared with wild-type littermates, Clca1 (Gob5), Gkn1, Gkn2, Nox1, Tff2. We also analyzed the expression of Tff1, Tff2, and Tff3 in the pancreas, liver, and lung of Tff1KO and wild-type animals, indicating a cross-regulation of Tff gene expression. Furthermore, on the protein level, heteromeric Tff1-Fcgbp and various monomeric Tff1 forms were identified in the duodenum and a high-molecular-mass Tff2/Muc6 complex was identified in the proximal colon (FPLC, proteomics).
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Affiliation(s)
- Franz Salm
- Institute of Molecular Biology and Medicinal Chemistry, Otto-von-Guericke University Magdeburg, Leipziger Str. 44, 39120 Magdeburg, Germany
| | - Eva B. Znalesniak
- Institute of Molecular Biology and Medicinal Chemistry, Otto-von-Guericke University Magdeburg, Leipziger Str. 44, 39120 Magdeburg, Germany
| | - Aikaterini Laskou
- Institute of Molecular Biology and Medicinal Chemistry, Otto-von-Guericke University Magdeburg, Leipziger Str. 44, 39120 Magdeburg, Germany
| | - Sönke Harder
- Section Mass Spectrometry and Proteomics, Diagnostic Center, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Hartmut Schlüter
- Section Mass Spectrometry and Proteomics, Diagnostic Center, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Werner Hoffmann
- Institute of Molecular Biology and Medicinal Chemistry, Otto-von-Guericke University Magdeburg, Leipziger Str. 44, 39120 Magdeburg, Germany
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Stadlhofer R, Moritz M, Fuh MM, Heeren J, Zech H, Clauditz TS, Schlüter H, Betz CS, Eggert D, Böttcher A, Hahn J. Lipidome Analysis of Oropharyngeal Tumor Tissues Using Nanosecond Infrared Laser (NIRL) Tissue Sampling and Subsequent Mass Spectrometry. Int J Mol Sci 2023; 24:ijms24097820. [PMID: 37175533 PMCID: PMC10178251 DOI: 10.3390/ijms24097820] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/16/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
Ultrashort pulse infrared lasers can simultaneously sample and homogenize biological tissue using desorption by impulsive vibrational excitation (DIVE). With growing attention on alterations in lipid metabolism in malignant disease, mass spectrometry (MS)-based lipidomic analysis has become an emerging topic in cancer research. In this pilot study, we investigated the feasibility of tissue sampling with a nanosecond infrared laser (NIRL) for the subsequent lipidomic analysis of oropharyngeal tissues, and its potential to discriminate oropharyngeal squamous cell carcinoma (OPSCC) from non-tumorous oropharyngeal tissue. Eleven fresh frozen oropharyngeal tissue samples were ablated. The produced aerosols were collected by a glass fiber filter, and the lipidomes were analyzed with mass spectrometry. Data was evaluated by principal component analysis and Welch's t-tests. Lipid profiles comprised 13 lipid classes and up to 755 lipid species. We found significant inter- and intrapatient alterations in lipid profiles for tumor and non-tumor samples (p-value < 0.05, two-fold difference). Thus, NIRL tissue sampling with consecutive MS lipidomic analysis is a feasible and promising approach for the differentiation of OPSCC and non-tumorous oropharyngeal tissue and may provide new insights into lipid composition alterations in OPSCC.
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Affiliation(s)
- Rupert Stadlhofer
- Department of Otorhinolaryngology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Manuela Moritz
- Section/Core Facility Mass Spectrometric Proteomics, Diagnostic Center, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Marceline M Fuh
- Department of Biochemistry and Molecular Cell Biology, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Jörg Heeren
- Department of Biochemistry and Molecular Cell Biology, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Henrike Zech
- Department of Otorhinolaryngology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
- Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Till S Clauditz
- Department of Pathology, Diagnostic Center, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Hartmut Schlüter
- Section/Core Facility Mass Spectrometric Proteomics, Diagnostic Center, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Christian S Betz
- Department of Otorhinolaryngology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Dennis Eggert
- Department of Otorhinolaryngology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Arne Böttcher
- Department of Otorhinolaryngology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Jan Hahn
- Section/Core Facility Mass Spectrometric Proteomics, Diagnostic Center, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
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20
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Znalesniak EB, Laskou A, Salm F, Haupenthal K, Harder S, Schlüter H, Hoffmann W. The Forms of the Lectin Tff2 Differ in the Murine Stomach and Pancreas: Indications for Different Molecular Functions. Int J Mol Sci 2023; 24:ijms24087059. [PMID: 37108221 PMCID: PMC10138697 DOI: 10.3390/ijms24087059] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 03/30/2023] [Accepted: 04/03/2023] [Indexed: 04/29/2023] Open
Abstract
The lectin TFF2 belongs to the trefoil factor family (TFF). This polypeptide is typically co-secreted with the mucin MUC6 from gastric mucous neck cells, antral gland cells, and duodenal Brunner glands. Here, TFF2 fulfills a protective function by forming a high-molecular-mass complex with the MUC6, physically stabilizing the mucus barrier. In pigs and mice, and slightly in humans, TFF2 is also synthesized in the pancreas. Here, we investigated the murine stomach, pancreas, and duodenum by fast protein liquid chromatography (FPLC) and proteomics and identified different forms of Tff2. In both the stomach and duodenum, the predominant form is a high-molecular-mass complex with Muc6, whereas, in the pancreas, only low-molecular-mass monomeric Tff2 was detectable. We also investigated the expression of Tff2 and other selected genes in the stomach, pancreas, and the proximal, medial, and distal duodenum (RT-PCR analysis). The absence of the Tff2/Muc6 complex in the pancreas is due to a lack of Muc6. Based on its known motogenic, anti-apoptotic, and anti-inflammatory effects, we propose a protective receptor-mediated function of monomeric Tff2 for the pancreatic ductal epithelium. This view is supported by a report that a loss of Tff2 promotes the formation of pancreatic intraductal mucinous neoplasms.
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Affiliation(s)
- Eva B Znalesniak
- Institute of Molecular Biology and Medicinal Chemistry, Otto-von-Guericke University Magdeburg, Leipziger Str. 44, 39120 Magdeburg, Germany
| | - Aikaterini Laskou
- Institute of Molecular Biology and Medicinal Chemistry, Otto-von-Guericke University Magdeburg, Leipziger Str. 44, 39120 Magdeburg, Germany
| | - Franz Salm
- Institute of Molecular Biology and Medicinal Chemistry, Otto-von-Guericke University Magdeburg, Leipziger Str. 44, 39120 Magdeburg, Germany
| | - Katharina Haupenthal
- Institute of Molecular Biology and Medicinal Chemistry, Otto-von-Guericke University Magdeburg, Leipziger Str. 44, 39120 Magdeburg, Germany
| | - Sönke Harder
- Section Mass Spectrometry and Proteomics, Diagnostic Center, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Hartmut Schlüter
- Section Mass Spectrometry and Proteomics, Diagnostic Center, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246 Hamburg, Germany
| | - Werner Hoffmann
- Institute of Molecular Biology and Medicinal Chemistry, Otto-von-Guericke University Magdeburg, Leipziger Str. 44, 39120 Magdeburg, Germany
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21
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Bartkowiak K, Mossahebi Mohammadi P, Gärtner S, Kwiatkowski M, Andreas A, Geffken M, Peine S, Verpoort K, Scholz U, Deutsch TM, Michel LL, Schneeweiss A, Thewes V, Trumpp A, Müller V, Riethdorf S, Schlüter H, Pantel K. Detection and Isolation of Circulating Tumor Cells from Breast Cancer Patients Using CUB Domain-Containing Protein 1. J Proteome Res 2023; 22:1213-1230. [PMID: 36926972 DOI: 10.1021/acs.jproteome.2c00739] [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] [Indexed: 03/18/2023]
Abstract
In cancer metastasis, single circulating tumor cells (CTCs) in the blood and disseminated tumor cells (DTCs) in the bone marrow mediate cancer metastasis. Because suitable biomarker proteins are lacking, CTCs and DTCs with mesenchymal attributes are difficult to isolate from the bulk of normal blood cells. To establish a procedure allowing the isolation of such cells, we analyzed the cell line BC-M1 established from DTCs in the bone marrow of a breast cancer patient by stable isotope labeling by amino acids in cell culture (SILAC) and mass spectrometry. We found high levels of the transmembrane protein CUB domain-containing protein 1 (CDCP1) in breast cancer cell lines with mesenchymal attributes. Peripheral blood mononuclear cells were virtually negative for CDCP1. Confirmation in vivo by CellSearch revealed CDCP1-positive CTCs in 8 of 30 analyzed breast cancer patients. Only EpCam-positive CTCs were enriched by CellSearch. Using the extracellular domain of CDCP1, we established a magnetic-activated cell sorting (MACS) approach enabling also the enrichment of EpCam-negative CTCs. Thus, our approach is particularly suited for the isolation of mesenchymal CTCs with downregulated epithelial cancer that occur, for example, in triple-negative breast cancer patients who are prone to therapy failure.
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Affiliation(s)
- Kai Bartkowiak
- Department of Tumour Biology, University Medical Centre Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Parinaz Mossahebi Mohammadi
- Department of Tumour Biology, University Medical Centre Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Sebastian Gärtner
- Department of Tumour Biology, University Medical Centre Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Marcel Kwiatkowski
- Laboratory for Metabolic Signaling, Institute of Biochemistry, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Antje Andreas
- Department of Tumour Biology, University Medical Centre Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Maria Geffken
- Department of Transfusion Medicine, University Medical Centre Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Sven Peine
- Department of Transfusion Medicine, University Medical Centre Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Karl Verpoort
- Practice for Haematology and Oncology, Hohe Weide 17b, 20295 Hamburg, Germany
| | - Ursula Scholz
- Gynecological Oncology, Asklepios Klinik Hamburg-Barmbek, Rübenkamp 220, 22307 Hamburg, Germany
| | - Thomas M Deutsch
- Department of Obstetrics and Gynecology, University of Heidelberg, Im Neuenheimer Feld 440, 69120 Heidelberg, Germany
| | - Laura L Michel
- National Center for Tumor Diseases, Heidelberg University Hospital and German Cancer Research Center, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Andreas Schneeweiss
- National Center for Tumor Diseases, Heidelberg University Hospital and German Cancer Research Center, Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Verena Thewes
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Andreas Trumpp
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Volkmar Müller
- Department of Gynecology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Sabine Riethdorf
- Department of Tumour Biology, University Medical Centre Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Hartmut Schlüter
- Department of Clinical Chemistry and Laboratory Medicine, University Medical Centre Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Klaus Pantel
- Department of Tumour Biology, University Medical Centre Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
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22
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Von Amsberg G, Dyshlovoy S, Hauschild J, Sailer V, Perner S, Offermann A, Merkens L, Krisp C, Werner S, Pantel K, Kaune M, Tilki D, Schlüter H, Graefen M, Bokemeyer C. Long-term taxane exposure and transdifferentiation of prostate cancer in vitro. J Clin Oncol 2023. [DOI: 10.1200/jco.2023.41.6_suppl.254] [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: 03/18/2023] Open
Abstract
254 Background: Development of aggressive variants of metastatic castration-resistant prostate cancer (AVPC) is a major challenge in the course of therapy but the underlying mechanisms of aggressive transdifferentiation are not completely understood and appropriate tumor models are missing. Here, we investigated the consequences of long-term taxane exposure on hormone-independent, BRCA2-mutated, AR-V7-positive 22Rv1 cells. Methods: 22Rv1 cells were treated with stepwise increased taxane concentrations for 10 months. Individual clones were picked and further cultured in media containing either docetaxel (Doce) or cabazitaxel (Caba). Passage-matched cells were maintained in culture without treatment. Further characterization was carried out using proliferation, migration, metabolic, and colony formation assays as well as proteomics, RNAseq analyses and xenotransplantation in immunodeficient mice. Results: In total, three single cell 22Rv1-DR clones (50-100-fold resistance to Doce) and three 22Rv1-CR clones (80-150-fold resistance to Caba) were successfully established. All clones showed cross-resistance to either drug. Expectedly, treatment-induced overexpression of ABCB1 was detected and validated. Moreover, alteration of drug resistance related SLC7A5, SLC3A2, and SLC25A24 genes was observed. Additionally, an enrichment analyses identified, among others, neuroendocrine transdifferentiation (GO-term “Neuroendocrine tumors”, p=4.46e-5) to be stimulated in prostate 22Rv1 cells under long-term treatment with Doce or Caba. In line with this, the neuroendocrine features were validated in vitro as well as in xenotransplanted tumors in vivo with upregulation of synaptophysin, chromogranin and neuron specific enolase accompanied by downregulation of the androgen receptor (AR) and upregulation of AR spice variants. Additionally, neuritic morphology, shift to higher nuclear-plasma ratio, partial loss of adherent properties and growth slowdown, along with higher migratory activity were detected. Conclusions: Long-term taxane exposure of 22Rv1 cells resulted in the development of neuroendocrine traits in individual cell clones that have successfully been translated into stable cell lines. Thus, we provide a new cell line model for secondary therapy-induced neuroendocrine transdifferentiation. Further in-depth analysis to identify individual alterations in the course of therapy is currently ongoing.
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Affiliation(s)
| | | | | | - Verena Sailer
- Institute of Pathology, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Sven Perner
- Pathology of the University Hospital Schleswig-Holstein, Campus Luebeck and Research Center Borstel, Leibniz Center for Medicine and Biosciences, Lübeck, Germany
| | - Anne Offermann
- Pathology of the University Hospital Schleswig-Holstein, Campus Luebeck and Research Center Borstel, Leibniz Center for Medicine and Biosciences, Lübeck, Germany
| | - Lina Merkens
- Institute of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christoph Krisp
- Institute of Clinical Chemistry and Laboratory Medicine, Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Werner
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Klaus Pantel
- Institute of Tumour Biology, Center of Experimental Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Moritz Kaune
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Derya Tilki
- Martini-Klinik Prostate Cancer Center and Department of Urology, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Hartmut Schlüter
- Institute of Clinical Chemistry and Laboratory Medicine, Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Markus Graefen
- Martini-Klinik, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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23
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Nauth T, Bazgir F, Voß H, Brandenstein LI, Mosaddeghzadeh N, Rickassel V, Deden S, Gorzelanny C, Schlüter H, Ahmadian MR, Rosenberger G. Cutaneous manifestations in Costello syndrome: HRAS p.Gly12Ser affects RIN1-mediated integrin trafficking in immortalized epidermal keratinocytes. Hum Mol Genet 2023; 32:304-318. [PMID: 35981076 DOI: 10.1093/hmg/ddac188] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 07/15/2022] [Accepted: 08/07/2022] [Indexed: 01/18/2023] Open
Abstract
Heterozygous germline missense variants in the HRAS gene underlie Costello syndrome (CS). The molecular basis for cutaneous manifestations in CS is largely unknown. We used an immortalized human cell line, HaCaT keratinocytes, stably expressing wild-type or CS-associated (p.Gly12Ser) HRAS and defined RIN1 as quantitatively most prominent, high-affinity effector of active HRAS in these cells. As an exchange factor for RAB5 GTPases, RIN1 is involved in endosomal sorting of cell-adhesion integrins. RIN1-dependent RAB5A activation was strongly increased by HRASGly12Ser, and HRAS-RIN1-ABL1/2 signaling was induced in HRASWT- and HRASGly12Ser-expressing cells. Along with that, HRASGly12Ser expression decreased total integrin levels and enriched β1 integrin in RAB5- and EEA1-positive early endosomes. The intracellular level of active β1 integrin was increased in HRASGly12Ser HaCaT keratinocytes due to impaired recycling, whereas RIN1 disruption raised β1 integrin cell surface distribution. HRASGly12Ser induced co-localization of β1 integrin with SNX17 and RAB7 in early/sorting and late endosomes, respectively. Thus, by retaining β1 integrin in intracellular endosomal compartments, HRAS-RIN1 signaling affects the subcellular availability of β1 integrin. This may interfere with integrin-dependent processes as we detected for HRASGly12Ser cells spreading on fibronectin. We conclude that dysregulation of receptor trafficking and integrin-dependent processes such as cell adhesion are relevant in the pathobiology of CS.
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Affiliation(s)
- Theresa Nauth
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Farhad Bazgir
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine University, 40225 Düsseldorf, Germany
| | - Hannah Voß
- Institute of Clinical Chemistry and Laboratory Medicine, Section Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Laura I Brandenstein
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Niloufar Mosaddeghzadeh
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine University, 40225 Düsseldorf, Germany
| | - Verena Rickassel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Sophia Deden
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Christian Gorzelanny
- Department of Dermatology and Venereology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Hartmut Schlüter
- Institute of Clinical Chemistry and Laboratory Medicine, Section Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Mohammad R Ahmadian
- Institute of Biochemistry and Molecular Biology II, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine University, 40225 Düsseldorf, Germany
| | - Georg Rosenberger
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
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24
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Weste J, Houben T, Harder S, Schlüter H, Lücke E, Schreiber J, Hoffmann W. Different Molecular Forms of TFF3 in the Human Respiratory Tract: Heterodimerization with IgG Fc Binding Protein (FCGBP) and Proteolytic Cleavage in Bronchial Secretions. Int J Mol Sci 2022; 23:ijms232315359. [PMID: 36499686 PMCID: PMC9737082 DOI: 10.3390/ijms232315359] [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] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/25/2022] [Accepted: 11/25/2022] [Indexed: 12/12/2022] Open
Abstract
The polypeptide TFF3 belongs to the trefoil factor family (TFF) of lectins. TFF3 is typically secreted from mucous epithelia together with mucins. Both intestinal and salivary TFF3 mainly exist as disulfide-linked heterodimers with IgG Fc binding protein (FCGBP). Here, we investigated bronchial tissue specimens, bronchial secretions, and bronchoalveolar lavage (BAL) fluid from patients with a chronic obstructive pulmonary disease (COPD) background by fast protein liquid chromatography and proteomics. For the first time, we identified different molecular forms of TFF3 in the lung. The high-molecular mass form represents TFF3-FCGBP oligomers, whereas the low-molecular mass forms are homodimeric and monomeric TFF3 with possibly anti-apoptotic activities. In addition, disulfide-linked TFF3 heterodimers with an Mr of about 60k and 30k were detected in both bronchial secretions and BAL fluid. In these liquids, TFF3 is partly N-terminally truncated probably by neutrophil elastase cleavage. TFF3-FCGBP is likely involved in the mucosal innate immune defense against microbial infections. We discuss a hypothetical model how TFF3 might control FCGBP oligomerization. Furthermore, we did not find indications for interactions of TFF3-FCGBP with DMBT1gp340 or the mucin MUC5AC, glycoproteins involved in mucosal innate immunity. Surprisingly, bronchial MUC5AC appeared to be degraded when compared with gastric MUC5AC.
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Affiliation(s)
- Jens Weste
- Institute of Molecular Biology and Medicinal Chemistry, Otto-von-Guericke University Magdeburg, 39120 Magdeburg, Germany
| | - Till Houben
- Institute of Molecular Biology and Medicinal Chemistry, Otto-von-Guericke University Magdeburg, 39120 Magdeburg, Germany
| | - Sönke Harder
- Section Mass Spectrometry and Proteomics, Diagnostic Center, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Hartmut Schlüter
- Section Mass Spectrometry and Proteomics, Diagnostic Center, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Eva Lücke
- Department of Pneumology, Otto-von-Guericke University Magdeburg, 39120 Magdeburg, Germany
| | - Jens Schreiber
- Department of Pneumology, Otto-von-Guericke University Magdeburg, 39120 Magdeburg, Germany
| | - Werner Hoffmann
- Institute of Molecular Biology and Medicinal Chemistry, Otto-von-Guericke University Magdeburg, 39120 Magdeburg, Germany
- Correspondence:
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25
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Behrens CS, Freese J, Zech AT, Köhne M, Krisp C, Braren I, Loos M, Kolbe M, Huge A, Schlüter H, Hansen A, Carrier L, Ulmer B, Eschenhagen T. Modelling LMNA-cardiomyopathy with patient-specific human iPSC-derived engineered heart tissue and a partial rescue by gene replacement therapy. J Mol Cell Cardiol 2022. [DOI: 10.1016/j.yjmcc.2022.08.218] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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26
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Meyer-Jens M, Pietsch N, Voß H, Müller K, Krämer E, Schlüter H, Schlossarek S, Carrier L. Evaluation of the effect of LCZ696 in human iPSC-derived cardiomyocyte hypertrophy and tubulin detyrosination. J Mol Cell Cardiol 2022. [DOI: 10.1016/j.yjmcc.2022.08.110] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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27
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von Amsberg G, Zilles M, Mansour W, Gild P, Alsdorf W, Kaune M, Böckelmann L, Hauschild J, Krisp C, Rohlfing T, Saygi C, Alawi M, Zielinski A, Langebrake C, Oh-Hohenhorst SJ, Perner S, Tilki D, Schlüter H, Graefen M, Dyshlovoy SA, Bokemeyer C. Salvage Chemotherapy with Cisplatin, Ifosfamide, and Paclitaxel in Aggressive Variant of Metastatic Castration-Resistant Prostate Cancer. Int J Mol Sci 2022; 23:ijms232314948. [PMID: 36499277 PMCID: PMC9738104 DOI: 10.3390/ijms232314948] [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] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 11/12/2022] [Accepted: 11/24/2022] [Indexed: 12/05/2022] Open
Abstract
Significant progress has been achieved in the treatment of metastatic castration-resistant prostate cancer (mCRPC). However, results in patients with aggressive variant prostate cancer (AVPC) have been disappointing. Here, we report retrospectively collected data from intensively pretreated AVPC patients (n = 17; 88.2% visceral metastases; 82% elevation of neuroendocrine markers) treated with salvage chemotherapy consisting of cisplatin, ifosfamide, and paclitaxel (TIP). At the interim analysis, 60% of patients showed radiographic response or stable disease (PFS = 2.5 months; OS = 6 months). In men who responded to chemotherapy, an OS > 15 months was observed. Preclinical analyses confirmed the high activity of the TIP regimen, especially in docetaxel-resistant prostate cancer cells. This effect was primarily mediated by increased cisplatin sensitivity in the emergence of taxane resistance. Proteomic and functional analyses identified a lower DNA repair capacity and cell cycle machinery deficiency to be causative. In contrast, paclitaxel showed inconsistent effects, partially antagonizing cisplatin and ifosfamide in some AVPC models. Consequently, paclitaxel has been excluded from the TIP combination for future patients. In summary, we report for the first time the promising efficacy of TIP as salvage therapy in AVPC. Our preclinical data indicate a pivotal role for cisplatin in overcoming docetaxel resistance.
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Affiliation(s)
- Gunhild von Amsberg
- Department of Oncology, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- Martini-Klinik Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- Correspondence: ; Tel.: +49-179-5137710
| | - Mirjam Zilles
- Department of Oncology, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Wael Mansour
- Department of Radiotherapy and Radiooncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Philipp Gild
- Department of Urology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Winfried Alsdorf
- Department of Oncology, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Moritz Kaune
- Department of Oncology, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Lukas Böckelmann
- Department of Oncology, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Jessica Hauschild
- Department of Oncology, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- Martini-Klinik Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Christoph Krisp
- Institute of Clinical Chemistry and Laboratory Medicine, Section Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Tina Rohlfing
- Department of Oncology, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Ceren Saygi
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Malik Alawi
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Alexandra Zielinski
- Department of Radiotherapy and Radiooncology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Claudia Langebrake
- Pharmacy, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Su Jung Oh-Hohenhorst
- Martini-Klinik Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- Department of Urology, Centre Hospitalier de l’Université de Montreal (CHUM)/Centre de recherche du CHUM, Montreal, QC 3840, Canada
| | - Sven Perner
- Institute of Pathology, University of Lübeck and University Hospital Schleswig-Holstein, Campus Lübeck, 23562 Lübeck, Germany
- Pathology, Research Center Borstel, Leibniz Lung Center, 23845 Borstel, Germany
- German Center for Lung Research (DZL), 35392 Gießen, Germany
| | - Derya Tilki
- Martini-Klinik Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- Department of Urology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Hartmut Schlüter
- Institute of Clinical Chemistry and Laboratory Medicine, Section Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Markus Graefen
- Martini-Klinik Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Sergey A. Dyshlovoy
- Department of Oncology, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
- Martini-Klinik Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Carsten Bokemeyer
- Department of Oncology, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
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28
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Ricklefs F, Maire C, Wollmann K, Dührsen L, Fita K, Sahm F, Herold-Mende C, von Deimling A, Fuh M, Schlüter H, Westphal M, Lamszus K. BIOM-52. DIAGNOSTIC POTENTIAL OF EXTRACELLULAR VESICLES IN MENINGIOMA PATIENTS. Neuro Oncol 2022. [DOI: 10.1093/neuonc/noac209.062] [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] Open
Abstract
Abstract
Standard monitoring after meningioma resection relies on serial MRI examinations, which are time-consuming, expensive and provide no information on molecular alterations that may indicate progression towards a more aggressive tumor. Extracellular vesicles (EVs) secreted by tumor cells play an important role in cell-cell communication, and tumor-derived EVs circulating in patient blood can serve as biomarkers. We investigated the potential role of plasma EVs in meningioma patients for tumor detection and determined whether EVs secreted by meningioma cells reflect epigenetic, genomic and proteomic alterations of original tumors. EV concentrations were quantified in patient plasma (n = 46). Short-term meningioma cultures were established (n = 26) and secreted EVs were isolated. Methylation and copy number profiling was performed using 850k arrays, and mutations were identified by targeted gene panel sequencing. Differential quantitative mass spectrometry was employed for proteomic analysis. We found that the levels of circulating EVs were significantly elevated in meningioma patients compared to healthy individuals, and that plasma EV concentrations correlated with malignancy grade and extent of peritumoral edema. Postoperatively, EV counts dropped to normal levels, and the magnitude of the postoperative decrease was associated with extent of tumor resection (Simpson grade). Methylation profiling of EV-DNA allowed correct tumor classification as meningioma in all investigated cases, and accurate methylation subclass assignment in nearly all cases. Copy number variations present in tumors, as well as tumor-specific mutations were faithfully reflected in meningioma EV-DNA. Proteomic EV profiling did not permit original tumor identification but revealed tumor-associated proteins such as desmoplakin that could potentially be utilized to enrich meningioma EVs from biofluids. In conclusion, elevated EV levels in meningioma patient plasma may aid in tumor diagnosis and assessment of treatment response. Meningioma EV-DNA mirrors genetic and epigenetic tumor alterations and facilitates molecular tumor classification.
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Affiliation(s)
- Franz Ricklefs
- Universitry Medical Center Hamburg-Eppendorf , Hamburg , Germany
| | - Cecile Maire
- University Medical Center Hamburg-Eppendorf , Hamburg , Germany
| | | | - Lasse Dührsen
- University Medical Center Hamburg-Eppendorf , Hamburg , Germany
| | - Krystian Fita
- University Medical Center Hamburg-Eppendorf , Hamburg , Germany
| | - Felix Sahm
- Department of Neuropathology, University Hospital Heidelberg, and Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK) and German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | | | - Andreas von Deimling
- Department of Neuropathology, University Hospital Heidelberg, and Clinical Cooperation Unit Neuropathology, German Consortium for Translational Cancer Research (DKTK) and German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Marceline Fuh
- University Medical Center Hamburg-Eppendorf , Hamburg , Germany
| | | | | | - Katrin Lamszus
- University Medical Center Hamburg-Eppendorf , Hamburg , Germany
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29
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Guan Y, Zhang M, Gaikwad M, Voss H, Fazel R, Ansari S, Shen H, Wang J, Schlüter H. Correction to An Integrated Strategy Reveals Complex Glycosylation of Erythropoietin Using Mass Spectrometry. J Proteome Res 2022; 21:2552. [PMID: 36098618 PMCID: PMC9552228 DOI: 10.1021/acs.jproteome.2c00509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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30
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Zhang Y, Dreyer B, Govorukhina N, Heberle AM, Končarević S, Krisp C, Opitz CA, Pfänder P, Bischoff R, Schlüter H, Kwiatkowski M, Thedieck K, Horvatovich PL. Comparative Assessment of Quantification Methods for Tumor Tissue Phosphoproteomics. Anal Chem 2022; 94:10893-10906. [PMID: 35880733 PMCID: PMC9366746 DOI: 10.1021/acs.analchem.2c01036] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
With increasing sensitivity and accuracy in mass spectrometry,
the tumor phosphoproteome is getting into reach. However, the selection
of quantitation techniques best-suited to the biomedical question
and diagnostic requirements remains a trial and error decision as
no study has directly compared their performance for tumor tissue
phosphoproteomics. We compared label-free quantification (LFQ), spike-in-SILAC
(stable isotope labeling by amino acids in cell culture), and tandem
mass tag (TMT) isobaric tandem mass tags technology for quantitative
phosphosite profiling in tumor tissue. Compared to the classic SILAC
method, spike-in-SILAC is not limited to cell culture analysis, making
it suitable for quantitative analysis of tumor tissue samples. TMT
offered the lowest accuracy and the highest precision and robustness
toward different phosphosite abundances and matrices. Spike-in-SILAC
offered the best compromise between these features but suffered from
a low phosphosite coverage. LFQ offered the lowest precision but the
highest number of identifications. Both spike-in-SILAC and LFQ presented
susceptibility to matrix effects. Match between run (MBR)-based analysis
enhanced the phosphosite coverage across technical replicates in LFQ
and spike-in-SILAC but further reduced the precision and robustness
of quantification. The choice of quantitative methodology is critical
for both study design such as sample size in sample groups and quantified
phosphosites and comparison of published cancer phosphoproteomes.
Using ovarian cancer tissue as an example, our study builds a resource
for the design and analysis of quantitative phosphoproteomic studies
in cancer research and diagnostics.
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Affiliation(s)
- Yang Zhang
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV Groningen, The Netherlands.,Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, 6020 Innsbruck, Austria.,Laboratory of Pediatrics, Section Systems Medicine of Metabolism and Signaling, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands
| | - Benjamin Dreyer
- Section/Core Facility Mass Spectrometry and Proteomics, Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Natalia Govorukhina
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Alexander M Heberle
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, 6020 Innsbruck, Austria.,Laboratory of Pediatrics, Section Systems Medicine of Metabolism and Signaling, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands
| | - Saša Končarević
- Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt/Main, Germany
| | - Christoph Krisp
- Section/Core Facility Mass Spectrometry and Proteomics, Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Christiane A Opitz
- Metabolic Crosstalk in Cancer, German Consortium of Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,Department of Neurology, National Center for Tumor Diseases, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Pauline Pfänder
- Metabolic Crosstalk in Cancer, German Consortium of Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.,Faculty of Bioscience, Heidelberg University, 69117 Heidelberg, Germany
| | - Rainer Bischoff
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Hartmut Schlüter
- Section/Core Facility Mass Spectrometry and Proteomics, Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Marcel Kwiatkowski
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, 6020 Innsbruck, Austria.,Department of Molecular Pharmacology, Groningen Research Institute for Pharmacy, University of Groningen, Groningen 9700 AD, The Netherlands.,Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen 9700 AD, The Netherlands
| | - Kathrin Thedieck
- Institute of Biochemistry and Center for Molecular Biosciences Innsbruck, University of Innsbruck, 6020 Innsbruck, Austria.,Laboratory of Pediatrics, Section Systems Medicine of Metabolism and Signaling, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands.,Department of Neuroscience, School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, 26129 Oldenburg, Germany
| | - Peter L Horvatovich
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV Groningen, The Netherlands
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Voß H, Schlumbohm S, Wurlitzer M, Dottermusch M, Neumann P, Barwikowski P, Schlüter H, Krisp C, Neumann J. OTHR-07. A new framework for missing value tolerant data integration. Neuro Oncol 2022. [PMCID: PMC9164682 DOI: 10.1093/neuonc/noac079.546] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Dataset integration is common practice to overcome limitations, e.g., in statistically underpowered omics datasets. This is of particular importance when analyzing rare tumor entities. However, combining datasets leads to the introduction of biases, so called 'batch effects', which are due to differences in quantification techniques, laboratory equipment or used tissue type. A common problem is the missing quantification for features like gene transcripts or proteins within a dataset. These missing values can appear at random in a given dataset and also get introduced by combination of multiple datasets. Currently, strategies beyond common normalization for batch effect reduction are either missing entirely or are unable to handle absence of data points and therefore rely on error-prone data imputation. We introduce a framework that enables batch effect adjustments for combined datasets while avoiding data loss by appropriately handling missing values without imputation. The underlying idea is based on a matrix dissection approach, adjusting common information from the integrated dataset under guarantee of sufficient data presence. The strategy is implemented within the R environment and linked with popular software stacks that are built on top of R. Successful data adjustment is exemplarily shown for proteomic data generated by different quantification approaches and LC-MS/MS instrumentation setups.
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Affiliation(s)
- Hannah Voß
- University Medical Center Hamburg-Eppendorf , Hamburg , Germany
| | - Simon Schlumbohm
- University Medical Center Hamburg-Eppendorf , Hamburg , Germany
- Helmut-Schmidt-University , Hamburg , Germany
| | | | | | | | | | | | - Christoph Krisp
- University Medical Center Hamburg-Eppendorf , Hamburg , Germany
| | - Julia Neumann
- University Medical Center Hamburg-Eppendorf , Hamburg , Germany
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Voss H, Godbole S, Schlumbohm S, Dottermusch M, Schuhmann Y, Neumann P, Schlüter H, Schüller U, Peng B, Barwikowski P, Krisp C, Neumann JE. OTHR-42. Missing data tolerant integration of proteomic datasets enables the identification and characterization of brain cancer subtypes. Neuro Oncol 2022. [PMCID: PMC9164826 DOI: 10.1093/neuonc/noac079.580] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Investigating the proteome can add a significant layer of information to manifold existing methylation, mutation, and transcriptome data on brain tumors as proteins represent the pharmacologically addressable phenotype of a disease. Small cohorts limit the usability and validity of statistical methods, and variable technical setups and high numbers of missing values make data integration from public sources challenging. Using a newly developed framework being able to reduce batch effects without the need for data reduction or missing value imputation, we show –based on in-house and publicly available datasets- successful integration of proteomic data across different tissue types, quantification platforms, and technical setups. Exemplarily, data of a Sonic hedgehog (Shh) medulloblastoma mouse model were analyzed, showing efficient data integration independent of tissue preservation strategy or batch. We further integrated batches of publicly available data of human brain tumors, confirming proposed proteomic cancer subtypes correlating with clinical features. We show that, missing value tolerant reduction of technical variances may be helpful to identify biomarkers, proteomic signatures, and altered pathways characteristic for molecular brain cancer subtypes.
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Middelkamp M, Ruck L, Krisp C, Sumislawski P, Mohammadi B, Dottermusch M, Meister V, Küster L, Schlüter H, Windhorst S, Neumann JE. ETMR-02. Overexpression of Lin28A in neural progenitor cells in vivo does not lead to brain tumor formation but results in reduced spine density. Neuro Oncol 2022. [PMCID: PMC9165115 DOI: 10.1093/neuonc/noac079.180] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
The RNA binding protein LIN28A is a stem- and progenitor marker and one of the factors necessary to induce pluripotent stem cells. An overexpression of LIN28A has been identified in malignant brain tumors called embryonal tumors with multilayered rosettes (ETMR) but its specific role during brain development remains largely unknown. Radial glia cells of the ventricular zone (VZ) are proposed as a cell of origin for ETMR. We asked whether an overexpression of LIN28A in such cells might affect brain development or result in the formation of brain tumors. Constitutive overexpression of LIN28A in hGFAP-cre::lsl-Lin28A (GL) mice led to a transient increase of proliferation in the cortical VZ at embryonic stages but no postnatal brain tumor formation. Postnatally, GL mice displayed a pyramidal cell layer dispersion of the hippocampus and altered spine and dendrite morphology, including reduced dendritic spine densities in the hippocampus and cortex. GL mice displayed hyperkinetic activity and differential quantitative MS-based proteomics revealed altered time dependent molecular functions regarding mRNA processing and spine morphogenesis. Phosphoproteomic analyses indicated a downregulation of mTOR pathway modulated proteins such as Map1b being involved in microtubule dynamics within a crosstalk of Gsk3b/Rho-Rac/Map1b signaling. In conclusion, we show that Lin28A overexpression transiently increases proliferation of neural precursor cells but it is not sufficient to drive brain tumors in vivo. In contrast, Lin28A impacts on protein abundancy patterns related to spine morphogenesis and phosphorylation levels of proteins involved in microtubule dynamics, resulting in decreased spine densities of neurons in the hippocampus and cortex as well as in altered behavior. Our work provides new insights into the role of LIN28A for neuronal morphogenesis and development and may reveal future targets for treatment of ETMR patients.
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Affiliation(s)
- Maximilian Middelkamp
- Center for Molecular Neurobiology Hamburg (ZMNH), University Medical Center Hamburg-Eppendorf , Hamburg , Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf , Hamburg , Germany
| | - Lisa Ruck
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf , Hamburg , Germany
| | - Christoph Krisp
- Institute of Clinical Chemistry and Laboratory Medicine, Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf , Hamburg , Germany
| | - Piotr Sumislawski
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf , Hamburg , Germany
| | - Behnam Mohammadi
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf , Hamburg , Germany
| | - Matthias Dottermusch
- Center for Molecular Neurobiology Hamburg (ZMNH), University Medical Center Hamburg-Eppendorf , Hamburg , Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf , Hamburg , Germany
| | - Valerie Meister
- Institute of Neuropathology, Ludwig-Maximilians-University Munich , Munich , Germany
| | - Lukas Küster
- Department of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf , Hamburg , Germany
| | - Hartmut Schlüter
- Institute of Clinical Chemistry and Laboratory Medicine, Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf , Hamburg , Germany
| | - Sabine Windhorst
- Department of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf , Hamburg , Germany
| | - Julia E Neumann
- Center for Molecular Neurobiology Hamburg (ZMNH), University Medical Center Hamburg-Eppendorf , Hamburg , Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf , Hamburg , Germany
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Navolic J, Middelkamp M, Sumislawski P, Ruck L, Krisp C, Dottermusch M, Schlüter H, Neumann JE. OTHR-19. Disordered cell migration in the cerebral cortex caused by Lin28A overexpression and Wnt pathway activation in neural precursor cells. Neuro Oncol 2022. [DOI: 10.1093/neuonc/noac079.558] [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: 11/14/2022] Open
Abstract
Abstract
LIN28A overexpression and mutations of the Wnt pathway gene CTNNB1 have been described in rare malignant brain tumors of early childhood. In order to investigate the interplay of the oncogenic proteins Lin28A and Ctnnb1 during embryonal brain development, we overexpressed these components in neural progenitor cells in vivo. The sole overexpression of either Lin28A, stabilized Ctnnb1 (Ctnnb1Δex3) or the combination of both in hGFAP-positive forebrain precursor cells did not lead to brain tumor formation but resulted in distinct phenotypes in the cerebral cortex during embryonal development. The hGFAP-cre::IsI-Lin28A (GL) mouse model showed transiently increased proliferation in the cerebral ventricular zone and proper isocortical layering. hGFAP-cre::Ctnnb1Δex3fl/+ (GB) and hGFAP-cre::Ctnnb1Δex3fl/+::IsI-Lin28A (GBL) mice developed a hydrocephalus and showed disturbed cortical layering. GB mice displayed cerebral hypoplasia with a thinned cortex, while the GBL cortices showed variable thickness. Immunostainings with the pial marker Laminin and dendritic marker Map2c revealed a porous pia mater and aggregations of neurons above the pial border in the GBL model at embryonal day 14 (E14.5). At later embryonal stage (E18.5), the GBL model showed also large blood vessels located in deeper cortical layers. Proteome analyses of GB and GBL cortices revealed decreased abundance of the Lissencephaly associated component Reelin-receptor Lrp8 compared to hGFAP-cre control mice. Additionally, we found 92 proteins, which were altered specifically in the GBL mouse model. These results indicate that the co-expression of Lin28A and Ctnnb1Δex3 in neural precursor cells does not lead to brain tumor formation but results in neuronal migration disturbances with ectopic neurons in the subarachnoid area. Whereas the GB phenotype is reminiscent of human lissencephaly type I, GBL brain morphology showed similarities to neuronal overmigration observed in the migration disorder of human Cobblestone (Type II) Lissencephaly.
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Affiliation(s)
- Jelena Navolic
- Center for Molecular Neurobiology Hamburg (ZMNH), University Medical Center Hamburg-Eppendorf , Hamburg , Germany
| | - Maximilian Middelkamp
- Center for Molecular Neurobiology Hamburg (ZMNH), University Medical Center Hamburg-Eppendorf , Hamburg , Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf , Hamburg , Germany
| | - Piotr Sumislawski
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf , Hamburg , Germany
| | - Lisa Ruck
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf , Hamburg , Germany
| | - Christoph Krisp
- Institute of Clinical Chemistry and Laboratory Medicine, Mass Spectrometric Proteomics, University Medical Center Hamburg- Eppendorf , Hamburg , Germany
| | - Matthias Dottermusch
- Center for Molecular Neurobiology Hamburg (ZMNH), University Medical Center Hamburg-Eppendorf , Hamburg , Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf , Hamburg , Germany
| | - Hartmut Schlüter
- Institute of Clinical Chemistry and Laboratory Medicine, Mass Spectrometric Proteomics, University Medical Center Hamburg- Eppendorf , Hamburg , Germany
| | - Julia E Neumann
- Center for Molecular Neurobiology Hamburg (ZMNH), University Medical Center Hamburg-Eppendorf , Hamburg , Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf , Hamburg , Germany
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Voß H, Moritz M, Pelczar P, Gagliani N, Huber S, Nippert V, Schlüter H, Hahn J. Tissue Sampling and Homogenization with NIRL Enables Spatially Resolved Cell Layer Specific Proteomic Analysis of the Murine Intestine. Int J Mol Sci 2022; 23:ijms23116132. [PMID: 35682811 PMCID: PMC9181169 DOI: 10.3390/ijms23116132] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/18/2022] [Accepted: 05/27/2022] [Indexed: 02/04/2023] Open
Abstract
For investigating the molecular physiology and pathophysiology in organs, the most exact data should be obtained; if not, organ-specific cell lines are analyzed, or the whole organ is homogenized, followed by the analysis of its biomolecules. However, if the morphological organization of the organ can be addressed, then, in the best case, the composition of molecules in single cells of the target organ can be analyzed. Laser capture microdissection (LCM) is a technique which enables the selection of specific cells of a tissue for further analysis of their molecules. However, LCM is a time-consuming two-dimensional technique, and optimal results are only obtained if the tissue is fixed, e.g., by formalin. Especially for proteome analysis, formalin fixation reduced the number of identifiable proteins, and this is an additional drawback. Recently, it was demonstrated that sampling of fresh-frozen (non-fixed) tissue with an infrared-laser is giving higher yields with respect to the absolute protein amount and number of identifiable proteins than conventional mechanical homogenization of tissues. In this study, the applicability of the infrared laser tissue sampling for the proteome analysis of different cell layers of murine intestine was investigated, using LC–MS/MS-based differential quantitative bottom-up proteomics. By laser ablation, eight consecutive layers of colon tissue were obtained and analyzed. However, a clear distinguishability of protein profiles between ascending, descending, and transversal colon was made, and we identified the different intestinal-cell-layer proteins, which are cell-specific, as confirmed by data from the Human Protein Atlas. Thus, for the first time, sampling directly from intact fresh-frozen tissue with three-dimensional resolution is giving access to the different proteomes of different cell layers of colon tissue.
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Affiliation(s)
- Hannah Voß
- Section/Core Facility Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246 Hamburg, Germany; (H.V.); (M.M.); (V.N.)
| | - Manuela Moritz
- Section/Core Facility Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246 Hamburg, Germany; (H.V.); (M.M.); (V.N.)
| | - Penelope Pelczar
- Section of Molecular Immunology und Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246 Hamburg, Germany; (P.P.); (N.G.); (S.H.)
| | - Nicola Gagliani
- Section of Molecular Immunology und Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246 Hamburg, Germany; (P.P.); (N.G.); (S.H.)
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246 Hamburg, Germany
| | - Samuel Huber
- Section of Molecular Immunology und Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246 Hamburg, Germany; (P.P.); (N.G.); (S.H.)
| | - Vivien Nippert
- Section/Core Facility Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246 Hamburg, Germany; (H.V.); (M.M.); (V.N.)
| | - Hartmut Schlüter
- Section/Core Facility Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246 Hamburg, Germany; (H.V.); (M.M.); (V.N.)
- Correspondence: (H.S.); (J.H.); Tel.: +49-1575-6085997 (H.S.); +49-1522-2827168 (J.H.)
| | - Jan Hahn
- Section/Core Facility Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Martinistraße 52, 20246 Hamburg, Germany; (H.V.); (M.M.); (V.N.)
- Correspondence: (H.S.); (J.H.); Tel.: +49-1575-6085997 (H.S.); +49-1522-2827168 (J.H.)
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Ricklefs FL, Maire CL, Wollmann K, Dührsen L, Fita KD, Sahm F, Herold-Mende C, von Deimling A, Kolbe K, Holz M, Bergmann L, Fuh MM, Schlüter H, Alawi M, Reimer R, Peine S, Glatzel M, Westphal M, Lamszus K. Diagnostic potential of extracellular vesicles in meningioma patients. Neuro Oncol 2022; 24:2078-2090. [PMID: 35551407 PMCID: PMC9883720 DOI: 10.1093/neuonc/noac127] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 02/02/2023] Open
Abstract
BACKGROUND Extracellular vesicles (EVs) play an important role in cell-cell communication, and tumor-derived EVs circulating in patient blood can serve as biomarkers. Here, we investigated the potential role of plasma EVs in meningioma patients for tumor detection and determined whether EVs secreted by meningioma cells reflect epigenetic, genomic, and proteomic alterations of original tumors. METHODS EV concentrations were quantified in patient plasma (n = 46). Short-term meningioma cultures were established (n = 26) and secreted EVs were isolated. Methylation and copy number profiling was performed using 850k arrays, and mutations were identified by targeted gene panel sequencing. Differential quantitative mass spectrometry was employed for proteomic analysis. RESULTS Levels of circulating EVs were elevated in meningioma patients compared to healthy individuals, and the plasma EV concentration correlated with malignancy grade and extent of peritumoral edema. Postoperatively, EV counts dropped to normal levels, and the magnitude of the postoperative decrease was associated with extent of tumor resection. Methylation profiling of EV-DNA allowed correct tumor classification as meningioma in all investigated cases, and accurate methylation subclass assignment in almost all cases. Copy number variations present in tumors, as well as tumor-specific mutations were faithfully reflected in meningioma EV-DNA. Proteomic EV profiling did not permit original tumor identification but revealed tumor-associated proteins that could potentially be utilized to enrich meningioma EVs from biofluids. CONCLUSIONS Elevated EV levels in meningioma patient plasma could aid in tumor diagnosis and assessment of treatment response. Meningioma EV-DNA mirrors genetic and epigenetic tumor alterations and facilitates molecular tumor classification.
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Affiliation(s)
- Franz L Ricklefs
- Corresponding Authors: Katrin Lamszus, MD, Laboratory for Brain Tumor Biology, Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany (); Franz Ricklefs, MD, Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany ()
| | - Cecile L Maire
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kathrin Wollmann
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lasse Dührsen
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Krystian D Fita
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Felix Sahm
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Christel Herold-Mende
- Division of Neurosurgical Research, Department of Neurosurgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Katharina Kolbe
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mareike Holz
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Leonie Bergmann
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marceline M Fuh
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hartmut Schlüter
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Malik Alawi
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Rudolph Reimer
- Heinrich-Pette-Institut, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Sven Peine
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Markus Glatzel
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Manfred Westphal
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katrin Lamszus
- Corresponding Authors: Katrin Lamszus, MD, Laboratory for Brain Tumor Biology, Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany (); Franz Ricklefs, MD, Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany ()
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Lassé M, Bonin LL, El Saghir J, Eddy SF, Hutzfeldt A, Hoxha E, Dumoulin B, Lindenmeyer M, Schlüter H, Beck BB, Brandts P, Kretzler M, Demir F, Harder JL, Rinschen M. MO059: Trajectory Analysis of the Kidney Organoid Proteome Extends its Modelling Potential of Disease. Nephrol Dial Transplant 2022. [DOI: 10.1093/ndt/gfac063.011] [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: 11/12/2022] Open
Abstract
Abstract
BACKGROUND AND AIMS
Kidney organoids are a valuable and innovative model to understand genetic diseases, kidney development and transcriptomic dynamics. However, their proteome has not been analyzed so far. It is unclear how their proteome changes during differentiation, and if more complex disease processes such as inflammatory tissue responses could be modelled with this approach.
METHOD
Here, we used proteomics to compare organoids with existing model systems such as native glomeruli and cultured cells. We characterize the trajectory of organoid differentiation and delineate innate immune responses in organoids to expand its scope as a model system in nephrology. We also compared our proteomics with bulk and single cell transcriptomic data.
RESULTS
Genes involved in podocytopathies and cystic kidney diseases were abundantly expressed on protein level, distinguishing organoids from almost every available cell culture model. On their pathway to terminal differentiation, organoids developed increased deposition of extracellular matrix. Single cell transcriptomic analysis suggests that most changes locate to podocytes and early podocyte progenitors. This matrix deposition is different from commonly used animal models of glomerular disease. A novel signaling system discovered was the TNFα system, a system also available in podocytes. Incubation of organoids with high concentrations of TNFα led to an activation of NF-kB signaling, and secretion of cytokines and complement components, alongside with extracellular matrix components.
CONCLUSION
Interestingly, this signaling system directly links inflammatory signaling, production of cytokines and complement, and production of extracellular matrix. Thus, we provide a repository of human kidney organoid proteins that revealed the potential to model pathophysiological pathways beyond genetic diseases.
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Affiliation(s)
- Moritz Lassé
- Universitätsklinikum Hamburg-Eppendorf (UKE), Hamburg, Germany, Zentrum für Innere Medizin, III. Medizinische Klinik und Poliklinik (Nephrologie/Rheumatologie/Endokrinologie), Hamburg, Germany
| | - Léna L Bonin
- Aarhus University, Aarhus, Denmark, Department of Biomedicine, Denmark
| | - Jamal El Saghir
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Sean F Eddy
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Arvid Hutzfeldt
- Universitätsklinikum Hamburg-Eppendorf (UKE), Hamburg, Germany, Zentrum für Innere Medizin, III. Medizinische Klinik und Poliklinik (Nephrologie/Rheumatologie/Endokrinologie), Hamburg, Germany
| | - Elion Hoxha
- Universitätsklinikum Hamburg-Eppendorf (UKE), Hamburg, Germany, Zentrum für Innere Medizin, III. Medizinische Klinik und Poliklinik (Nephrologie/Rheumatologie/Endokrinologie), Hamburg, Germany
| | - Bernhard Dumoulin
- Universitätsklinikum Hamburg-Eppendorf (UKE), Hamburg, Germany, Zentrum für Innere Medizin, III. Medizinische Klinik und Poliklinik (Nephrologie/Rheumatologie/Endokrinologie), Hamburg, Germany
| | - Maja Lindenmeyer
- Universitätsklinikum Hamburg-Eppendorf (UKE), Hamburg, Germany, Zentrum für Innere Medizin, III. Medizinische Klinik und Poliklinik (Nephrologie/Rheumatologie/Endokrinologie), Hamburg, Germany
| | - Hartmut Schlüter
- Universitätsklinikum Hamburg-Eppendorf (UKE), Hamburg, Germany, Institute of Clinical Chemistry and Laboratory Medicine, Germany
| | - Bodo B Beck
- University Hospital Cologne, Human Genetics, Germany
| | - Paul Brandts
- Universitätsklinikum Hamburg-Eppendorf (UKE), Hamburg, Germany, Zentrum für Innere Medizin, III. Medizinische Klinik und Poliklinik (Nephrologie/Rheumatologie/Endokrinologie), Hamburg, Germany
| | - Matthias Kretzler
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Fatih Demir
- Aarhus University, Aarhus, Denmark, Department of Biomedicine, Denmark
| | - Jennifer L Harder
- Department of Internal Medicine, Division of Nephrology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Markus Rinschen
- Aarhus University, Aarhus, Denmark, Department of Biomedicine, Denmark
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Aypek H, Krisp C, Lu S, Liu S, Kylies D, Kretz O, Wu G, Moritz M, Amann K, Benz K, Tong P, Hu ZM, Alsulaiman SM, Khan AO, Grohmann M, Wagner T, Müller-Deile J, Schlüter H, Puelles VG, Bergmann C, Huber TB, Grahammer F. Loss of the collagen IV modifier prolyl 3-hydroxylase 2 causes thin basement membrane nephropathy. J Clin Invest 2022; 132:147253. [PMID: 35499085 PMCID: PMC9057608 DOI: 10.1172/jci147253] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 03/16/2022] [Indexed: 01/12/2023] Open
Abstract
The glomerular filtration barrier (GFB) produces primary urine and is composed of a fenestrated endothelium, a glomerular basement membrane (GBM), podocytes, and a slit diaphragm. Impairment of the GFB leads to albuminuria and microhematuria. The GBM is generated via secreted proteins from both endothelial cells and podocytes and is supposed to majorly contribute to filtration selectivity. While genetic mutations or variations of GBM components have been recently proposed to be a common cause of glomerular diseases, pathways modifying and stabilizing the GBM remain incompletely understood. Here, we identified prolyl 3-hydroxylase 2 (P3H2) as a regulator of the GBM in an a cohort of patients with albuminuria. P3H2 hydroxylates the 3' of prolines in collagen IV subchains in the endoplasmic reticulum. Characterization of a P3h2ΔPod mouse line revealed that the absence of P3H2 protein in podocytes induced a thin basement membrane nephropathy (TBMN) phenotype with a thinner GBM than that in WT mice and the development of microhematuria and microalbuminuria over time. Mechanistically, differential quantitative proteomics of the GBM identified a significant decrease in the abundance of collagen IV subchains and their interaction partners in P3h2ΔPod mice. To our knowledge, P3H2 protein is the first identified GBM modifier, and loss or mutation of P3H2 causes TBMN and focal segmental glomerulosclerosis in mice and humans.
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Affiliation(s)
| | - Christoph Krisp
- Institute of Clinical Chemistry and Laboratory Medicine, Mass Spectrometric Proteomics Group, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Shun Lu
- III. Department of Medicine and
| | | | | | | | | | - Manuela Moritz
- Institute of Clinical Chemistry and Laboratory Medicine, Mass Spectrometric Proteomics Group, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kerstin Amann
- Department of Nephropathology, Institute of Pathology and
| | - Kerstin Benz
- Department of Pediatrics, University of Erlangen, Erlangen, Germany
| | - Ping Tong
- Department of Ophthalmology, The Second Xiangya Hospital and
| | - Zheng-mao Hu
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | | | - Arif O. Khan
- Eye Institute, Cleveland Clinic Abu Dhabi, Abu Dhabi, United Arab Emirates.,Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine of Case Western University, Cleveland, Ohio, USA
| | - Maik Grohmann
- Medizinische Genetik Mainz, Limbach Genetics, Mainz, Germany
| | - Timo Wagner
- Medizinische Genetik Mainz, Limbach Genetics, Mainz, Germany
| | - Janina Müller-Deile
- Department of Nephrology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Hartmut Schlüter
- Institute of Clinical Chemistry and Laboratory Medicine, Mass Spectrometric Proteomics Group, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Carsten Bergmann
- Medizinische Genetik Mainz, Limbach Genetics, Mainz, Germany.,Department of Medicine IV, Faculty of Medicine, Medical Center-University of Freiburg, Freiburg, Germany
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Meka DP, Kobler O, Hong S, Friedrich CM, Wuesthoff S, Henis M, Schwanke B, Krisp C, Schmuelling N, Rueter R, Ruecker T, Betleja E, Cheng T, Mahjoub MR, Soba P, Schlüter H, Fornasiero EF, Calderon de Anda F. Centrosome-dependent microtubule modifications set the conditions for axon formation. Cell Rep 2022; 39:110686. [PMID: 35443171 PMCID: PMC10150443 DOI: 10.1016/j.celrep.2022.110686] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 02/04/2021] [Revised: 12/27/2021] [Accepted: 03/24/2022] [Indexed: 11/29/2022] Open
Abstract
Microtubule (MT) modifications are critical during axon development, with stable MTs populating the axon. How these modifications are spatially coordinated is unclear. Here, via high-resolution microscopy, we show that early developing neurons have fewer somatic acetylated MTs restricted near the centrosome. At later stages, however, acetylated MTs spread out in soma and concentrate in growing axon. Live imaging in early plated neurons of the MT plus-end protein, EB3, show increased displacement and growth rate near the MTOC, suggesting local differences that might support axon selection. Moreover, F-actin disruption in early developing neurons, which show fewer somatic acetylated MTs, does not induce multiple axons, unlike later stages. Overexpression of centrosomal protein 120 (Cep120), which promotes MT acetylation/stabilization, induces multiple axons, while its knockdown downregulates proteins modulating MT dynamics and stability, hampering axon formation. Collectively, we show how centrosome-dependent MT modifications contribute to axon formation.
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Affiliation(s)
- Durga Praveen Meka
- Institute of Developmental Neurophysiology, Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Oliver Kobler
- Combinatorial Neuroimaging Core Facility, Leibniz Institute for Neurobiology, 39118 Magdeburg, Germany
| | - Shuai Hong
- Institute of Developmental Neurophysiology, Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Carina Meta Friedrich
- Institute of Developmental Neurophysiology, Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Souhaila Wuesthoff
- Institute of Developmental Neurophysiology, Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Melad Henis
- Institute of Developmental Neurophysiology, Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany; Department of Anatomy and Histology, Faculty of Veterinary Medicine, New Valley University, 72511 El-Kharga, Egypt
| | - Birgit Schwanke
- Institute of Developmental Neurophysiology, Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Christoph Krisp
- Institute for Clinical Chemistry and Laboratory Medicine, Mass Spectrometric Proteomics Group, Campus Forschung, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Nessa Schmuelling
- Institute of Developmental Neurophysiology, Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - René Rueter
- Institute of Developmental Neurophysiology, Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Tabitha Ruecker
- Institute of Developmental Neurophysiology, Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Ewelina Betleja
- Department of Medicine (Nephrology Division), Washington University, St. Louis, MO 63110, USA
| | - Tao Cheng
- Department of Medicine (Nephrology Division), Washington University, St. Louis, MO 63110, USA
| | - Moe R Mahjoub
- Department of Medicine (Nephrology Division), Washington University, St. Louis, MO 63110, USA
| | - Peter Soba
- LIMES Institute, Department of Molecular Brain Physiology and Behavior, University of Bonn, 53115 Bonn, Germany; Institute of Physiology and Pathophysiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Hartmut Schlüter
- Institute for Clinical Chemistry and Laboratory Medicine, Mass Spectrometric Proteomics Group, Campus Forschung, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Eugenio F Fornasiero
- Department of Neuro- and Sensory Physiology, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Froylan Calderon de Anda
- Institute of Developmental Neurophysiology, Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany.
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40
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Herbertz M, Harder S, Schlüter H, Lohr C, Dobler S. Na,K-ATPase α1 and β-subunits show distinct localizations in the nervous tissue of the large milkweed bug. Cell Tissue Res 2022; 388:503-519. [PMID: 35332371 PMCID: PMC9110512 DOI: 10.1007/s00441-022-03580-6] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 01/11/2022] [Indexed: 11/28/2022]
Abstract
The Na,K-ATPase (NKA) is an essential ion transporter and signaling molecule in all animal tissues and believed to consist at least one α and one ß-subunit to form a functional enzyme. In the large milkweed bug, Oncopeltus fasciatus, adaptation to dietary cardiac glycosides (CGs), which can fatally block the NKA, has resulted in gene duplications leading to four α1-subunits. These differ in sensitivity to CGs, but resistance trades off against ion pumping activity, thus influencing the α1-subunits’ suitability for specific tissues. Besides, O. fasciatus possesses four different ß-subunits that can alter the NKA's kinetics and should play an essential role in the formation of cellular junctions. Proteomic analyses revealed the distribution and composition of α1/ß-complexes in the nervous tissue of O. fasciatus. The highly CG-resistant, but less active α1B and the highly active, but less resistant α1C predominated in the nervous tissue and co-occurred with ß2 and ß3, partly forming larger complexes than just heterodimers. Immunohistochemical analyses provided a fine scale resolution of the subunits’ distribution in different morphological structures of the nervous tissue. This may suggest that α1 as well as ß-subunits occur in isolation without the other subunit, which contradicts the present understanding that the two types of subunits have to associate to form functional complexes. An isolated occurrence was especially prominent for ß3 and βx, the enigmatic fourth and N-terminally largely truncated ß-subunit. We hypothesize that dimerization of these ß-subunits plays a role in cell–cell contacts.
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Affiliation(s)
- Marlena Herbertz
- Institute of Cell and Systems Biology of Animals, Molecular Evolutionary Biology, Universität Hamburg, 20146, Hamburg, Germany.
| | - Sönke Harder
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Hartmut Schlüter
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Christian Lohr
- Institute of Cell and Systems Biology of Animals, Neurophysiology, Universität Hamburg, 20146, Hamburg, Germany
| | - Susanne Dobler
- Institute of Cell and Systems Biology of Animals, Molecular Evolutionary Biology, Universität Hamburg, 20146, Hamburg, Germany
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Zickler M, Stanelle-Bertram S, Ehret S, Heinrich F, Lange P, Schaumburg B, Kouassi NM, Beck S, Jaeckstein MY, Mann O, Krasemann S, Schroeder M, Jarczak D, Nierhaus A, Kluge S, Peschka M, Schlüter H, Renné T, Pueschel K, Kloetgen A, Scheja L, Ondruschka B, Heeren J, Gabriel G. Replication of SARS-CoV-2 in adipose tissue determines organ and systemic lipid metabolism in hamsters and humans. Cell Metab 2022; 34:1-2. [PMID: 34895500 PMCID: PMC8663969 DOI: 10.1016/j.cmet.2021.12.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/05/2021] [Accepted: 12/02/2021] [Indexed: 12/21/2022]
Abstract
Zickler et al. describe SARS-CoV-2 RNA in post-mortem samples of human adipose tissue. In the hamster model, SARS-CoV-2 propagation in adipose tissue leads to specific changes in lipid metabolism, which are reflected in lipidome patterns of hamster and human plasma.
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Affiliation(s)
- Martin Zickler
- Leibniz Institute for Experimental Virology, Hamburg, Germany
| | | | - Sandra Ehret
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fabian Heinrich
- Institute of Legal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Philine Lange
- Institute of Legal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | | | - Sebastian Beck
- Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Michelle Y Jaeckstein
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Oliver Mann
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Susanne Krasemann
- Institute of Neuropathology, University Medical Center, Hamburg-Eppendorf, Hamburg, Germany
| | - Maria Schroeder
- Department of Intensive Care Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Dominik Jarczak
- Department of Intensive Care Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Axel Nierhaus
- Department of Intensive Care Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Kluge
- Department of Intensive Care Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Manuela Peschka
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hartmut Schlüter
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thomas Renné
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Klaus Pueschel
- Institute of Legal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andreas Kloetgen
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Ludger Scheja
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Benjamin Ondruschka
- Institute of Legal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Joerg Heeren
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Guelsah Gabriel
- Leibniz Institute for Experimental Virology, Hamburg, Germany; Institute for Virology, University for Veterinary Medicine Hanover, Hanover, Germany.
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42
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Schuster R, Steffen P, Dreyer B, Rohn S, Schlüter H, Riedner M. Identifying Circulating Urotensin II and Urotensin II-Related Peptide-Generating Enzymes in the Human Plasma Fraction Cohn IV-4. J Proteome Res 2021; 20:5368-5378. [PMID: 34734734 DOI: 10.1021/acs.jproteome.1c00521] [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] [Indexed: 11/30/2022]
Abstract
Urotensin II (UII) and UII-related peptide (URP) are vasoactive peptide hormones causing strong vasoconstriction or vasodilation, depending on the type of blood vessel. In humans, the active forms are resulting from proteolytic cleavage of their inactive precursor protein. In blood plasma, a defined protease converting the inactive UII and URP precursors into their active forms has not been identified yet. Using mass spectrometry-based enzyme screening for detecting UII- and URP-converting enzymes, the human plasma fraction Cohn IV-4 was chromatographed, and the resulting fractions were screened for UII- or URP-generating activity. Plasma kallikrein (PK) as a UII- and URP-generating protease was identified. URP generation was also found for the serine protease factor XIa, plasmin, thrombin, and, to a smaller extent, factor XIIa. It was demonstrated that in the Cohn IV-4 fraction, PK accounts for a significant amount of UII- and URP-generating activity.
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Affiliation(s)
- Raphael Schuster
- Institute of Organic Chemistry, Department of Chemistry, Universität Hamburg, 20146 Hamburg, Germany
| | - Pascal Steffen
- Bowel Cancer & Biomarker Lab, Faculty of Medicine and Health, Northern Clinical School, University of Sydney, Sydney, New South Wales 2065, Australia
| | - Benjamin Dreyer
- Mass Spectrometric Proteomics, Institute of Clinical Chemistry, University Hospital Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Sascha Rohn
- Hamburg School of Food Science, Institute of Food Chemistry, Universität Hamburg, Grindelallee 117, 20146 Hamburg, Germany.,Institute of Food Technology and Food Chemistry, Technische Universität Berlin, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
| | - Hartmut Schlüter
- Mass Spectrometric Proteomics, Institute of Clinical Chemistry, University Hospital Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Maria Riedner
- Institute of Organic Chemistry, Department of Chemistry, Universität Hamburg, 20146 Hamburg, Germany
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43
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Feridouni Khamaneh Y, Kiani P, Miller RJD, Schlüter H, Friedrich RE. Complementing the pulp proteome via sampling with a picosecond infrared laser (PIRL). Clin Oral Investig 2021; 25:6757-6768. [PMID: 33977388 PMCID: PMC8602158 DOI: 10.1007/s00784-021-03962-0] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 04/20/2021] [Indexed: 11/27/2022]
Abstract
OBJECTIVES The aim of this investigation was the detailed analysis of the human pulp proteome using the new picosecond infrared laser (PIRL)-based sampling technique, which is based on a completely different mechanism compared to mechanical sampling. Proteome analysis of healthy pulp can provide data to define changes in the proteome associated with dental disease. MATERIAL AND METHODS Immediately after extraction of the entire, undamaged tooth, 15 wisdom teeth were deep frozen in liquid nitrogen and preserved at -80°C. Teeth were crushed, and the excised frozen pulps were conditioned for further analysis. The pulps were sampled using PIRL, and the aspirates digested with trypsin and analyzed with mass spectrometry. Pulp proteins were categorized according to their gene ontology terminus. Proteins identified exclusively in this study were searched in the Human Protein Atlas (HPA) for gaining information about the main known localization and function. RESULTS A total of 1348 proteins were identified in this study. The comparison with prior studies showed a match of 72%. Twenty-eight percent of the proteins were identified exclusively in this study. Considering HPA, almost half of these proteins were assigned to tissues that could be pulp specific. CONCLUSION PIRL is releasing proteins from the dental pulp which are not dissolved by conventional sampling techniques. Clinical Relevance The presented data extend current knowledge on dental pulp proteomics in healthy teeth and can serve as a reference for studies on pulp proteomics in dental disease.
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Affiliation(s)
- Yaghoup Feridouni Khamaneh
- Department of Oral and Maxillofacial Surgery, University Medical Center Hamburg-Eppendorf, University of Hamburg, Hamburg, Germany.
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, University of Hamburg, Hamburg, Germany.
- Department of Periodontics, Preventive and Restorative Dentistry, University Medical Center Hamburg-Eppendorf, University of Hamburg, Hamburg, Germany.
- DMD, Dental Clinic Zahnvitalis, Julius-Vosseler-Str. 42, D-22527, Hamburg, Germany.
| | - Parnian Kiani
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, University of Hamburg, Hamburg, Germany
- Department of Chemistry, Lash Miller Chemical Laboratories, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
| | - R J Dwayne Miller
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, University of Hamburg, Hamburg, Germany
- Department of Chemistry, Lash Miller Chemical Laboratories, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
| | - Hartmut Schlüter
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, University of Hamburg, Hamburg, Germany
| | - Reinhard E Friedrich
- Department of Oral and Maxillofacial Surgery, University Medical Center Hamburg-Eppendorf, University of Hamburg, Hamburg, Germany
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Krösser D, Dreyer B, Siebels B, Voß H, Krisp C, Schlüter H. Investigation of the Proteomes of the Truffles Tuber albidum pico, T. aestivum, T. indicum, T. magnatum, and T. melanosporum. Int J Mol Sci 2021; 22:ijms222312999. [PMID: 34884803 PMCID: PMC8658033 DOI: 10.3390/ijms222312999] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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] [Received: 10/21/2021] [Revised: 11/29/2021] [Accepted: 11/29/2021] [Indexed: 11/17/2022] Open
Abstract
Truffles of the Tuber species are known as expensive foods, mainly for their distinct aroma and taste. This high price makes them a profitable target of food fraud, e.g., the misdeclaration of cheaper truffle species as expensive ones. While many studies investigated truffles on the metabolomic level or the volatile organic compounds extruded by them, research at the proteome level as a phenotype determining basis is limited. In this study, a bottom-up proteomic approach based on LC-MS/MS measurements in data-independent acquisition mode was performed to analyze the truffle species Tuber aestivum, Tuber albidum pico, Tuber indicum, Tuber magnatum, and Tuber melanosporum, and a protein atlas of the investigated species was obtained. The yielded proteomic fingerprints are unique for each of the of the five truffle species and can now be used in case of suspected food fraud. First, a comprehensive spectral library containing 9000 proteins and 50,000 peptides was generated by two-dimensional liquid chromatography coupled to tandem mass spectrometry (2D-LC-MS/MS). Then, samples of the truffle species were analyzed in data-independent acquisition (DIA) proteomics mode yielding 2715 quantified proteins present in all truffle samples. Individual species were clearly distinguishable by principal component analysis (PCA). Quantitative proteome fingerprints were generated from 2066 ANOVA significant proteins, and side-by-side comparisons of truffles were done by T-tests. A further aim of this study was the annotation of functions for the identified proteins. For Tuber magnatum and Tuber melanosporum conclusive links to their superior aroma were found by enrichment of proteins responsible for sulfur-metabolic processes in comparison with other truffles. The obtained data in this study may serve as a reference library for food analysis laboratories in the future to tackle food fraud by misdeclaration of truffles. Further identified proteins with their corresponding abundance values in the different truffle species may serve as potential protein markers in the establishment of targeted analysis methods. Lastly, the obtained data may serve in the future as a basis for deciphering the biochemistry of truffles more deeply as well, when protein databases of the different truffle species will be more complete.
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Hahn J, Moritz M, Voß H, Pelczar P, Huber S, Schlüter H. Tissue Sampling and Homogenization in the Sub-Microliter Scale with a Nanosecond Infrared Laser (NIRL) for Mass Spectrometric Proteomics. Int J Mol Sci 2021; 22:ijms221910833. [PMID: 34639174 PMCID: PMC8509473 DOI: 10.3390/ijms221910833] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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] [Received: 08/25/2021] [Revised: 09/30/2021] [Accepted: 10/02/2021] [Indexed: 12/12/2022] Open
Abstract
It was recently shown that ultrashort pulse infrared (IR) lasers, operating at the wavelength of the OH vibration stretching band of water, are highly efficient for sampling and homogenizing biological tissue. In this study we utilized a tunable nanosecond infrared laser (NIRL) for tissue sampling and homogenization with subsequent liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis for mass spectrometric proteomics. For the first time, laser sampling was performed with murine spleen and colon tissue. An ablation volume of 1.1 × 1.1 × 0.4 mm³ (approximately 0.5 µL) was determined with optical coherence tomography (OCT). The results of bottom-up proteomics revealed proteins with significant abundance differences for both tissue types, which are in accordance with the corresponding data of the Human Protein Atlas. The results demonstrate that tissue sampling and homogenization of small tissue volumes less than 1 µL for subsequent mass spectrometric proteomics is feasible with a NIRL.
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Affiliation(s)
- Jan Hahn
- Section/Core Facility Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Martinistr. 52, 20246 Hamburg, Germany; (M.M.); (H.V.); (H.S.)
- Correspondence: ; Tel.: +49-1522-2827-168
| | - Manuela Moritz
- Section/Core Facility Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Martinistr. 52, 20246 Hamburg, Germany; (M.M.); (H.V.); (H.S.)
| | - Hannah Voß
- Section/Core Facility Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Martinistr. 52, 20246 Hamburg, Germany; (M.M.); (H.V.); (H.S.)
| | - Penelope Pelczar
- Section of Molecular Immunology and Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Martinistr. 52, 20246 Hamburg, Germany; (P.P.); (S.H.)
| | - Samuel Huber
- Section of Molecular Immunology and Gastroenterology, I. Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), Martinistr. 52, 20246 Hamburg, Germany; (P.P.); (S.H.)
| | - Hartmut Schlüter
- Section/Core Facility Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf (UKE), Martinistr. 52, 20246 Hamburg, Germany; (M.M.); (H.V.); (H.S.)
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Bartkowiak K, Heidrich I, Kwiatkowski M, Banys-Paluchowski M, Andreas A, Wurlitzer M, Geffken M, Voß H, Zeller T, Blankenberg S, Peine S, Joosse SA, Müller V, Schlüter H, Oliveira-Ferrer L, Pantel K. Circulating Cellular Communication Network Factor 1 Protein as a Sensitive Liquid Biopsy Marker for Early Detection of Breast Cancer. Clin Chem 2021; 68:344-353. [PMID: 34458901 DOI: 10.1093/clinchem/hvab153] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 07/01/2021] [Accepted: 07/16/2021] [Indexed: 11/13/2022]
Abstract
BACKGROUND Despite recent progress in liquid biopsy technologies, early blood-based detection of breast cancer is still a challenge. METHODS We analyzed secretion of the protein cellular communication network factor 1 (CCN1, formerly cysteine-rich angiogenic inducer 61) in breast cancer cell lines by an enzyme-linked immunosorbent assay (ELISA). Soluble CCN1 in the plasma (2.5 µL) of 544 patients with breast cancer and 427 healthy controls was analyzed by ELISA. The breast cancer samples were acquired at the time of primary diagnosis prior to neoadjuvant therapy or surgery. A classifier was established on a training cohort of patients with breast cancer and age-adapted healthy controls and further validated on an independent cohort comprising breast cancer patients and healthy controls. Samples from patients with benign breast diseases were investigated as additional controls. Samples from patients with acute heart diseases (n = 127) were investigated as noncancer controls. The diagnostic accuracy was determined by receiver operating characteristic using the parameters area under the curve, sensitivity, and specificity. RESULTS CCN1 was frequently secreted by breast cancer cell lines into the extracellular space. Subsequent analysis of clinical blood samples from patients with breast cancer and age-adjusted healthy controls revealed an overall specificity of 99.0% and sensitivity of 80.0% for cancer detection. Remarkably, 81.5% of small T1 cancers were already CCN1-positive, while CCN1 concentrations in patients with benign breast lesions were below the threshold for breast cancer detection. CONCLUSIONS Circulating CCN1 is a potentially novel blood biomarker for the detection of breast cancer at the earliest invasive stage.
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Affiliation(s)
- Kai Bartkowiak
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Isabel Heidrich
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marcel Kwiatkowski
- Department of Functional Proteo-Metabolomics, Institute of Biochemistry, University of Innsbruck, Innsbruck, Austria
| | - Maggie Banys-Paluchowski
- Department of Gynecology and Obstetrics, University Hospital Schleswig-Holstein, Lübeck, Germany.,Department Working Group Gynecological Oncology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Antje Andreas
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marcus Wurlitzer
- Department of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maria Geffken
- Department of Transfusion Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hannah Voß
- Department of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tanja Zeller
- Department of General and Interventional Cardiology, University Heart Center Hamburg -Eppendorf, Hamburg, Germany.,German Center of Cardiovascular Disease (DZHK), Partner Site Hamburg, Lübeck, Kiel, Hamburg, Germany
| | - Stefan Blankenberg
- Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Department of Gynecology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sven Peine
- Department of Transfusion Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Simon A Joosse
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Volkmar Müller
- Department of Gynecology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hartmut Schlüter
- Department of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Klaus Pantel
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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47
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Omidi M, Ahmad Agha N, Müller A, Feyerabend F, Helmholz H, Willumeit-Römer R, Schlüter H, Luthringer-Feyerabend BJC. Investigation of the impact of magnesium versus titanium implants on protein composition in osteoblast by label free quantification. Metallomics 2021; 12:916-934. [PMID: 32352129 DOI: 10.1039/d0mt00028k] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Metallic implant biomaterials predominate in orthopaedic surgery. Compared to titanium-based permanent implants, magnesium-based ones offer new possibilities as they possess mechanical properties closer to the ones of bones and they are biodegradable. Furthermore, magnesium is more and more considered to be "bioactive" i.e., able to elicit a specific tissue response or to strengthen the intimate contact between the implant and the osseous tissue. Indeed, several studies demonstrated the overall beneficial effect of magnesium-based materials on bone tissue (in vivo and in vitro). Here, the direct effects of titanium and magnesium on osteoblasts were measured on proteomes levels in order to highlight metal-specific and relevant proteins. Out of 2100 identified proteins, only 10 and 81 differentially regulated proteins, compare to the control, were isolated for titanium and magnesium samples, respectively. Selected ones according to their relationship to bone tissue were further discussed. Most of them were involved in extracellular matrix maturation and remodelling (two having a negative effect on mineralisation). A fine-tuned balanced between osteoblast maturation, differentiation and viability was observed.
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Affiliation(s)
- M Omidi
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Centre Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - N Ahmad Agha
- Institute of Materials Research, Division for Metallic Biomaterials, Helmholtz-Zentrum Geesthacht (HZG), 21502 Geesthacht, Germany.
| | - A Müller
- Institute of Materials Research, Division for Metallic Biomaterials, Helmholtz-Zentrum Geesthacht (HZG), 21502 Geesthacht, Germany.
| | - F Feyerabend
- Institute of Materials Research, Division for Metallic Biomaterials, Helmholtz-Zentrum Geesthacht (HZG), 21502 Geesthacht, Germany.
| | - H Helmholz
- Institute of Materials Research, Division for Metallic Biomaterials, Helmholtz-Zentrum Geesthacht (HZG), 21502 Geesthacht, Germany.
| | - R Willumeit-Römer
- Institute of Materials Research, Division for Metallic Biomaterials, Helmholtz-Zentrum Geesthacht (HZG), 21502 Geesthacht, Germany.
| | - H Schlüter
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Centre Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - B J C Luthringer-Feyerabend
- Institute of Materials Research, Division for Metallic Biomaterials, Helmholtz-Zentrum Geesthacht (HZG), 21502 Geesthacht, Germany.
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48
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Maire CL, Fuh MM, Kaulich K, Fita KD, Stevic I, Heiland DH, Welsh JA, Jones JC, Görgens A, Ricklefs T, Dührsen L, Sauvigny T, Joosse SA, Reifenberger G, Pantel K, Glatzel M, Miklosi AG, Felce JH, Caselli M, Pereno V, Reimer R, Schlüter H, Westphal M, Schüller U, Lamszus K, Ricklefs FL. Genome-wide methylation profiling of glioblastoma cell-derived extracellular vesicle DNA allows tumor classification. Neuro Oncol 2021; 23:1087-1099. [PMID: 33508126 DOI: 10.1093/neuonc/noab012] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [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: 12/14/2022] Open
Abstract
BACKGROUND Genome-wide DNA methylation profiling has recently been developed into a tool that allows tumor classification in central nervous system tumors. Extracellular vesicles (EVs) are released by tumor cells and contain high molecular weight DNA, rendering EVs a potential biomarker source to identify tumor subgroups, stratify patients and monitor therapy by liquid biopsy. We investigated whether the DNA in glioblastoma cell-derived EVs reflects genome-wide tumor methylation and mutational profiles and allows noninvasive tumor subtype classification. METHODS DNA was isolated from EVs secreted by glioblastoma cells as well as from matching cultured cells and tumors. EV-DNA was localized and quantified by direct stochastic optical reconstruction microscopy. Methylation and copy number profiling was performed using 850k arrays. Mutations were identified by targeted gene panel sequencing. Proteins were differentially quantified by mass spectrometric proteomics. RESULTS Genome-wide methylation profiling of glioblastoma-derived EVs correctly identified the methylation class of the parental cells and original tumors, including the MGMT promoter methylation status. Tumor-specific mutations and copy number variations (CNV) were detected in EV-DNA with high accuracy. Different EV isolation techniques did not affect the methylation profiling and CNV results. DNA was present inside EVs and on the EV surface. Proteome analysis did not allow specific tumor identification or classification but identified tumor-associated proteins that could potentially be useful for enriching tumor-derived circulating EVs from biofluids. CONCLUSIONS This study provides proof of principle that EV-DNA reflects the genome-wide methylation, CNV, and mutational status of glioblastoma cells and enables their molecular classification.
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Affiliation(s)
- Cecile L Maire
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marceline M Fuh
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kerstin Kaulich
- Institute of Neuropathology, University of Duesseldorf, Duesseldorf, Germany
| | - Krystian D Fita
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ines Stevic
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Dieter H Heiland
- Department of Neurosurgery, Medical Center University of Freiburg, Freiburg, Germany
| | - Joshua A Welsh
- Translational Nanobiology Section, Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jennifer C Jones
- Translational Nanobiology Section, Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - André Görgens
- Department of Laboratory Medicine, Clinical Research Center, Karolinska Institute, Stockholm, Sweden.,Institute for Transfusion Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Evox Therapeutics Limited, Oxford, UK
| | - Tammo Ricklefs
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lasse Dührsen
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thomas Sauvigny
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Simon A Joosse
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Guido Reifenberger
- Institute of Neuropathology, University of Duesseldorf, Duesseldorf, Germany
| | - Klaus Pantel
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Markus Glatzel
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | | | | | | | - Rudolph Reimer
- Heinrich-Pette-Institut, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Hartmut Schlüter
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Manfred Westphal
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ulrich Schüller
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Department of Pediatric Hematology and Oncology, and Research Institute Children's Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katrin Lamszus
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Franz L Ricklefs
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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49
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Ali A, Ellinger B, Brandt SC, Betzel C, Rühl M, Wrenger C, Schlüter H, Schäfer W, Brognaro H, Gand M. Genome and Secretome Analysis of Staphylotrichum longicolleum DSM105789 Cultured on Agro-Residual and Chitinous Biomass. Microorganisms 2021; 9:1581. [PMID: 34442660 PMCID: PMC8398502 DOI: 10.3390/microorganisms9081581] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 11/17/2022] Open
Abstract
Staphylotrichum longicolleum FW57 (DSM105789) is a prolific chitinolytic fungus isolated from wood, with a chitinase activity of 0.11 ± 0.01 U/mg. We selected this strain for genome sequencing and annotation, and compiled its growth characteristics on four different chitinous substrates as well as two agro-industrial waste products. We found that the enzymatic mixture secreted by FW57 was not only able to digest pre-treated sugarcane bagasse, but also untreated sugarcane bagasse and maize leaves. The efficiency was comparable to a commercial enzymatic cocktail, highlighting the potential of the S. longicolleum enzyme mixture as an alternative pretreatment method. To further characterize the enzymes, which efficiently digested polymers such as cellulose, hemicellulose, pectin, starch, and lignin, we performed in-depth mass spectrometry-based secretome analysis using tryptic peptides from in-gel and in-solution digestions. Depending on the growth conditions, we were able to detect from 442 to 1092 proteins, which were annotated to identify from 134 to 224 putative carbohydrate-active enzymes (CAZymes) in five different families: glycoside hydrolases, auxiliary activities, carbohydrate esterases, polysaccharide lyases, glycosyl transferases, and proteins containing a carbohydrate-binding module, as well as combinations thereof. The FW57 enzyme mixture could be used to replace commercial enzyme cocktails for the digestion of agro-residual substrates.
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Affiliation(s)
- Arslan Ali
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Martin Luther King Platz 6, 20146 Hamburg, Germany; (A.A.); (C.B.); (C.W.); (H.S.); (H.B.)
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, University Road, Karachi 75270, Pakistan
- Institute of Clinical Chemistry and Laboratory Medicine, Diagnostic Center, Section Mass Spectrometry & Proteomics, Campus Research, Martinistr. 2, N27, Medical Center Hamburg-Eppendorf, Universität Hamburg, 20246 Hamburg, Germany
| | - Bernhard Ellinger
- Department ScreeningPort, Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Schnackenburgallee 114, 22525 Hamburg, Germany;
| | - Sophie C. Brandt
- Department of Molecular Phytopathology, Biocenter Klein Flottbek, University of Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany; (S.C.B.); (W.S.)
| | - Christian Betzel
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Martin Luther King Platz 6, 20146 Hamburg, Germany; (A.A.); (C.B.); (C.W.); (H.S.); (H.B.)
| | - Martin Rühl
- Institute of Food Chemistry and Food Biotechnology, Department Biology and Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Gießen, Germany;
| | - Carsten Wrenger
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Martin Luther King Platz 6, 20146 Hamburg, Germany; (A.A.); (C.B.); (C.W.); (H.S.); (H.B.)
- Biomedical Science Institute, University of São Paulo, Av. Lineu Prestes, 2415, São Paulo CEP 05508-900, Brazil
| | - Hartmut Schlüter
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Martin Luther King Platz 6, 20146 Hamburg, Germany; (A.A.); (C.B.); (C.W.); (H.S.); (H.B.)
- Institute of Clinical Chemistry and Laboratory Medicine, Diagnostic Center, Section Mass Spectrometry & Proteomics, Campus Research, Martinistr. 2, N27, Medical Center Hamburg-Eppendorf, Universität Hamburg, 20246 Hamburg, Germany
| | - Wilhelm Schäfer
- Department of Molecular Phytopathology, Biocenter Klein Flottbek, University of Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany; (S.C.B.); (W.S.)
| | - Hévila Brognaro
- Institute of Biochemistry and Molecular Biology, University of Hamburg, Martin Luther King Platz 6, 20146 Hamburg, Germany; (A.A.); (C.B.); (C.W.); (H.S.); (H.B.)
- Biomedical Science Institute, University of São Paulo, Av. Lineu Prestes, 2415, São Paulo CEP 05508-900, Brazil
| | - Martin Gand
- Department of Molecular Phytopathology, Biocenter Klein Flottbek, University of Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany; (S.C.B.); (W.S.)
- Institute of Food Chemistry and Food Biotechnology, Department Biology and Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Gießen, Germany;
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50
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Rosenbaum FP, Poehlein A, Egelkamp R, Daniel R, Harder S, Schlüter H, Schoelmerich MC. Lactate metabolism in strictly anaerobic microorganisms with a soluble NAD + -dependent l-lactate dehydrogenase. Environ Microbiol 2021; 23:4661-4672. [PMID: 34190373 DOI: 10.1111/1462-2920.15657] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 06/28/2021] [Indexed: 11/30/2022]
Abstract
Lactate is a universal metabolite and energy source, yet the mode of lactate metabolism in many strictly anaerobic microorganisms is still enigmatic. This sparked us to investigate the biochemistry and bioenergetics of lactate metabolism in the model acetogenic bacterium Moorella thermoacetica. Growth and metabolism were dependent on CO2 and the chemiosmotic gradient. We discovered a l-lactate:NAD+ oxidoreductase (LDH) in cell-free extracts, exhibiting an average specific activity of 362.8 ± 22.9 mU mg-1 . The enzyme was reversible, most active at 65°C and pH 9, with Km values of 23.1 ± 3.7 mM for l-lactate and 273.3 ± 39.1 μM for NAD+ . In-gel activity assays and mass spectrometric proteomics revealed that the ldh gene encoded the characterized LDH. Transcriptomic and genomic analyses showed that ldh expression was induced by lactate and there was a single nucleotide polymorphism near the predicted NAD+ binding site. Genes encoding central redox and energy metabolism complexes, such as, the energetic coupling site Ech2, menaquinone, and the electron bifurcating EtfABCX and MTHFR were also upregulated in cells grown on lactate. These findings ultimately lead to a redox-balanced metabolic model that shows how growth on lactate can proceed in a microorganism that only has a conventional NAD+ -reducing LDH.
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Affiliation(s)
- Florian P Rosenbaum
- Microbiology & Biotechnology, Institute of Plant Sciences and Microbiology, University of Hamburg, Hamburg, 22609, Germany
| | - Anja Poehlein
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg-August University Göttingen, Göttingen, 37077, Germany
| | - Richard Egelkamp
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg-August University Göttingen, Göttingen, 37077, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg-August University Göttingen, Göttingen, 37077, Germany
| | - Sönke Harder
- Mass Spectrometric Proteomics Group, Department of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, 20246, Germany
| | - Hartmut Schlüter
- Mass Spectrometric Proteomics Group, Department of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, 20246, Germany
| | - Marie Charlotte Schoelmerich
- Microbiology & Biotechnology, Institute of Plant Sciences and Microbiology, University of Hamburg, Hamburg, 22609, Germany
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