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Abou Kors T, Hofmann L, Betzler A, Payer K, Bens M, Truong J, von Witzleben A, Thomas J, Kraus JM, Kalaajieh R, Huber D, Ezić J, Benckendorff J, Greve J, Schuler PJ, Ottensmeier CH, Kestler HA, Hoffmann TK, Theodoraki MN, Brunner C, Laban S. INHBA is Enriched in HPV-negative Oropharyngeal Squamous Cell Carcinoma and Promotes Cancer Progression. Cancer Res Commun 2024; 4:571-587. [PMID: 38329386 PMCID: PMC10901070 DOI: 10.1158/2767-9764.crc-23-0258] [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: 07/04/2023] [Revised: 12/15/2023] [Accepted: 02/06/2024] [Indexed: 02/09/2024]
Abstract
Patients with oropharyngeal squamous cell carcinoma (OPSCC) caused by human papilloma virus (HPV) exhibit a better prognosis than those with HPV-negative OPSCC. This study investigated the distinct molecular pathways that delineate HPV-negative from HPV-positive OPSCC to identify biologically relevant therapeutic targets. Bulk mRNA from 23 HPV-negative and 39 HPV-positive OPSCC tumors (n = 62) was sequenced to uncover the transcriptomic profiles. Differential expression followed by gene set enrichment analysis was performed to outline the top enriched biological process in the HPV-negative compared with HPV-positive entity. INHBA, the highest overexpressed gene in the HPV-negative tumor, was knocked down. Functional assays (migration, proliferation, cell death, stemness) were conducted to confirm the target's oncogenic role. Correlation analyses to reveal its impact on the tumor microenvironment were performed. We revealed that epithelial-to-mesenchymal transition (EMT) is the most enriched process in HPV-negative compared with HPV-positive OPSCC, with INHBA (inhibin beta A subunit) being the top upregulated gene. INHBA knockdown downregulated the expression of EMT transcription factors and attenuated migration, proliferation, stemness, and cell death resistance of OPSCC cells. We uncovered that INHBA associates with a pro-tumor microenvironment by negatively correlating with antitumor CD8+ T and B cells while positively correlating with pro-tumor M1 macrophages. We identified three miRNAs that are putatively involved in repressing INHBA expression. Our results indicate that the upregulation of INHBA is tumor-promoting. We propose INHBA as an attractive therapeutic target for the treatment of INHBA-enriched tumors in patients with HPV-negative OPSCC to ameliorate prognosis. SIGNIFICANCE Patients with HPV-negative OPSCC have a poorer prognosis due to distinct molecular pathways. This study reveals significant transcriptomic differences between HPV-negative and HPV-positive OPSCC, identifying INHBA as a key upregulated gene in HPV-negative OPSCC's oncogenic pathways. INHBA is crucial in promoting EMT, cell proliferation, and an immunosuppressive tumor environment, suggesting its potential as a therapeutic target for HPV-negative OPSCC.
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Affiliation(s)
- Tsima Abou Kors
- Department of Otorhinolaryngology, Head and Neck Surgery, Ulm University Medical Center, Ulm, Germany
| | - Linda Hofmann
- Department of Otorhinolaryngology, Head and Neck Surgery, Ulm University Medical Center, Ulm, Germany
| | - Annika Betzler
- Department of Otorhinolaryngology, Head and Neck Surgery, Ulm University Medical Center, Ulm, Germany
| | - Kathrina Payer
- Department of Otorhinolaryngology, Head and Neck Surgery, Ulm University Medical Center, Ulm, Germany
| | - Martin Bens
- Fritz Lipmann Institute, Leibniz Institute on Aging, University of Jena, Jena, Germany
| | - Jens Truong
- Department of Otorhinolaryngology, Head and Neck Surgery, Ulm University Medical Center, Ulm, Germany
| | - Adrian von Witzleben
- Department of Otorhinolaryngology, Head and Neck Surgery, Ulm University Medical Center, Ulm, Germany
| | - Jaya Thomas
- Cancer Sciences Unit, University of Southampton, Faculty of Medicine, Southampton, United Kingdom
| | - Johann M Kraus
- Institute for Medical Systems Biology, Ulm University, Ulm, Germany
| | - Randa Kalaajieh
- Department of Otorhinolaryngology, Head and Neck Surgery, Ulm University Medical Center, Ulm, Germany
| | - Diana Huber
- Department of Otorhinolaryngology, Head and Neck Surgery, Ulm University Medical Center, Ulm, Germany
| | - Jasmin Ezić
- Department of Otorhinolaryngology, Head and Neck Surgery, Ulm University Medical Center, Ulm, Germany
| | | | - Jens Greve
- Department of Otorhinolaryngology, Head and Neck Surgery, Ulm University Medical Center, Ulm, Germany
| | - Patrick J Schuler
- Department of Otorhinolaryngology, Head and Neck Surgery, Ulm University Medical Center, Ulm, Germany
| | - Christian H Ottensmeier
- Institute of Systems, Molecular and Integrative Biology, Liverpool Head and Neck Center, University of Liverpool, Faculty of Medicine, Liverpool, United Kingdom
| | - Hans A Kestler
- Institute for Medical Systems Biology, Ulm University, Ulm, Germany
| | - Thomas K Hoffmann
- Department of Otorhinolaryngology, Head and Neck Surgery, Ulm University Medical Center, Ulm, Germany
| | - Marie-Nicole Theodoraki
- Department of Otorhinolaryngology, Head and Neck Surgery, Ulm University Medical Center, Ulm, Germany
| | - Cornelia Brunner
- Department of Otorhinolaryngology, Head and Neck Surgery, Ulm University Medical Center, Ulm, Germany
| | - Simon Laban
- Department of Otorhinolaryngology, Head and Neck Surgery, Ulm University Medical Center, Ulm, Germany
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2
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Huber LT, Kraus JM, Ezić J, Wanli A, Groth M, Laban S, Hoffmann TK, Wollenberg B, Kestler HA, Brunner C. Liquid biopsy: an examination of platelet RNA obtained from head and neck squamous cell carcinoma patients for predictive molecular tumor markers. Explor Target Antitumor Ther 2023; 4:422-446. [PMID: 37455825 PMCID: PMC10344902 DOI: 10.37349/etat.2023.00143] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 03/01/2023] [Indexed: 07/18/2023] Open
Abstract
Aim Recently, a tumor cell-platelet interaction was identified in different tumor entities, resulting in a transfer of tumor-derived RNA into platelets, named further "tumor-educated platelets (TEP)". The present pilot study aims to investigate whether such a tumor-platelet transfer of RNA occurs also in patients suffering from head and neck squamous cell carcinoma (HNSCC). Methods Sequencing analysis of RNA derived from platelets of tumor patients (TPs) and healthy donors (HDs) were performed. Subsequently, quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was used for verification of differentially expressed genes in platelets from TPs and HDs in a second cohort of patients and HDs. Data were analyzed by applying bioinformatic tools. Results Sequencing of RNA derived from the tumor as well as from platelets of TPs and HDs revealed 426 significantly differentially existing RNA, at which 406 RNA were more and 20 RNA less abundant in platelets from TPs in comparison to that of HDs. In TPs' platelets, abundantly existing RNA coding for 49 genes were detected, characteristically expressed in epithelial cells and RNA, the products of which are involved in tumor progression. Applying bioinformatic tools and verification on a second TP/HD cohort, collagen type I alpha 1 chain (COL1A1) and zinc finger protein 750 (ZNF750) were identified as the strongest potentially platelet-RNA-sequencing (RNA-seq)-based biomarkers for HNSCC. Conclusions These results indicate a transfer of tumor-derived messenger RNA (mRNA) into platelets of HNSCC patients. Therefore, analyses of a patient's platelet RNA could be an efficient option for liquid biopsy in order to diagnose HNSCC or to monitor tumorigenesis as well as therapeutic responses at any time and in real time.
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Affiliation(s)
- Lisa T. Huber
- Department of Oto-Rhino-Laryngology, Head and Neck Surgery, Ulm University Medical Center, 89075 Ulm, Germany
| | - Johann M. Kraus
- Institute of Medical Systems Biology, Ulm University, 89081 Ulm, Germany
| | - Jasmin Ezić
- Department of Oto-Rhino-Laryngology, Head and Neck Surgery, Ulm University Medical Center, 89075 Ulm, Germany
| | - Amin Wanli
- Department of Oto-Rhino-Laryngology, Head and Neck Surgery, Ulm University Medical Center, 89075 Ulm, Germany
| | - Marco Groth
- Leibniz Institute of Aging – Fritz Lipmann Institute, CF DNA sequencing, 07745 Jena, Germany
| | - Simon Laban
- Department of Oto-Rhino-Laryngology, Head and Neck Surgery, Ulm University Medical Center, 89075 Ulm, Germany
| | - Thomas K. Hoffmann
- Department of Oto-Rhino-Laryngology, Head and Neck Surgery, Ulm University Medical Center, 89075 Ulm, Germany
| | - Barbara Wollenberg
- Clinic for Otorhinolaryngology, Head and Neck Surgery, Technical University of Munich, 80333 Munich, Germany
| | - Hans A. Kestler
- Institute of Medical Systems Biology, Ulm University, 89081 Ulm, Germany
| | - Cornelia Brunner
- Department of Oto-Rhino-Laryngology, Head and Neck Surgery, Ulm University Medical Center, 89075 Ulm, Germany
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3
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Mühlenbruch L, Abou-Kors T, Dubbelaar ML, Bichmann L, Kohlbacher O, Bens M, Thomas J, Ezić J, Kraus JM, Kestler HA, von Witzleben A, Mytilineos J, Fürst D, Engelhardt D, Doescher J, Greve J, Schuler PJ, Theodoraki MN, Brunner C, Hoffmann TK, Rammensee HG, Walz JS, Laban S. The HLA ligandome of oropharyngeal squamous cell carcinomas reveals shared tumour-exclusive peptides for semi-personalised vaccination. Br J Cancer 2023; 128:1777-1787. [PMID: 36823366 PMCID: PMC9949688 DOI: 10.1038/s41416-023-02197-y] [Citation(s) in RCA: 2] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 01/24/2023] [Accepted: 02/01/2023] [Indexed: 02/25/2023] Open
Abstract
BACKGROUND The immune peptidome of OPSCC has not previously been studied. Cancer-antigen specific vaccination may improve clinical outcome and efficacy of immune checkpoint inhibitors such as PD1/PD-L1 antibodies. METHODS Mapping of the OPSCC HLA ligandome was performed by mass spectrometry (MS) based analysis of naturally presented HLA ligands isolated from tumour tissue samples (n = 40) using immunoaffinity purification. The cohort included 22 HPV-positive (primarily HPV-16) and 18 HPV-negative samples. A benign reference dataset comprised of the HLA ligandomes of benign haematological and tissue datasets was used to identify tumour-associated antigens. RESULTS MS analysis led to the identification of naturally HLA-presented peptides in OPSCC tumour tissue. In total, 22,769 peptides from 9485 source proteins were detected on HLA class I. For HLA class II, 15,203 peptides from 4634 source proteins were discovered. By comparative profiling against the benign HLA ligandomic datasets, 29 OPSCC-associated HLA class I ligands covering 11 different HLA allotypes and nine HLA class II ligands were selected to create a peptide warehouse. CONCLUSION Tumour-associated peptides are HLA-presented on the cell surfaces of OPSCCs. The established warehouse of OPSCC-associated peptides can be used for downstream immunogenicity testing and peptide-based immunotherapy in (semi)personalised strategies.
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Affiliation(s)
- Lena Mühlenbruch
- grid.10392.390000 0001 2190 1447Institute for Cell Biology, Department of Immunology, Eberhard Karls University of Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.10392.390000 0001 2190 1447Department of Peptide-based Immunotherapy, Eberhard Karls University and University Hospital Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.10392.390000 0001 2190 1447Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,German Cancer Consortium (DKTK), Partner Site Tübingen, 72076 Tübingen, Baden-Württemberg Germany
| | - Tsima Abou-Kors
- grid.410712.10000 0004 0473 882XDepartment of Otorhinolaryngology and Head & Neck Surgery, Ulm University Medical Center, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Marissa L. Dubbelaar
- grid.10392.390000 0001 2190 1447Institute for Cell Biology, Department of Immunology, Eberhard Karls University of Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.10392.390000 0001 2190 1447Department of Peptide-based Immunotherapy, Eberhard Karls University and University Hospital Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.10392.390000 0001 2190 1447Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.10392.390000 0001 2190 1447Quantitative Biology Center (QBiC), Eberhard Karls University Tübingen, 72076 Tübingen, Baden-Württemberg Germany
| | - Leon Bichmann
- grid.10392.390000 0001 2190 1447Institute for Cell Biology, Department of Immunology, Eberhard Karls University of Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.10392.390000 0001 2190 1447Applied Bioinformatics, Department of Computer Science, Eberhard Karls University Tübingen, 72076 Tübingen, Baden-Württemberg Germany
| | - Oliver Kohlbacher
- grid.10392.390000 0001 2190 1447Applied Bioinformatics, Department of Computer Science, Eberhard Karls University Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.10392.390000 0001 2190 1447Cluster of Excellence Machine Learning in the Sciences (EXC2064), Eberhard Karls University Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.411544.10000 0001 0196 8249Institute for Translational Bioinformatics, University Hospital Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.10392.390000 0001 2190 1447Institute for Bioinformatics and Medical Informatics, Eberhard Karls University Tübingen, 72076 Tübingen, Baden-Württemberg Germany
| | - Martin Bens
- grid.418245.e0000 0000 9999 5706Leibniz-Institute on Aging, Fritz-Lipmann-Institute, 07745 Jena, Thüringen Germany
| | - Jaya Thomas
- grid.5491.90000 0004 1936 9297CRUK and NIHR Experimental Cancer Medicine Center & School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, SO17 1BJ UK
| | - Jasmin Ezić
- grid.410712.10000 0004 0473 882XDepartment of Otorhinolaryngology and Head & Neck Surgery, Ulm University Medical Center, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Johann M. Kraus
- grid.6582.90000 0004 1936 9748Ulm University, Institute of Medical Systems Biology, Ulm, Germany
| | - Hans A. Kestler
- grid.6582.90000 0004 1936 9748Ulm University, Institute of Medical Systems Biology, Ulm, Germany
| | - Adrian von Witzleben
- grid.410712.10000 0004 0473 882XDepartment of Otorhinolaryngology and Head & Neck Surgery, Ulm University Medical Center, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Joannis Mytilineos
- grid.410712.10000 0004 0473 882XInstitute of Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden–Württemberg–Hessen, and University Hospital Ulm, Ulm, Germany ,grid.6582.90000 0004 1936 9748Institute of Transfusion Medicine, Ulm University, Ulm, Germany ,German Stem Cell Donor Registry, German Red Cross Blood Transfusion Service, Ulm, Germany
| | - Daniel Fürst
- grid.410712.10000 0004 0473 882XInstitute of Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Transfusion Service, Baden–Württemberg–Hessen, and University Hospital Ulm, Ulm, Germany ,grid.6582.90000 0004 1936 9748Institute of Transfusion Medicine, Ulm University, Ulm, Germany
| | - Daphne Engelhardt
- grid.410712.10000 0004 0473 882XDepartment of Otorhinolaryngology and Head & Neck Surgery, Ulm University Medical Center, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Johannes Doescher
- grid.410712.10000 0004 0473 882XDepartment of Otorhinolaryngology and Head & Neck Surgery, Ulm University Medical Center, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Jens Greve
- grid.410712.10000 0004 0473 882XDepartment of Otorhinolaryngology and Head & Neck Surgery, Ulm University Medical Center, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Patrick J. Schuler
- grid.410712.10000 0004 0473 882XDepartment of Otorhinolaryngology and Head & Neck Surgery, Ulm University Medical Center, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Marie-Nicole Theodoraki
- grid.410712.10000 0004 0473 882XDepartment of Otorhinolaryngology and Head & Neck Surgery, Ulm University Medical Center, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Cornelia Brunner
- grid.410712.10000 0004 0473 882XDepartment of Otorhinolaryngology and Head & Neck Surgery, Ulm University Medical Center, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Thomas K. Hoffmann
- grid.410712.10000 0004 0473 882XDepartment of Otorhinolaryngology and Head & Neck Surgery, Ulm University Medical Center, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Hans-Georg Rammensee
- grid.10392.390000 0001 2190 1447Institute for Cell Biology, Department of Immunology, Eberhard Karls University of Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.10392.390000 0001 2190 1447Department of Peptide-based Immunotherapy, Eberhard Karls University and University Hospital Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.10392.390000 0001 2190 1447Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,German Cancer Consortium (DKTK), Partner Site Tübingen, 72076 Tübingen, Baden-Württemberg Germany
| | - Juliane S. Walz
- grid.10392.390000 0001 2190 1447Institute for Cell Biology, Department of Immunology, Eberhard Karls University of Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.10392.390000 0001 2190 1447Department of Peptide-based Immunotherapy, Eberhard Karls University and University Hospital Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.10392.390000 0001 2190 1447Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, 72076 Tübingen, Baden-Württemberg Germany ,grid.411544.10000 0001 0196 8249Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Baden-Württemberg 72076 Germany
| | - Simon Laban
- Department of Otorhinolaryngology and Head & Neck Surgery, Ulm University Medical Center, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany.
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4
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Werle SD, Ikonomi N, Schwab JD, Kraus JM, Weidner FM, Lenhard Rudolph K, Pfister AS, Schuler R, Kühl M, Kestler HA. Identification of dynamic driver sets controlling phenotypical landscapes. Comput Struct Biotechnol J 2022; 20:1603-1617. [PMID: 35465155 PMCID: PMC9010550 DOI: 10.1016/j.csbj.2022.03.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/30/2022] [Accepted: 03/30/2022] [Indexed: 11/03/2022] Open
Abstract
Controlling phenotypical landscapes is of vital interest to modern biology. This task becomes highly demanding because cellular decisions involve complex networks engaging in crosstalk interactions. Previous work on control theory indicates that small sets of compounds can control single phenotypes. However, a dynamic approach is missing to determine the drivers of the whole network dynamics. By analyzing 35 biologically motivated Boolean networks, we developed a method to identify small sets of compounds sufficient to decide on the entire phenotypical landscape. These compounds do not strictly prefer highly related compounds and show a smaller impact on the stability of the attractor landscape. The dynamic driver sets include many intervention targets and cellular reprogramming drivers in human networks. Finally, by using a new comprehensive model of colorectal cancer, we provide a complete workflow on how to implement our approach to shift from in silico to in vitro guided experiments.
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5
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Schön M, Nosanova A, Jacob C, Kraus JM, Kestler HAK, Mayer B, Feldengut S, Amunts K, Del Tredici K, Boeckers TM, Braak H. A comparative study of pre-alpha islands in the entorhinal cortex from selected primates and in lissencephaly. J Comp Neurol 2021; 530:683-704. [PMID: 34402535 DOI: 10.1002/cne.25233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/08/2021] [Accepted: 08/12/2021] [Indexed: 11/11/2022]
Abstract
The entorhinal cortex (EC) is the main interface between the sensory association areas of the neocortex and the hippocampus. It is crucial for the evaluation and processing of sensory data for long-term memory consolidation, and shows damage in many brain diseases, e.g., neurodegenerative diseases, such as Alzheimer's disease and developmental disorders. The pre-alpha layer of the EC in humans (layer II) displays a remarkable distribution of neurons in islands. These cellular islands give rise to a portion of the perforant path - the major reciprocal data stream for neocortical information into the hippocampal formation. However, the functional relevance of the morphological appearance of the pre-alpha layer in cellular islands and the precise timing of their initial appearance during primate evolution are largely unknown. Here, we conducted a comparative study of the EC from 38 non-human primates and Homo sapiens and found a strong relationship between gyrification index (GI) and the presence of the pre-alpha cellular islands. The formation of cellular islands also correlated wih brain and body weight as well as neopallial volume. In the two human lissencephalic cases, the cellular islands in the pre-alpha layer were lacking. These findings emphasize the relationship between cortical folding and island formation in the entorhinal cortex from an evolutionary perspective, and suggest a role in the pathomechanism of developmental brain disorders. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- M Schön
- Institute for Anatomy and Cell Biology, Ulm University, Ulm, Germany
| | - A Nosanova
- Institute for Anatomy and Cell Biology, Ulm University, Ulm, Germany
| | - C Jacob
- Institute for Anatomy and Cell Biology, Ulm University, Ulm, Germany
| | - J M Kraus
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - H A K Kestler
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - B Mayer
- Institute of Epidemiology and Medical Biometry, Ulm University, Ulm, Germany
| | - S Feldengut
- Clinical Neuroanatomy, Department of Neurology, Center for Clinical Research, Ulm University, Ulm, Germany
| | - K Amunts
- Institute of Neuroscience and Medicine (INM-1), Research Center Jülich, Jülich, Germany.,C. and O. Vogt Institute for Brain Research, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - K Del Tredici
- Clinical Neuroanatomy, Department of Neurology, Center for Clinical Research, Ulm University, Ulm, Germany
| | - T M Boeckers
- Institute for Anatomy and Cell Biology, Ulm University, Ulm, Germany.,DZNE, Ulm site, Ulm, Germany
| | - H Braak
- Clinical Neuroanatomy, Department of Neurology, Center for Clinical Research, Ulm University, Ulm, Germany
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6
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Völkel G, Laban S, Fürstberger A, Kühlwein SD, Ikonomi N, Hoffmann TK, Brunner C, Neuberg DS, Gaidzik V, Döhner H, Kraus JM, Kestler HA. Erratum to: Analysis, identification and visualization of subgroups in genomics. Brief Bioinform 2021; 22:6314775. [PMID: 34226916 PMCID: PMC8575006 DOI: 10.1093/bib/bbab280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 11/24/2022] Open
Affiliation(s)
- Gunnar Völkel
- Institute of Medical Systems Biology (MSB), Ulm University, Ulm, Germany
| | - Simon Laban
- Department of Otorhinolaryngology, Head and Neck Surgery, Ulm University Medical Center, Germany
| | - Axel Fürstberger
- MSB and deputy of Core Unit Bioinformatics, Ulm University, Ulm, Germany
| | - Silke D Kühlwein
- International Graduate School of Molecular Medicine, Ulm University, Germany
| | - Nensi Ikonomi
- International Graduate School of Molecular Medicine, Ulm University, Germany
| | - Thomas K Hoffmann
- Department of Otorhinolaryngology, Head and Neck Surgery, Ulm University Medical Center, Germany
| | - Cornelia Brunner
- Department of Otorhinolaryngology, Head and Neck Surgery, Ulm University Medical Center, Germany
| | - Donna S Neuberg
- Department of Biostatistics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Verena Gaidzik
- Department of Internal Medicine III, Ulm University Medical Center, Germany
| | - Hartmut Döhner
- Department of Internal Medicine III, Ulm University Medical Center, Germany
| | | | - Hans A Kestler
- Institute of Medical Systems Biology, and head of Core Unit Bioinformatics, Ulm University, Ulm, Germany
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7
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Arnold F, Mahaddalkar PU, Kraus JM, Zhong X, Bergmann W, Srinivasan D, Gout J, Roger E, Beutel AK, Zizer E, Tharehalli U, Daiss N, Russell R, Perkhofer L, Oellinger R, Lin Q, Azoitei N, Weiss F, Lerch MM, Liebau S, Katz S, Lechel A, Rad R, Seufferlein T, Kestler HA, Ott M, Sharma AD, Hermann PC, Kleger A. Functional Genomic Screening During Somatic Cell Reprogramming Identifies DKK3 as a Roadblock of Organ Regeneration. Adv Sci (Weinh) 2021; 8:2100626. [PMID: 34306986 PMCID: PMC8292873 DOI: 10.1002/advs.202100626] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Indexed: 05/06/2023]
Abstract
Somatic cell reprogramming and tissue repair share relevant factors and molecular programs. Here, Dickkopf-3 (DKK3) is identified as novel factor for organ regeneration using combined transcription-factor-induced reprogramming and RNA-interference techniques. Loss of Dkk3 enhances the generation of induced pluripotent stem cells but does not affect de novo derivation of embryonic stem cells, three-germ-layer differentiation or colony formation capacity of liver and pancreatic organoids. However, DKK3 expression levels in wildtype animals and serum levels in human patients are elevated upon injury. Accordingly, Dkk3-null mice display less liver damage upon acute and chronic failure mediated by increased proliferation in hepatocytes and LGR5+ liver progenitor cell population, respectively. Similarly, recovery from experimental pancreatitis is accelerated. Regeneration onset occurs in the acinar compartment accompanied by virtually abolished canonical-Wnt-signaling in Dkk3-null animals. This results in reduced expression of the Hedgehog repressor Gli3 and increased Hedgehog-signaling activity upon Dkk3 loss. Collectively, these data reveal Dkk3 as a key regulator of organ regeneration via a direct, previously unacknowledged link between DKK3, canonical-Wnt-, and Hedgehog-signaling.
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Affiliation(s)
- Frank Arnold
- Department of Internal Medicine IUniversity Hospital UlmAlbert‐Einstein Allee 2389081 UlmGermany
| | - Pallavi U Mahaddalkar
- Institute for Diabetes and RegenerationHelmholtz Zentrum MünchenIngolstädter Landstraße 185764 NeuherbergGermany
| | - Johann M. Kraus
- Institute of Medical Systems BiologyUlm UniversityAlbert‐Einstein Allee 1189081 UlmGermany
| | - Xiaowei Zhong
- Department of GastroenterologyHepatology and EndocrinologyHannover Medical SchoolFeodor‐Lynen‐Str. 730625 HannoverGermany
| | - Wendy Bergmann
- Core Facility for Cell Sorting and Cell AnalysisUniversity Medical Center RostockSchillingallee 7018057 RostockGermany
| | - Dharini Srinivasan
- Department of Internal Medicine IUniversity Hospital UlmAlbert‐Einstein Allee 2389081 UlmGermany
| | - Johann Gout
- Department of Internal Medicine IUniversity Hospital UlmAlbert‐Einstein Allee 2389081 UlmGermany
| | - Elodie Roger
- Department of Internal Medicine IUniversity Hospital UlmAlbert‐Einstein Allee 2389081 UlmGermany
| | - Alica K. Beutel
- Department of Internal Medicine IUniversity Hospital UlmAlbert‐Einstein Allee 2389081 UlmGermany
| | - Eugen Zizer
- Department of Internal Medicine IUniversity Hospital UlmAlbert‐Einstein Allee 2389081 UlmGermany
| | - Umesh Tharehalli
- Department of Internal Medicine IUniversity Hospital UlmAlbert‐Einstein Allee 2389081 UlmGermany
| | - Nora Daiss
- Department of Internal Medicine IUniversity Hospital UlmAlbert‐Einstein Allee 2389081 UlmGermany
| | - Ronan Russell
- Diabetes CenterUniversity of CaliforniaSan FranciscoCA94143USA
| | - Lukas Perkhofer
- Department of Internal Medicine IUniversity Hospital UlmAlbert‐Einstein Allee 2389081 UlmGermany
| | - Rupert Oellinger
- Institute of Molecular Oncology and Functional GenomicsTranslaTUM Cancer CenterTechnical University of MunichIsmaninger Str. 2281675 MunichGermany
| | - Qiong Lin
- Bayer AG Research & DevelopmentPharmaceuticalsMüllerstraße 17813353 BerlinGermany
| | - Ninel Azoitei
- Department of Internal Medicine IUniversity Hospital UlmAlbert‐Einstein Allee 2389081 UlmGermany
| | - Frank‐Ulrich Weiss
- Department of Medicine AUniversity Medicine GreifswaldFerdinand‐Sauerbruch‐Straße17475 GreifswaldGermany
| | - Markus M. Lerch
- Department of Medicine AUniversity Medicine GreifswaldFerdinand‐Sauerbruch‐Straße17475 GreifswaldGermany
- Klinikum der Ludwig‐Maximilians‐Universität München‐GroßhadernMarchioninistraße 1581377 MünchenGermany
| | - Stefan Liebau
- Institute of Neuroanatomy & Developmental Biology INDBEberhard Karls University TübingenÖsterbergstr. 372074 TübingenGermany
| | - Sarah‐Fee Katz
- Department of Internal Medicine IUniversity Hospital UlmAlbert‐Einstein Allee 2389081 UlmGermany
| | - André Lechel
- Department of Internal Medicine IUniversity Hospital UlmAlbert‐Einstein Allee 2389081 UlmGermany
| | - Roland Rad
- Institute of Molecular Oncology and Functional GenomicsTranslaTUM Cancer CenterTechnical University of MunichIsmaninger Str. 2281675 MunichGermany
| | - Thomas Seufferlein
- Department of Internal Medicine IUniversity Hospital UlmAlbert‐Einstein Allee 2389081 UlmGermany
| | - Hans A. Kestler
- Institute of Medical Systems BiologyUlm UniversityAlbert‐Einstein Allee 1189081 UlmGermany
| | - Michael Ott
- Department of GastroenterologyHepatology and EndocrinologyHannover Medical SchoolFeodor‐Lynen‐Str. 730625 HannoverGermany
| | - Amar Deep Sharma
- Department of GastroenterologyHepatology and EndocrinologyHannover Medical SchoolFeodor‐Lynen‐Str. 730625 HannoverGermany
| | - Patrick C. Hermann
- Department of Internal Medicine IUniversity Hospital UlmAlbert‐Einstein Allee 2389081 UlmGermany
| | - Alexander Kleger
- Department of Internal Medicine IUniversity Hospital UlmAlbert‐Einstein Allee 2389081 UlmGermany
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Völkel G, Fürstberger A, Schwab JD, Werle SD, Ikonomi N, Gscheidmeier T, Kraus JM, Groß A, Holderried M, Balig J, Jobst F, Kuhn P, Kuhn KA, Kohlbacher O, Kaisers UX, Seufferlein T, Kestler HA. Metadata Correction: Patient Empowerment During the COVID-19 Pandemic by Ensuring Safe and Fast Communication of Test Results: Implementation and Performance of a Tracking System. J Med Internet Res 2021; 23:e31253. [PMID: 34152993 PMCID: PMC8277404 DOI: 10.2196/31253] [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] [Received: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 11/13/2022] Open
Abstract
[This corrects the article DOI: 10.2196/27348.].
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Affiliation(s)
- Gunnar Völkel
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Axel Fürstberger
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Julian D Schwab
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Silke D Werle
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Nensi Ikonomi
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | | | - Johann M Kraus
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Alexander Groß
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Martin Holderried
- Department of Medical Development and Quality Management, University Hospital Tübingen, Tübingen, Germany
| | - Julien Balig
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | | | - Peter Kuhn
- Comprehensive Cancer Center, University Hospital Ulm, Ulm, Germany
| | - Klaus A Kuhn
- Institute of Medical Informatics, Statistics and Epidemiology, Technical University of Munich, Ulm, Germany
| | - Oliver Kohlbacher
- Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany
| | | | - Thomas Seufferlein
- Department of Internal Medicine I, University Hospital Ulm, Ulm, Germany
| | - Hans A Kestler
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
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9
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Völkel G, Fürstberger A, Schwab JD, Werle SD, Ikonomi N, Gscheidmeier T, Kraus JM, Groß A, Holderried M, Balig J, Jobst F, Kuhn P, Kuhn KA, Kohlbacher O, Kaisers UX, Seufferlein T, Kestler HA. Patient Empowerment During the COVID-19 Pandemic by Ensuring Safe and Fast Communication of Test Results: Implementation and Performance of a Tracking System. J Med Internet Res 2021; 23:e27348. [PMID: 33999836 PMCID: PMC8189287 DOI: 10.2196/27348] [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] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/23/2021] [Accepted: 05/12/2021] [Indexed: 11/13/2022] Open
Abstract
Background Overcoming the COVID-19 crisis requires new ideas and strategies for online communication of personal medical information and patient empowerment. Rapid testing of a large number of subjects is essential for monitoring and delaying the spread of SARS-CoV-2 in order to mitigate the pandemic’s consequences. People who do not know that they are infected may not stay in quarantine and, thus, risk infecting others. Unfortunately, the massive number of COVID-19 tests performed is challenging for both laboratories and the units that conduct throat swabs and communicate the results. Objective The goal of this study was to reduce the communication burden for health care professionals. We developed a secure and easy-to-use tracking system to report COVID-19 test results online that is simple to understand for the tested subjects as soon as these results become available. Instead of personal calls, the system updates the status and the results of the tests automatically. This aims to reduce the delay when informing testees about their results and, consequently, to slow down the virus spread. Methods The application in this study draws on an existing tracking tool. With this open-source and browser-based online tracking system, we aim to minimize the time required to inform the tested person and the testing units (eg, hospitals or the public health care system). The system can be integrated into the clinical workflow with very modest effort and avoids excessive load to telephone hotlines. Results The test statuses and results are published on a secured webpage, enabling regular status checks by patients; status checks are performed without the use of smartphones, which has some importance, as smartphone usage diminishes with age. Stress tests and statistics show the performance of our software. CTest is currently running at two university hospitals in Germany—University Hospital Ulm and University Hospital Tübingen—with thousands of tests being performed each week. Results show a mean number of 10 (SD 2.8) views per testee. Conclusions CTest runs independently of existing infrastructures, aims at straightforward integration, and aims for the safe transmission of information. The system is easy to use for testees. QR (Quick Response) code links allow for quick access to the test results. The mean number of views per entry indicates a reduced amount of time for both health care professionals and testees. The system is quite generic and can be extended and adapted to other communication tasks.
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Affiliation(s)
- Gunnar Völkel
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Axel Fürstberger
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Julian D Schwab
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Silke D Werle
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Nensi Ikonomi
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | | | - Johann M Kraus
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Alexander Groß
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Martin Holderried
- Department of Medical Development and Quality Management, University Hospital Tübingen, Tübingen, Germany
| | - Julien Balig
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | | | - Peter Kuhn
- Comprehensive Cancer Center, University Hospital Ulm, Ulm, Germany
| | - Klaus A Kuhn
- Institute of Medical Informatics, Statistics and Epidemiology, Technical University of Munich, Ulm, Germany
| | - Oliver Kohlbacher
- Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany
| | | | - Thomas Seufferlein
- Department of Internal Medicine I, University Hospital Ulm, Ulm, Germany
| | - Hans A Kestler
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
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10
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Kestler AMR, Kühlwein SD, Kraus JM, Schwab JD, Szekely R, Thiam P, Hühne R, Jahn N, Fürstberger A, Ikonomi N, Balig J, Schuler R, Kuhn P, Steger F, Seufferlein T, Kestler HA. Digitalization of adverse event management in oncology to improve treatment outcome-A prospective study protocol. PLoS One 2021; 16:e0252493. [PMID: 34086740 PMCID: PMC8177479 DOI: 10.1371/journal.pone.0252493] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 05/15/2021] [Indexed: 11/18/2022] Open
Abstract
The occurrence of adverse events frequently accompanies tumor treatments. Side effects should be detected and treated as soon as possible to maintain the best possible treatment outcome. Besides the standard reporting system Common Terminology Criteria for Adverse Events (CTCAE), physicians have recognized the potential of patient-reporting systems. These are based on a more subjective description of current patient reporting symptoms. Patient-reported symptoms are essential to define the impact of a given treatment on the quality of life and the patient's wellbeing. They also act against an underreporting of side effects which are paramount to define the actual value of a treatment for the individual patient. Here, we present a study protocol for a clinical trial that assesses the potential of a smartphone application for CTCAE conform symptom reporting and tracking that is adjusted to the standard clinical reporting system rather than symptom oriented descriptive trial tools. The presented study will be implemented in two parts, both lasting over six months. The first part will assess the feasibility of the application with 30 patients non-randomly divided into three equally-sized age groups (<55years, 55-75years, >75years). In the second part 36 other patients will be randomly assigned to two groups, one reporting using the smartphone and one not. This prospective second part will compare the impact of smartphone reported adverse events regarding applied therapy doses and quality of life to those of patients receiving standard care. We aim for early detection and treatment of adverse events in oncological treatment to improve patients' safety and outcomes. For this purpose, we will capture frequent adverse events of chemotherapies, immunotherapies, or other targeted therapies with our smartphone application. The presented trial is registered at the U.S. National Library of Medicine ClinicalTrials.gov (NCT04493450) on July 30, 2020.
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Affiliation(s)
| | | | - Johann M. Kraus
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Julian D. Schwab
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Robin Szekely
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Patrick Thiam
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Rolf Hühne
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Niels Jahn
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Axel Fürstberger
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Nensi Ikonomi
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Julien Balig
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Rainer Schuler
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Peter Kuhn
- Comprehensive Cancer Center, University Hospital Ulm, Ulm, Germany
| | - Florian Steger
- Institute of the History, Philosophy and Ethics of Medicine, Ulm University, Ulm, Germany
| | - Thomas Seufferlein
- Department of Internal Medicine I, University Hospital Ulm, Ulm, Germany
| | - Hans A. Kestler
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
- * E-mail:
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11
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Gout J, Perkhofer L, Morawe M, Arnold F, Ihle M, Biber S, Lange S, Roger E, Kraus JM, Stifter K, Hahn SA, Zamperone A, Engleitner T, Müller M, Walter K, Rodriguez-Aznar E, Sainz Jr B, Hermann PC, Hessmann E, Müller S, Azoitei N, Lechel A, Liebau S, Wagner M, Simeone DM, Kestler HA, Seufferlein T, Wiesmüller L, Rad R, Frappart PO, Kleger A. Synergistic targeting and resistance to PARP inhibition in DNA damage repair-deficient pancreatic cancer. Gut 2021; 70:743-760. [PMID: 32873698 PMCID: PMC7948173 DOI: 10.1136/gutjnl-2019-319970] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 06/22/2020] [Accepted: 07/01/2020] [Indexed: 12/11/2022]
Abstract
OBJECTIVE ATM serine/threonine kinase (ATM) is the most frequently mutated DNA damage response gene, involved in homologous recombination (HR), in pancreatic ductal adenocarcinoma (PDAC). DESIGN Combinational synergy screening was performed to endeavour a genotype-tailored targeted therapy. RESULTS Synergy was found on inhibition of PARP, ATR and DNA-PKcs (PAD) leading to synthetic lethality in ATM-deficient murine and human PDAC. Mechanistically, PAD-induced PARP trapping, replication fork stalling and mitosis defects leading to P53-mediated apoptosis. Most importantly, chemical inhibition of ATM sensitises human PDAC cells toward PAD with long-term tumour control in vivo. Finally, we anticipated and elucidated PARP inhibitor resistance within the ATM-null background via whole exome sequencing. Arising cells were aneuploid, underwent epithelial-mesenchymal-transition and acquired multidrug resistance (MDR) due to upregulation of drug transporters and a bypass within the DNA repair machinery. These functional observations were mirrored in copy number variations affecting a region on chromosome 5 comprising several of the upregulated MDR genes. Using these findings, we ultimately propose alternative strategies to overcome the resistance. CONCLUSION Analysis of the molecular susceptibilities triggered by ATM deficiency in PDAC allow elaboration of an efficient mutation-specific combinational therapeutic approach that can be also implemented in a genotype-independent manner by ATM inhibition.
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Affiliation(s)
- Johann Gout
- Department of Internal Medicine I, Ulm University Hospital, Ulm, Germany
| | - Lukas Perkhofer
- Department of Internal Medicine I, Ulm University Hospital, Ulm, Germany
| | - Mareen Morawe
- Department of Internal Medicine I, Ulm University Hospital, Ulm, Germany
| | - Frank Arnold
- Department of Internal Medicine I, Ulm University Hospital, Ulm, Germany
| | - Michaela Ihle
- Department of Obstetrics and Gynecology, Ulm University, Ulm, Germany
| | - Stephanie Biber
- Department of Obstetrics and Gynecology, Ulm University, Ulm, Germany
| | - Sebastian Lange
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany,Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technische Universität München, Munich, Germany
| | - Elodie Roger
- Department of Internal Medicine I, Ulm University Hospital, Ulm, Germany
| | - Johann M Kraus
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Katja Stifter
- Department of Internal Medicine I, Ulm University Hospital, Ulm, Germany
| | - Stephan A Hahn
- Department of Molecular GI Oncology, Faculty of Medicine, Ruhr University Bochum, Bochum, Germany
| | - Andrea Zamperone
- Department of Surgery, NYU Langone Health, New York, NY, USA,Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Thomas Engleitner
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
| | - Martin Müller
- Department of Internal Medicine I, Ulm University Hospital, Ulm, Germany
| | - Karolin Walter
- Department of Internal Medicine I, Ulm University Hospital, Ulm, Germany
| | | | - Bruno Sainz Jr
- Cancer Stem Cell and Tumor Microenvironment Group, Instituto de Investigaciones Biomédicas "Alberto Sols" CSIC-UAM, Madrid, Spain,Cancer Stem Cell and Fibroinflammatory Microenvironment Group, Area 3 - Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Patrick C Hermann
- Department of Internal Medicine I, Ulm University Hospital, Ulm, Germany
| | - Elisabeth Hessmann
- Department of Gastroenterology and Gastrointestinal Oncology, University Medical Center Göttingen, Göttingen, Germany
| | - Sebastian Müller
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany
| | - Ninel Azoitei
- Department of Internal Medicine I, Ulm University Hospital, Ulm, Germany
| | - André Lechel
- Department of Internal Medicine I, Ulm University Hospital, Ulm, Germany
| | - Stefan Liebau
- Institute of Neuroanatomy & Developmental Biology INDB, Eberhard Karls Universitat Tübingen, Tübingen, Germany
| | - Martin Wagner
- Department of Internal Medicine I, Ulm University Hospital, Ulm, Germany
| | - Diane M Simeone
- Department of Surgery, NYU Langone Health, New York, NY, USA,Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA,Department of Pathology, NYU Langone Health, New York, NY, USA
| | - Hans A Kestler
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Thomas Seufferlein
- Department of Internal Medicine I, Ulm University Hospital, Ulm, Germany
| | - Lisa Wiesmüller
- Department of Obstetrics and Gynecology, Ulm University, Ulm, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, Munich, Germany,Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, Munich, Germany,Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technische Universität München, Munich, Germany,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Pierre-Olivier Frappart
- Department of Internal Medicine I, Ulm University Hospital, Ulm, Germany,Institute of Toxicology, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Alexander Kleger
- Department of Internal Medicine I, Ulm University Hospital, Ulm, Germany
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12
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von Witzleben A, Fehn A, Grages A, Ezić J, Jeske SS, Puntigam LK, Brunner C, Kraus JM, Kestler HA, Doescher J, Brand M, Theodoraki MN, Ottensmeier CH, Hoffmann TK, Schuler PJ, Laban S. Prospective longitudinal study of immune checkpoint molecule (ICM) expression in immune cell subsets during curative conventional therapy of head and neck squamous cell carcinoma (HNSCC). Int J Cancer 2020; 148:2023-2035. [PMID: 33336372 DOI: 10.1002/ijc.33446] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 07/18/2020] [Revised: 11/01/2020] [Accepted: 11/13/2020] [Indexed: 12/31/2022]
Abstract
Programmed-death-1 (PD1) antibodies are approved for recurrent and metastatic head and neck squamous cell carcinoma. Multiple drugs targeting costimulatory and coinhibitory immune checkpoint molecules (ICM) have been discovered. However, it remains unknown how these ICM are affected by curative conventional therapy on different immune cell subsets during the course of treatment. In the prospective noninterventional clinical study titled "Immune Response Evaluation to Curative conventional Therapy" (NCT03053661), 22 patients were prospectively enrolled. Blood samples were drawn at defined time points throughout curative conventional treatment and follow-up. Immune cells (IC) from the different time points were assessed by multicolor flow cytometry. The following ICM were measured by flow cytometry: PD1, CTLA4, BTLA, CD137, CD27, GITR, OX40, LAG3 and TIM3. Dynamics of ICM expression were assessed using nonparametric paired samples tests. Significant changes were noted for PD1, BTLA and CD27 on multiple IC types during or after radiotherapy. Nonsignificant trends for increased expression of OX40 and GITR from baseline until the end of RT were observed on CD4 T cells and CD4+ CD39+ T cells. In patients with samples at recurrence of disease, a nonsignificant increase of TIM3 and LAG3 positive CD4+ CD39+ T cells was evident, accompanied by an increase of double positive cells for TIM3/LAG3. Potential future targets to be combined with RT in the conventional treatment and anti-PD1/PD-L could be BTLA agonists, or agonistic antibodies to costimulatory ICM like CD137, OX40 or GITR. The combination of cetuximab with CD27 agonistic antibodies enhancing ADCC or the targeting of TIM3/LAG3 may be another promising strategy.
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Affiliation(s)
- Adrian von Witzleben
- Department of Otorhinolaryngology and Head & Neck Surgery, University Medical Center Ulm, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany.,University of Southampton, Faculty of Medicine, Cancer Sciences Unit, Southampton, UK.,Southampton University Hospitals NHS foundation Trust, Southampton, UK
| | - Adrian Fehn
- Department of Otorhinolaryngology and Head & Neck Surgery, University Medical Center Ulm, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Ayla Grages
- Department of Otorhinolaryngology and Head & Neck Surgery, University Medical Center Ulm, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Jasmin Ezić
- Department of Otorhinolaryngology and Head & Neck Surgery, University Medical Center Ulm, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Sandra S Jeske
- Department of Otorhinolaryngology and Head & Neck Surgery, University Medical Center Ulm, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Lisa K Puntigam
- Department of Otorhinolaryngology and Head & Neck Surgery, University Medical Center Ulm, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Cornelia Brunner
- Department of Otorhinolaryngology and Head & Neck Surgery, University Medical Center Ulm, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Johann M Kraus
- Ulm University, Institute for Medical Systems Biology, Ulm, Germany
| | - Hans A Kestler
- Ulm University, Institute for Medical Systems Biology, Ulm, Germany
| | - Johannes Doescher
- Department of Otorhinolaryngology and Head & Neck Surgery, University Medical Center Ulm, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Matthias Brand
- Department of Otorhinolaryngology and Head & Neck Surgery, University Medical Center Ulm, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Marie-Nicole Theodoraki
- Department of Otorhinolaryngology and Head & Neck Surgery, University Medical Center Ulm, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Christian H Ottensmeier
- University of Southampton, Faculty of Medicine, Cancer Sciences Unit, Southampton, UK.,Southampton University Hospitals NHS foundation Trust, Southampton, UK
| | - Thomas K Hoffmann
- Department of Otorhinolaryngology and Head & Neck Surgery, University Medical Center Ulm, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Patrick J Schuler
- Department of Otorhinolaryngology and Head & Neck Surgery, University Medical Center Ulm, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Simon Laban
- Department of Otorhinolaryngology and Head & Neck Surgery, University Medical Center Ulm, Head and Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
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13
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Völkel G, Laban S, Fürstberger A, Kühlwein SD, Ikonomi N, Hoffmann TK, Brunner C, Neuberg DS, Gaidzik V, Döhner H, Kraus JM, Kestler HA. Analysis, identification and visualization of subgroups in genomics. Brief Bioinform 2020; 22:5909009. [PMID: 32954413 PMCID: PMC8138884 DOI: 10.1093/bib/bbaa217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 12/22/2022] Open
Abstract
Motivation Cancer is a complex and heterogeneous disease involving multiple somatic mutations that accumulate during its progression. In the past years, the wide availability of genomic data from patients’ samples opened new perspectives in the analysis of gene mutations and alterations. Hence, visualizing and further identifying genes mutated in massive sets of patients are nowadays a critical task that sheds light on more personalized intervention approaches. Results Here, we extensively review existing tools for visualization and analysis of alteration data. We compare different approaches to study mutual exclusivity and sample coverage in large-scale omics data. We complement our review with the standalone software AVAtar (‘analysis and visualization of alteration data’) that integrates diverse aspects known from different tools into a comprehensive platform. AVAtar supplements customizable alteration plots by a multi-objective evolutionary algorithm for subset identification and provides an innovative and user-friendly interface for the evaluation of concurrent solutions. A use case from personalized medicine demonstrates its unique features showing an application on vaccination target selection. Availability AVAtar is available at: https://github.com/sysbio-bioinf/avatar Contact hans.kestler@uni-ulm.de, phone: +49 (0) 731 500 24 500, fax: +49 (0) 731 500 24 502
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Affiliation(s)
| | | | | | | | | | - Thomas K Hoffmann
- Department of Otorhinolaryngology, Head and Neck Surgery, Ulm University Medical Center, Germany
| | - Cornelia Brunner
- Department of Otorhinolaryngology, Head and Neck Surgery, Ulm University Medical Center, Germany
| | - Donna S Neuberg
- Department of Biostatistics, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Verena Gaidzik
- Department of Internal Medicine III, Ulm University Medical Center, Germany
| | - Hartmut Döhner
- Department of Internal Medicine III, Ulm University Medical Center, Germany
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14
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Armacki M, Polaschek S, Waldenmaier M, Morawe M, Ruhland C, Schmid R, Lechel A, Tharehalli U, Steup C, Bektas Y, Li H, Kraus JM, Kestler HA, Kruger S, Ormanns S, Walther P, Eiseler T, Seufferlein T. Protein Kinase D1, Reduced in Human Pancreatic Tumors, Increases Secretion of Small Extracellular Vesicles From Cancer Cells That Promote Metastasis to Lung in Mice. Gastroenterology 2020; 159:1019-1035.e22. [PMID: 32446697 DOI: 10.1053/j.gastro.2020.05.052] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 04/21/2020] [Accepted: 05/13/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND & AIMS Pancreatic tumor cells release small extracellular vesicles (sEVs, exosomes) that contain lipids and proteins, RNA, and DNA molecules that might promote formation of metastases. It is not clear what cargo these vesicles contain and how they are released. Protein kinase D1 (PRKD1) inhibits cell motility and is believed to be dysregulated in pancreatic ductal adenocarcinomas. We investigated whether it regulates production of sEVs in pancreatic cancer cells and their ability to form premetastatic niches for pancreatic cancer cells in mice. METHODS We analyzed data from UALCAN and human pancreatic tissue microarrays to compare levels of PRKD1 between tumor and nontumor tissues. We studied mice with pancreas-specific disruption of Prkd1 (PRKD1KO mice), mice that express oncogenic KRAS (KC mice), and KC mice with disruption of Prkd1 (PRKD1KO-KC mice). Subcutaneous xenograft tumors were grown in NSG mice from Panc1 cells; some mice were then given injections of sEVs. Pancreata and lung tissues from mice were analyzed by histology, immunohistochemistry, and/or quantitative polymerase chain reaction; we performed nanoparticle tracking analysis of plasma sEVs. The Prkd1 gene was disrupted in Panc1 cells using CRISPR-Cas9 or knocked down with small hairpin RNAs, or PRKD1 activity was inhibited with the selective inhibitor CRT0066101. Pancreatic cancer cell lines were analyzed by gene-expression microarray, quantitative polymerase chain reaction, immunoblot, and immunofluorescence analyses. sEVs secreted by Panc1 cell lines were analyzed by flow cytometry, transmission electron microscopy, and mass spectrometry. RESULTS Levels of PRKD1 were reduced in human pancreatic ductal adenocarcinoma tissues compared with nontumor tissues. PRKD1KO-KC mice developed more pancreatic intraepithelial neoplasia, at a faster rate, than KC mice, and had more lung metastases and significantly shorter average survival time. Serum from PRKD1KO-KC mice had increased levels of sEVs compared with KC mice. Pancreatic cancer cells with loss or inhibition of PRKD1 increased secretion of sEVs; loss of PRKD1 reduced phosphorylation of its substrate, cortactin, resulting in increased F-actin levels at the plasma membrane. sEVs from cells with loss or reduced expression of PRKD1 had altered content, and injection of these sEVs into mice increased metastasis of xenograft tumors to lung, compared with sEVs from pancreatic cells that expressed PRKD1. PRKD1-deficient pancreatic cancer cells showed increased loading of integrin α6β4 into sEVs-a process that required CD82. CONCLUSIONS Human pancreatic ductal adenocarcinoma has reduced levels of PRKD1 compared with nontumor pancreatic tissues. Loss of PRKD1 results in reduced phosphorylation of cortactin in pancreatic cancer cell lines, resulting in increased in F-actin at the plasma membrane and increased release of sEVs, with altered content. These sEVs promote metastasis of xenograft and pancreatic tumors to lung in mice.
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Affiliation(s)
- Milena Armacki
- Department of Internal Medicine I, University Hospital Ulm, Ulm, Germany
| | - Sandra Polaschek
- Department of Internal Medicine I, University Hospital Ulm, Ulm, Germany
| | | | - Mareen Morawe
- Department of Internal Medicine I, University Hospital Ulm, Ulm, Germany
| | - Claudia Ruhland
- Department of Internal Medicine I, University Hospital Ulm, Ulm, Germany
| | - Rebecca Schmid
- Department of Internal Medicine I, University Hospital Ulm, Ulm, Germany
| | - André Lechel
- Department of Internal Medicine I, University Hospital Ulm, Ulm, Germany
| | - Umesh Tharehalli
- Department of Internal Medicine I, University Hospital Ulm, Ulm, Germany
| | - Christoph Steup
- Department of Internal Medicine I, University Hospital Ulm, Ulm, Germany
| | - Yasin Bektas
- Department of Internal Medicine I, University Hospital Ulm, Ulm, Germany
| | - Hongxia Li
- Department of Internal Medicine I, University Hospital Ulm, Ulm, Germany
| | - Johann M Kraus
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Hans A Kestler
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Stephan Kruger
- Department of Medicine III, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Steffen Ormanns
- Institute of Pathology, Faculty of Medicine, Ludwig Maximilian University of Munich, Munich, Germany
| | - Paul Walther
- Central Facility for Electron Microscopy, University of Ulm, Ulm, Germany
| | - Tim Eiseler
- Department of Internal Medicine I, University Hospital Ulm, Ulm, Germany.
| | - Thomas Seufferlein
- Department of Internal Medicine I, University Hospital Ulm, Ulm, Germany.
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15
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Zinngrebe J, Schlichtig F, Kraus JM, Meyer M, Boldrin E, Kestler HA, Meyer L, Fischer‐Posovszky P, Debatin K. Biomarker profile for prediction of response to SMAC mimetic monotherapy in pediatric precursor B‐cell acute lymphoblastic leukemia. Int J Cancer 2020; 146:3219-3231. [DOI: 10.1002/ijc.32799] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/04/2019] [Indexed: 12/23/2022]
Affiliation(s)
- Julia Zinngrebe
- Department of Pediatrics and Adolescent MedicineUlm University Medical Center Ulm Germany
| | - Ferdinand Schlichtig
- Department of Pediatrics and Adolescent MedicineUlm University Medical Center Ulm Germany
| | - Johann M. Kraus
- Institute of Medical Systems Biology, Ulm University Ulm Germany
| | - Malcolm Meyer
- Department of Pediatrics and Adolescent MedicineUlm University Medical Center Ulm Germany
| | - Elena Boldrin
- Department of Pediatrics and Adolescent MedicineUlm University Medical Center Ulm Germany
| | - Hans A. Kestler
- Institute of Medical Systems Biology, Ulm University Ulm Germany
| | - Lüder‐Hinrich Meyer
- Department of Pediatrics and Adolescent MedicineUlm University Medical Center Ulm Germany
| | | | - Klaus‐Michael Debatin
- Department of Pediatrics and Adolescent MedicineUlm University Medical Center Ulm Germany
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16
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Feder K, Edmaier-Schröger K, Rawat VPS, Kirsten N, Metzeler K, Kraus JM, Döhner K, Döhner H, Kestler HA, Feuring-Buske M, Buske C. Differences in expression and function of LEF1 isoforms in normal versus leukemic hematopoiesis. Leukemia 2019; 34:1027-1037. [DOI: 10.1038/s41375-019-0635-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 08/06/2019] [Indexed: 12/12/2022]
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17
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Scheffold A, Baig AH, Chen Z, von Löhneysen SE, Becker F, Morita Y, Avila AI, Groth M, Lechel A, Schmid F, Kraus JM, Kestler HA, Stilgenbauer S, Philipp M, Burkhalter MD. Elevated Hedgehog activity contributes to attenuated DNA damage responses in aged hematopoietic cells. Leukemia 2019; 34:1125-1134. [PMID: 31728056 PMCID: PMC7214262 DOI: 10.1038/s41375-019-0641-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 10/04/2019] [Accepted: 11/03/2019] [Indexed: 01/13/2023]
Abstract
Accumulation of DNA damage and myeloid-skewed differentiation characterize aging of the hematopoietic system, yet underlying mechanisms remain incompletely understood. Here, we show that aging hematopoietic progenitor cells particularly of the myeloid branch exhibit enhanced resistance to bulky DNA lesions—a relevant type of DNA damage induced by toxins such as cancer drugs or endogenous aldehydes. We identified aging-associated activation of the Hedgehog (Hh) pathway to be connected to this phenotype. Inhibition of Hh signaling reverts DNA damage tolerance and DNA damage-resistant proliferation in aged hematopoietic progenitors. Vice versa, elevating Hh activity in young hematopoietic progenitors is sufficient to impair DNA damage responses. Altogether, these findings provide experimental evidence for aging-associated increases in Hh activity driving DNA damage tolerance in myeloid progenitors and myeloid-skewed differentiation. Modulation of Hh activity could thus be explored as a therapeutic strategy to prevent DNA damage tolerance, myeloid skewing, and disease development in the aging hematopoietic system.
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Affiliation(s)
- Annika Scheffold
- Department of Internal Medicine III, University Hospital Ulm, 89081, Ulm, Germany
| | - Ali H Baig
- Leibniz Institute on Aging, Fritz Lipmann Institute, 07745, Jena, Germany
| | - Zhiyang Chen
- Leibniz Institute on Aging, Fritz Lipmann Institute, 07745, Jena, Germany
| | | | - Friedrich Becker
- Leibniz Institute on Aging, Fritz Lipmann Institute, 07745, Jena, Germany
| | - Yohei Morita
- Leibniz Institute on Aging, Fritz Lipmann Institute, 07745, Jena, Germany
| | - Alush I Avila
- Leibniz Institute on Aging, Fritz Lipmann Institute, 07745, Jena, Germany
| | - Marco Groth
- Leibniz Institute on Aging, Fritz Lipmann Institute, 07745, Jena, Germany
| | - André Lechel
- Department of Internal Medicine I, University Hospital Ulm, 89081, Ulm, Germany
| | - Florian Schmid
- Institute of Medical Systems Biology, Ulm University, 89081, Ulm, Germany
| | - Johann M Kraus
- Institute of Medical Systems Biology, Ulm University, 89081, Ulm, Germany
| | - Hans A Kestler
- Institute of Medical Systems Biology, Ulm University, 89081, Ulm, Germany
| | - Stephan Stilgenbauer
- Department of Internal Medicine III, University Hospital Ulm, 89081, Ulm, Germany
| | - Melanie Philipp
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081, Ulm, Germany.,Department of Experimental and Clinical Pharmacology and Pharmacogenomics, Division of Pharmacogenomics, University of Tübingen, 72074, Tübingen, Germany
| | - Martin D Burkhalter
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081, Ulm, Germany. .,Department of Experimental and Clinical Pharmacology and Pharmacogenomics, Division of Pharmacogenomics, University of Tübingen, 72074, Tübingen, Germany.
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18
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Gangkofner DS, Holzinger D, Schroeder L, Eichmüller SB, Zörnig I, Jäger D, Wichmann G, Dietz A, Broglie MA, Herold-Mende C, Dyckhoff G, Boscolo-Rizzo P, Ezic J, Marienfeld RB, Möller P, Völkel G, Kraus JM, Kestler HA, Brunner C, Schuler PJ, Wigand M, Theodoraki MN, Doescher J, Hoffmann TK, Pawlita M, Butt J, Waterboer T, Laban S. Patterns of antibody responses to nonviral cancer antigens in head and neck squamous cell carcinoma patients differ by human papillomavirus status. Int J Cancer 2019; 145:3436-3444. [PMID: 31407331 DOI: 10.1002/ijc.32623] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/20/2019] [Accepted: 07/22/2019] [Indexed: 12/24/2022]
Abstract
There have been hints that nonviral cancer antigens are differentially expressed in human papillomavirus (HPV)-positive and HPV-negative head and neck squamous cell carcinoma (HNSCC). Antibody responses (AR) to cancer antigens may be used to indirectly determine cancer antigen expression in the tumor using a noninvasive and tissue-saving liquid biopsy. Here, we set out to characterize AR to a panel of nonviral cancer antigens in HPV-positive and HPV-negative HNSCC patients. A fluorescent microbead multiplex serology to 29 cancer antigens (16 cancer-testis antigens, 5 cancer-retina antigens and 8 oncogenes) and 29 HPV-antigens was performed in 382 HNSCC patients from five independent cohorts (153 HPV-positive and 209 HPV-negative). AR to any of the cancer antigens were found in 272/382 patients (72%). The ten most frequent AR were CT47, cTAGE5a, c-myc, LAGE-1, MAGE-A1, -A3, -A4, NY-ESO-1, SpanX-a1 and p53. AR to MAGE-A3, MAGE-A9 and p53 were found at significantly different prevalences by HPV status. An analysis of AR mean fluorescent intensity values uncovered remarkably different AR clusters by HPV status. To identify optimal antigen selections covering a maximum of patients with ≤10 AR, multiobjective optimization revealed distinct antigen selections by HPV status. We identified that AR to nonviral antigens differ by HPV status indicating differential antigen expression. Multiplex serology may be used to characterize antigen expression using serum or plasma as a tissue-sparing liquid biopsy. Cancer antigen panels should address the distinct antigen repertoire of HPV-positive and HPV-negative HNSCC.
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Affiliation(s)
- Dominik S Gangkofner
- Department of Otorhinolaryngology and Head & Neck Surgery, University Medical Center Ulm, Head & Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Dana Holzinger
- Infections and Cancer Epidemiology (F022), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lea Schroeder
- Infections and Cancer Epidemiology (F022), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan B Eichmüller
- Research Group GMP & T Cell Therapy (D210), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Inka Zörnig
- National Center for Tumor Diseases (NCT) and Heidelberg University Hospital, Heidelberg, Germany.,National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Applied Tumor Immunity (D120), Heidelberg, Germany
| | - Dirk Jäger
- National Center for Tumor Diseases (NCT) and Heidelberg University Hospital, Heidelberg, Germany.,National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Applied Tumor Immunity (D120), Heidelberg, Germany
| | - Gunnar Wichmann
- Department of Otorhinolaryngology, University Hospital Leipzig, Leipzig, Germany
| | - Andreas Dietz
- Department of Otorhinolaryngology, University Hospital Leipzig, Leipzig, Germany
| | - Martina A Broglie
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Zurich, Zurich, Switzerland
| | - Christel Herold-Mende
- Department of Otorhinolaryngology, Head and Neck Surgery, Heidelberg University Hospital, Heidelberg, Germany.,Department of Neurosurgery, Division of Experimental Neurosurgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Gerhard Dyckhoff
- Department of Otorhinolaryngology, Head and Neck Surgery, Heidelberg University Hospital, Heidelberg, Germany
| | - Paolo Boscolo-Rizzo
- Department of Neurosciences, ENT Clinic and Regional Center for Head and Neck Cancer, University of Padua, Treviso, Italy
| | - Jasmin Ezic
- Department of Otorhinolaryngology and Head & Neck Surgery, University Medical Center Ulm, Head & Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | | | - Peter Möller
- Institute of Pathology, University Medical Center Ulm, Ulm, Germany
| | - Gunnar Völkel
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Johann M Kraus
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Hans A Kestler
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Cornelia Brunner
- Department of Otorhinolaryngology and Head & Neck Surgery, University Medical Center Ulm, Head & Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Patrick J Schuler
- Department of Otorhinolaryngology and Head & Neck Surgery, University Medical Center Ulm, Head & Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Marlene Wigand
- Department of Otorhinolaryngology and Head & Neck Surgery, University Medical Center Ulm, Head & Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Marie N Theodoraki
- Department of Otorhinolaryngology and Head & Neck Surgery, University Medical Center Ulm, Head & Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Johannes Doescher
- Department of Otorhinolaryngology and Head & Neck Surgery, University Medical Center Ulm, Head & Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Thomas K Hoffmann
- Department of Otorhinolaryngology and Head & Neck Surgery, University Medical Center Ulm, Head & Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
| | - Michael Pawlita
- Infections and Cancer Epidemiology (F022), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Julia Butt
- Infections and Cancer Epidemiology (F022), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tim Waterboer
- Infections and Cancer Epidemiology (F022), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Simon Laban
- Department of Otorhinolaryngology and Head & Neck Surgery, University Medical Center Ulm, Head & Neck Cancer Center of the Comprehensive Cancer Center Ulm, Ulm, Germany
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19
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Groß A, Kracher B, Kraus JM, Kühlwein SD, Pfister AS, Wiese S, Luckert K, Pötz O, Joos T, Van Daele D, De Raedt L, Kühl M, Kestler HA. Representing dynamic biological networks with multi-scale probabilistic models. Commun Biol 2019; 2:21. [PMID: 30675519 PMCID: PMC6336720 DOI: 10.1038/s42003-018-0268-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 12/07/2018] [Indexed: 12/26/2022] Open
Abstract
Dynamic models analyzing gene regulation and metabolism face challenges when adapted to modeling signal transduction networks. During signal transduction, molecular reactions and mechanisms occur in different spatial and temporal frames and involve feedbacks. This impedes the straight-forward use of methods based on Boolean networks, Bayesian approaches, and differential equations. We propose a new approach, ProbRules, that combines probabilities and logical rules to represent the dynamics of a system across multiple scales. We demonstrate that ProbRules models can represent various network motifs of biological systems. As an example of a comprehensive model of signal transduction, we provide a Wnt network that shows remarkable robustness under a range of phenotypical and pathological conditions. Its simulation allows the clarification of controversially discussed molecular mechanisms of Wnt signaling by predicting wet-lab measurements. ProbRules provides an avenue in current computational modeling by enabling systems biologists to integrate vast amounts of available data on different scales.
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Affiliation(s)
- Alexander Groß
- Institute of Medical Systems Biology, Ulm University, 89081 Ulm, Germany
| | - Barbara Kracher
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Johann M. Kraus
- Institute of Medical Systems Biology, Ulm University, 89081 Ulm, Germany
| | - Silke D. Kühlwein
- Institute of Medical Systems Biology, Ulm University, 89081 Ulm, Germany
| | - Astrid S. Pfister
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Sebastian Wiese
- Core Unit Mass Spectrometry and Proteomics, Ulm University, 89081 Ulm, Germany
| | - Katrin Luckert
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
| | - Oliver Pötz
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
| | - Thomas Joos
- NMI Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
| | - Dries Van Daele
- Department of Computer Science, Katholieke Universiteit Leuven, 3001 Heverlee, Belgium
| | - Luc De Raedt
- Department of Computer Science, Katholieke Universiteit Leuven, 3001 Heverlee, Belgium
| | - Michael Kühl
- Institute of Biochemistry and Molecular Biology, Ulm University, 89081 Ulm, Germany
| | - Hans A. Kestler
- Institute of Medical Systems Biology, Ulm University, 89081 Ulm, Germany
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20
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Chen Z, Amro EM, Becker F, Hölzer M, Rasa SMM, Njeru SN, Han B, Di Sanzo S, Chen Y, Tang D, Tao S, Haenold R, Groth M, Romanov VS, Kirkpatrick JM, Kraus JM, Kestler HA, Marz M, Ori A, Neri F, Morita Y, Rudolph KL. Cohesin-mediated NF-κB signaling limits hematopoietic stem cell self-renewal in aging and inflammation. J Exp Med 2019; 216:152-175. [PMID: 30530755 PMCID: PMC6314529 DOI: 10.1084/jem.20181505] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 11/06/2018] [Accepted: 11/19/2018] [Indexed: 01/02/2023] Open
Abstract
Organism aging is characterized by increased inflammation and decreased stem cell function, yet the relationship between these factors remains incompletely understood. This study shows that aged hematopoietic stem and progenitor cells (HSPCs) exhibit increased ground-stage NF-κB activity, which enhances their responsiveness to undergo differentiation and loss of self-renewal in response to inflammation. The study identifies Rad21/cohesin as a critical mediator of NF-κB signaling, which increases chromatin accessibility in the vicinity of NF-κB target genes in response to inflammation. Rad21 is required for normal differentiation, but limits self-renewal of hematopoietic stem cells (HSCs) during aging and inflammation in an NF-κB-dependent manner. HSCs from aged mice fail to down-regulate Rad21/cohesin and inflammation/differentiation signals in the resolution phase of inflammation. Inhibition of cohesin/NF-κB reverts hypersensitivity of aged HSPCs to inflammation-induced differentiation and myeloid-biased HSCs with disrupted/reduced expression of Rad21/cohesin are increasingly selected during aging. Together, Rad21/cohesin-mediated NF-κB signaling limits HSPC function during aging and selects for cohesin-deficient HSCs with myeloid-skewed differentiation.
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Affiliation(s)
- Zhiyang Chen
- Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Jena, Germany
| | - Elias Moris Amro
- Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Jena, Germany
| | - Friedrich Becker
- Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Jena, Germany
| | - Martin Hölzer
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Jena, Germany
- European Virus Bioinformatics Center (EVBC), Jena, Germany
| | | | | | - Bing Han
- Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Jena, Germany
| | - Simone Di Sanzo
- Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Jena, Germany
| | - Yulin Chen
- Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Jena, Germany
| | - Duozhuang Tang
- Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Jena, Germany
| | - Si Tao
- Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Jena, Germany
| | - Ronny Haenold
- Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Jena, Germany
- Matthias Schleiden Institute for Genetics, Bioinformatics and Molecular Botany, Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany
| | - Marco Groth
- Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Jena, Germany
| | - Vasily S Romanov
- Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Jena, Germany
| | | | - Johann M Kraus
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Hans A Kestler
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Manja Marz
- Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Jena, Germany
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University Jena, Jena, Germany
- European Virus Bioinformatics Center (EVBC), Jena, Germany
| | - Alessandro Ori
- Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Jena, Germany
| | - Francesco Neri
- Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Jena, Germany
| | - Yohei Morita
- Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Jena, Germany
| | - K Lenhard Rudolph
- Leibniz Institute on Aging, Fritz Lipmann Institute (FLI), Jena, Germany
- Faculty of Medicine, Friedrich-Schiller-University, Jena, Germany
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21
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Armacki M, Trugenberger AK, Ellwanger AK, Eiseler T, Schwerdt C, Bettac L, Langgartner D, Azoitei N, Halbgebauer R, Groß R, Barth T, Lechel A, Walter BM, Kraus JM, Wiegreffe C, Grimm J, Scheffold A, Schneider MR, Peuker K, Zeißig S, Britsch S, Rose-John S, Vettorazzi S, Wolf E, Tannapfel A, Steinestel K, Reber SO, Walther P, Kestler HA, Radermacher P, Barth TF, Huber-Lang M, Kleger A, Seufferlein T. Thirty-eight-negative kinase 1 mediates trauma-induced intestinal injury and multi-organ failure. J Clin Invest 2018; 128:5056-5072. [PMID: 30320600 DOI: 10.1172/jci97912] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 08/28/2018] [Indexed: 12/17/2022] Open
Abstract
Dysregulated intestinal epithelial apoptosis initiates gut injury, alters the intestinal barrier, and can facilitate bacterial translocation leading to a systemic inflammatory response syndrome (SIRS) and/or multi-organ dysfunction syndrome (MODS). A variety of gastrointestinal disorders, including inflammatory bowel disease, have been linked to intestinal apoptosis. Similarly, intestinal hyperpermeability and gut failure occur in critically ill patients, putting the gut at the center of SIRS pathology. Regulation of apoptosis and immune-modulatory functions have been ascribed to Thirty-eight-negative kinase 1 (TNK1), whose activity is regulated merely by expression. We investigated the effect of TNK1 on intestinal integrity and its role in MODS. TNK1 expression induced crypt-specific apoptosis, leading to bacterial translocation, subsequent septic shock, and early death. Mechanistically, TNK1 expression in vivo resulted in STAT3 phosphorylation, nuclear translocation of p65, and release of IL-6 and TNF-α. A TNF-α neutralizing antibody partially blocked development of intestinal damage. Conversely, gut-specific deletion of TNK1 protected the intestinal mucosa from experimental colitis and prevented cytokine release in the gut. Finally, TNK1 was found to be deregulated in the gut in murine and porcine trauma models and human inflammatory bowel disease. Thus, TNK1 might be a target during MODS to prevent damage in several organs, notably the gut.
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Affiliation(s)
- Milena Armacki
- Department of Internal Medicine I, University Hospital Ulm, Ulm, Germany
| | | | - Ann K Ellwanger
- Department of Internal Medicine I, University Hospital Ulm, Ulm, Germany
| | - Tim Eiseler
- Department of Internal Medicine I, University Hospital Ulm, Ulm, Germany
| | - Christiane Schwerdt
- Waldkrankenhaus "Rudolph Elle" Eisenberg, Lehrstuhl für Orthopädie Uniklinik Jena, Jena, Germany
| | - Lucas Bettac
- Department of Internal Medicine I, University Hospital Ulm, Ulm, Germany
| | - Dominik Langgartner
- Laboratory for Molecular Psychosomatics, Clinic for Psychosomatic Medicine and Psychotherapy, and
| | - Ninel Azoitei
- Department of Internal Medicine I, University Hospital Ulm, Ulm, Germany
| | - Rebecca Halbgebauer
- Institute of Clinical and Experimental Trauma Immunology, University Hospital Ulm, Ulm, Germany
| | - Rüdiger Groß
- Department of Internal Medicine I, University Hospital Ulm, Ulm, Germany
| | - Tabea Barth
- Department of Internal Medicine I, University Hospital Ulm, Ulm, Germany
| | - André Lechel
- Department of Internal Medicine I, University Hospital Ulm, Ulm, Germany
| | - Benjamin M Walter
- Department of Internal Medicine I, University Hospital Ulm, Ulm, Germany
| | | | | | | | - Annika Scheffold
- Department of Internal Medicine III, University Hospital Ulm, Ulm, Germany
| | | | - Kenneth Peuker
- Center for Regenerative Therapies Dresden, TU Dresden, Dresden, Germany
| | - Sebastian Zeißig
- Center for Regenerative Therapies Dresden, TU Dresden, Dresden, Germany
| | - Stefan Britsch
- Institute of Molecular and Cellular Anatomy, Ulm University, Ulm, Germany
| | | | - Sabine Vettorazzi
- Institute of Comparative Molecular Endocrinology, Ulm University, Ulm, Germany
| | | | | | - Konrad Steinestel
- Institute of Pathology and Molecular Pathology, Bundeswehrkrankenhaus Ulm, Ulm, Germany
| | - Stefan O Reber
- Laboratory for Molecular Psychosomatics, Clinic for Psychosomatic Medicine and Psychotherapy, and
| | - Paul Walther
- Central Facility for Electron Microscopy, University of Ulm, Ulm, Germany
| | | | - Peter Radermacher
- Institute of Anesthesiological Pathophysiology and Process Engineering, Ulm University, Ulm, Germany
| | | | - Markus Huber-Lang
- Institute of Clinical and Experimental Trauma Immunology, University Hospital Ulm, Ulm, Germany
| | - Alexander Kleger
- Department of Internal Medicine I, University Hospital Ulm, Ulm, Germany
| | - Thomas Seufferlein
- Department of Internal Medicine I, University Hospital Ulm, Ulm, Germany
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Kraus JM, Lausser L, Kuhn P, Jobst F, Bock M, Halanke C, Hummel M, Heuschmann P, Kestler HA. Big data and precision medicine: challenges and strategies with healthcare data. Int J Data Sci Anal 2018. [DOI: 10.1007/s41060-018-0095-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Meena JK, Cerutti A, Beichler C, Morita Y, Bruhn C, Kumar M, Kraus JM, Speicher MR, Wang ZQ, Kestler HA, Fagagna FDD, Günes C, Rudolph KL. Telomerase abrogates aneuploidy-induced telomere replication stress, senescence and cell depletion. EMBO J 2017; 36:2922-2924. [PMID: 28971846 PMCID: PMC5623828 DOI: 10.15252/embj.201797470] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Gaidzik VI, Teleanu V, Papaemmanuil E, Weber D, Paschka P, Hahn J, Wallrabenstein T, Kolbinger B, Köhne CH, Horst HA, Brossart P, Held G, Kündgen A, Ringhoffer M, Götze K, Rummel M, Gerstung M, Campbell P, Kraus JM, Kestler HA, Thol F, Heuser M, Schlegelberger B, Ganser A, Bullinger L, Schlenk RF, Döhner K, Döhner H. RUNX1 mutations in acute myeloid leukemia are associated with distinct clinico-pathologic and genetic features. Leukemia 2016; 30:2282. [PMID: 27804971 DOI: 10.1038/leu.2016.207] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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25
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Völkel G, Wiese S, Holzmann K, Kraus JM, Schneider F, Görlach M, Kestler HA. TraqBio - Flexible Progress Tracking for Core Unit Projects. PLoS One 2016; 11:e0162857. [PMID: 27677174 PMCID: PMC5038959 DOI: 10.1371/journal.pone.0162857] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 08/30/2016] [Indexed: 11/28/2022] Open
Abstract
Motivation Core service units have become an organisational hallmark in many research institutions world wide. Such service cores provide complex state-of-the-art technologies and expertise to the research community. Typically, a user delivers material or raw data to a core. The core defines work packages for ensuing analysis and returns results back to the user. This core activity can be quite complex and time consuming and usually does not communicate itself to the outside. Naturally, the user is highly interested to follow the progress of a project once handed over to the core unit. This generates a time-intensive direct communication activity back and forth. A more effective, convenient and less disruptive way to track the status of a given project by the researcher, but also by core managers, appears highly desirable. Hence, we developed a lightweight and readily implementable web application that allows efficient progress tracking of core unit projects. Results The web application TraqBio allows for the convenient tracking of projects. Following project set-up by the core, the user receives an e-mail containing links for tracking the project status. Examples are provided for three common core units, namely genomics, proteomics, and bioinformatics units. TraqBio is a secure lightweight web application that can be either used in a standalone setup or incorporated into an existing web server infrastructure. Being accessible not only from classical desktop computers but also from mobile devices such as smartphones and tablets, TraqBio offers easy integration into every day work.
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Affiliation(s)
- Gunnar Völkel
- Institute of Medical Systems Biology, Ulm University, D-89069 Ulm, Germany
| | - Sebastian Wiese
- Core Unit Mass Spectrometry and Proteomics, Ulm University, D-89069 Ulm, Germany
| | | | - Johann M. Kraus
- Institute of Medical Systems Biology, Ulm University, D-89069 Ulm, Germany
| | - Fabian Schneider
- Institute of Medical Systems Biology, Ulm University, D-89069 Ulm, Germany
| | - Matthias Görlach
- Leibniz Institute on Aging – Fritz Lipmann Institute and FSU Jena, D-07745 Jena, Germany
| | - Hans A. Kestler
- Institute of Medical Systems Biology, Ulm University, D-89069 Ulm, Germany
- Leibniz Institute on Aging – Fritz Lipmann Institute and FSU Jena, D-07745 Jena, Germany
- * E-mail:
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26
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Gaidzik VI, Teleanu V, Papaemmanuil E, Weber D, Paschka P, Hahn J, Wallrabenstein T, Kolbinger B, Köhne CH, Horst HA, Brossart P, Held G, Kündgen A, Ringhoffer M, Götze K, Rummel M, Gerstung M, Campbell P, Kraus JM, Kestler HA, Thol F, Heuser M, Schlegelberger B, Ganser A, Bullinger L, Schlenk RF, Döhner K, Döhner H. RUNX1 mutations in acute myeloid leukemia are associated with distinct clinico-pathologic and genetic features. Leukemia 2016; 30:2160-2168. [DOI: 10.1038/leu.2016.126] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Revised: 04/13/2016] [Accepted: 04/21/2016] [Indexed: 12/16/2022]
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Schmid F, Schmid M, Müssel C, Sträng JE, Buske C, Bullinger L, Kraus JM, Kestler HA. GiANT: gene set uncertainty in enrichment analysis. Bioinformatics 2016; 32:1891-4. [DOI: 10.1093/bioinformatics/btw030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 01/12/2016] [Indexed: 11/14/2022] Open
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28
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Kaistha BP, Lorenz H, Schmidt H, Sipos B, Pawlak M, Gierke B, Kreider R, Lankat-Buttgereit B, Sauer M, Fiedler L, Krattenmacher A, Geisel B, Kraus JM, Frese KK, Kelkenberg S, Giese NA, Kestler HA, Gress TM, Buchholz M. PLAC8 Localizes to the Inner Plasma Membrane of Pancreatic Cancer Cells and Regulates Cell Growth and Disease Progression through Critical Cell-Cycle Regulatory Pathways. Cancer Res 2015; 76:96-107. [DOI: 10.1158/0008-5472.can-15-0216] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 08/22/2015] [Indexed: 11/16/2022]
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29
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Grieb M, Burkovski A, Sträng JE, Kraus JM, Groß A, Palm G, Kühl M, Kestler HA. Predicting Variabilities in Cardiac Gene Expression with a Boolean Network Incorporating Uncertainty. PLoS One 2015. [PMID: 26207376 PMCID: PMC4514755 DOI: 10.1371/journal.pone.0131832] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Gene interactions in cells can be represented by gene regulatory networks. A Boolean network models gene interactions according to rules where gene expression is represented by binary values (on / off or {1, 0}). In reality, however, the gene’s state can have multiple values due to biological properties. Furthermore, the noisy nature of the experimental design results in uncertainty about a state of the gene. Here we present a new Boolean network paradigm to allow intermediate values on the interval [0, 1]. As in the Boolean network, fixed points or attractors of such a model correspond to biological phenotypes or states. We use our new extension of the Boolean network paradigm to model gene expression in first and second heart field lineages which are cardiac progenitor cell populations involved in early vertebrate heart development. By this we are able to predict additional biological phenotypes that the Boolean model alone is not able to identify without utilizing additional biological knowledge. The additional phenotypes predicted by the model were confirmed by published biological experiments. Furthermore, the new method predicts gene expression propensities for modelled but yet to be analyzed genes.
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Affiliation(s)
- Melanie Grieb
- Core Unit Medical Systems Biology, Ulm University, Ulm, Germany
- International Graduate School of Molecular Medicine, Ulm University, Ulm, Germany
| | - Andre Burkovski
- Core Unit Medical Systems Biology, Ulm University, Ulm, Germany
- Neural Information Processing, Ulm University, Ulm, Germany
- International Graduate School of Molecular Medicine, Ulm University, Ulm, Germany
| | - J. Eric Sträng
- Core Unit Medical Systems Biology, Ulm University, Ulm, Germany
| | - Johann M. Kraus
- Core Unit Medical Systems Biology, Ulm University, Ulm, Germany
| | - Alexander Groß
- Leibniz Institute for Age Research, Fritz-Lipmann Institute, Jena, Germany
| | - Günther Palm
- Neural Information Processing, Ulm University, Ulm, Germany
| | - Michael Kühl
- Institute for Biochemistry and Molecular Biology, Ulm University, Ulm, Germany
- * E-mail: (MK); (HAK)
| | - Hans A. Kestler
- Leibniz Institute for Age Research, Fritz-Lipmann Institute, Jena, Germany
- Core Unit Medical Systems Biology, Ulm University, Ulm, Germany
- Neural Information Processing, Ulm University, Ulm, Germany
- * E-mail: (MK); (HAK)
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Meena JK, Cerutti A, Beichler C, Morita Y, Bruhn C, Kumar M, Kraus JM, Speicher MR, Wang ZQ, Kestler HA, d'Adda di Fagagna F, Günes C, Rudolph KL. Telomerase abrogates aneuploidy-induced telomere replication stress, senescence and cell depletion. EMBO J 2015; 34:1371-84. [PMID: 25820263 PMCID: PMC4491997 DOI: 10.15252/embj.201490070] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [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: 09/16/2014] [Revised: 03/03/2015] [Accepted: 03/04/2015] [Indexed: 11/09/2022] Open
Abstract
The causal role of aneuploidy in cancer initiation remains under debate since mutations of euploidy-controlling genes reduce cell fitness but aneuploidy strongly associates with human cancers. Telomerase activation allows immortal growth by stabilizing telomere length, but its role in aneuploidy survival has not been characterized. Here, we analyze the response of primary human cells and murine hematopoietic stem cells (HSCs) to aneuploidy induction and the role of telomeres and the telomerase in this process. The study shows that aneuploidy induces replication stress at telomeres leading to telomeric DNA damage and p53 activation. This results in p53/Rb-dependent, premature senescence of human fibroblast, and in the depletion of hematopoietic cells in telomerase-deficient mice. Endogenous telomerase expression in HSCs and enforced expression of telomerase in human fibroblasts are sufficient to abrogate aneuploidy-induced replication stress at telomeres and the consequent induction of premature senescence and hematopoietic cell depletion. Together, these results identify telomerase as an aneuploidy survival factor in mammalian cells based on its capacity to alleviate telomere replication stress in response to aneuploidy induction.
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Affiliation(s)
- Jitendra K Meena
- Leibniz Institute of Age Research, Fritz Lipmann Institute e.V., Jena, Germany
| | - Aurora Cerutti
- IFOM Foundation-FIRC Institute of Molecular Oncology Foundation, Milan, Italy
| | | | - Yohei Morita
- Leibniz Institute of Age Research, Fritz Lipmann Institute e.V., Jena, Germany
| | - Christopher Bruhn
- Leibniz Institute of Age Research, Fritz Lipmann Institute e.V., Jena, Germany
| | - Mukesh Kumar
- Institute of Experimental Cancer Research, University of Ulm, Ulm, Germany
| | - Johann M Kraus
- Medical Systems Biology Unit, Ulm University, Ulm, Germany
| | | | - Zhao-Qi Wang
- Leibniz Institute of Age Research, Fritz Lipmann Institute e.V., Jena, Germany
| | - Hans A Kestler
- Leibniz Institute of Age Research, Fritz Lipmann Institute e.V., Jena, Germany Medical Systems Biology Unit, Ulm University, Ulm, Germany
| | - Fabrizio d'Adda di Fagagna
- IFOM Foundation-FIRC Institute of Molecular Oncology Foundation, Milan, Italy Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia, Italy
| | - Cagatay Günes
- Leibniz Institute of Age Research, Fritz Lipmann Institute e.V., Jena, Germany
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Völkel G, Lausser L, Schmid F, Kraus JM, Kestler HA. Sputnik: ad hoc distributed computation. Bioinformatics 2015; 31:1298-301. [PMID: 25505087 DOI: 10.1093/bioinformatics/btu818] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 12/05/2014] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION In bioinformatic applications, computationally demanding algorithms are often parallelized to speed up computation. Nevertheless, setting up computational environments for distributed computation is often tedious. Aim of this project were the lightweight ad hoc set up and fault-tolerant computation requiring only a Java runtime, no administrator rights, while utilizing all CPU cores most effectively. RESULTS The Sputnik framework provides ad hoc distributed computation on the Java Virtual Machine which uses all supplied CPU cores fully. It provides a graphical user interface for deployment setup and a web user interface displaying the current status of current computation jobs. Neither a permanent setup nor administrator privileges are required. We demonstrate the utility of our approach on feature selection of microarray data. AVAILABILITY AND IMPLEMENTATION The Sputnik framework is available on Github http://github.com/sysbio-bioinf/sputnik under the Eclipse Public License. CONTACT hkestler@fli-leibniz.de or hans.kestler@uni-ulm.de SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Gunnar Völkel
- Core Unit Medical Systems Biology, Theoretical Computer Science, Ulm University, D-89069 Ulm, Germany and Leibniz Institute for Age Research-Fritz Lipmann Institute and FSU Jena, D-07745 Jena Core Unit Medical Systems Biology, Theoretical Computer Science, Ulm University, D-89069 Ulm, Germany and Leibniz Institute for Age Research-Fritz Lipmann Institute and FSU Jena, D-07745 Jena
| | - Ludwig Lausser
- Core Unit Medical Systems Biology, Theoretical Computer Science, Ulm University, D-89069 Ulm, Germany and Leibniz Institute for Age Research-Fritz Lipmann Institute and FSU Jena, D-07745 Jena
| | - Florian Schmid
- Core Unit Medical Systems Biology, Theoretical Computer Science, Ulm University, D-89069 Ulm, Germany and Leibniz Institute for Age Research-Fritz Lipmann Institute and FSU Jena, D-07745 Jena
| | - Johann M Kraus
- Core Unit Medical Systems Biology, Theoretical Computer Science, Ulm University, D-89069 Ulm, Germany and Leibniz Institute for Age Research-Fritz Lipmann Institute and FSU Jena, D-07745 Jena
| | - Hans A Kestler
- Core Unit Medical Systems Biology, Theoretical Computer Science, Ulm University, D-89069 Ulm, Germany and Leibniz Institute for Age Research-Fritz Lipmann Institute and FSU Jena, D-07745 Jena Core Unit Medical Systems Biology, Theoretical Computer Science, Ulm University, D-89069 Ulm, Germany and Leibniz Institute for Age Research-Fritz Lipmann Institute and FSU Jena, D-07745 Jena
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Wesner JS, Kraus JM, Schmidt TS, Walters DM, Clements WH. Metamorphosis enhances the effects of metal exposure on the mayfly, Centroptilum triangulifer. Environ Sci Technol 2014; 48:10415-10422. [PMID: 25093980 DOI: 10.1021/es501914y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The response of larval aquatic insects to stressors such as metals is used to assess the ecological condition of streams worldwide. However, nearly all larval insects metamorphose from aquatic larvae to winged adults, and recent surveys indicate that adults may be a more sensitive indicator of stream metal toxicity than larvae. One hypothesis to explain this pattern is that insects exposed to elevated metal in their larval stages have a reduced ability to successfully complete metamorphosis. To test this hypothesis we exposed late-instar larvae of the mayfly, Centroptilum triangulifer, to an aqueous Zn gradient (32-476 μg/L) in the laboratory. After 6 days of exposure, when metamorphosis began, larval survival was unaffected by zinc. However, Zn reduced wingpad development at concentrations above 139 μg/L. In contrast, emergence of subimagos and imagos tended to decline with any increase in Zn. At Zn concentrations below 105 μg/L (hardness-adjusted aquatic life criterion), survival between the wingpad and subimago stages declined 5-fold across the Zn gradient. These results support the hypothesis that metamorphosis may be a survival bottleneck, particularly in contaminated streams. Thus, death during metamorphosis may be a key mechanism explaining how stream metal contamination can impact terrestrial communities by reducing aquatic insect emergence.
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Affiliation(s)
- J S Wesner
- Colorado State University, Department of Fish, Wildlife, and Conservation Biology, Fort Collins, Colorado 80523 United States
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Katz SF, Lechel A, Obenauf AC, Begus-Nahrmann Y, Kraus JM, Hoffmann EM, Duda J, Eshraghi P, Hartmann D, Liss B, Schirmacher P, Kestler HA, Speicher MR, Rudolph KL. Disruption of Trp53 in livers of mice induces formation of carcinomas with bilineal differentiation. Gastroenterology 2012; 142:1229-1239.e3. [PMID: 22342966 DOI: 10.1053/j.gastro.2012.02.009] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Revised: 01/20/2012] [Accepted: 02/07/2012] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS p53 limits the self-renewal of stem cells from various tissues. Loss of p53, in combination with other oncogenic events, results in aberrant self-renewal and transformation of progenitor cells. It is not known whether loss of p53 is sufficient to induce tumor formation in liver. METHODS We used AlfpCre mice to create mice with liver-specific disruption of Trp53 (AlfpCre(+)Trp53(Δ2-10/Δ2-10) mice). We analyzed colony formation and genomic features and gene expression patterns in liver cells during hepatocarcinogenesis in mice with homozygous, heterozygous, and no disruption of Trp53. RESULTS Liver-specific disruption of Trp53 consistently induced formation of liver carcinomas that had bilineal differentiation. In nontransformed liver cells and cultured primary liver cells, loss of p53 (but not p21) resulted in chromosomal imbalances and increased clonogenic capacity of liver progenitor cells (LPCs) and hepatocytes. Primary cultures of hepatocytes and LPCs from AlfpCre(+)Trp53(Δ2-10/Δ2-10) mice, but not Cdkn1a(-/-) mice, formed tumors with bilineal differentiation when transplanted into immunocompromised mice. Spontaneous liver tumors that developed in AlfpCre(+)Trp53(Δ2-10/Δ2-10) mice had significant but complex alterations in expression of Rb checkpoint genes compared with chemically induced liver tumors that developed mice with wild-type Trp53. CONCLUSIONS Deletion of p53 from livers of mice is sufficient to induce tumor formation. The tumors have bilineal differentiation and dysregulation of Rb checkpoint genes.
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Affiliation(s)
- Sarah-Fee Katz
- Institute of Molecular Medicine and Max Planck Research Group on Stem Cell Aging, University of Ulm, Ulm, Germany
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Kleger A, Mahaddalkar PU, Katz SF, Lechel A, Joo JY, Loya K, Lin Q, Hartmann D, Liebau S, Kraus JM, Cantz T, Kestler HA, Zaehres H, Schöler H, Rudolph KL. Increased reprogramming capacity of mouse liver progenitor cells, compared with differentiated liver cells, requires the BAF complex. Gastroenterology 2012; 142:907-17. [PMID: 22245845 DOI: 10.1053/j.gastro.2012.01.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Revised: 12/01/2011] [Accepted: 01/03/2012] [Indexed: 01/01/2023]
Abstract
BACKGROUND & AIMS Ectopic expression of certain transcription factors can reprogram somatic cells to a pluripotent state. Hematopoietic and muscle stem cells can be more efficiently reprogrammed than differentiated blood or muscle cells, yet similar findings have not been shown in other primary organ systems. Moreover, molecular characteristics of the cellular hierarchy of tissues that influence reprogramming capacities need to be delineated. We analyzed the effect of differentiation stage of freshly isolated, mouse liver cells on the reprogramming efficiency. METHODS Liver progenitor cell (LPC)-enriched cell fractions were isolated from adult (6-8 wk) and fetal (embryonic day 14.5) livers of mice and reprogrammed to become induced pluripotent stem (iPS) cells. Different transcription factors were expressed in liver cells, and markers of pluripotency were examined, along with the ability of iPS cells to differentiate, in vitro and in vivo, into different germ layers. RESULTS Fetal and adult LPCs had significantly greater reprogramming efficiency after transduction with 3 or 4 reprogramming factors. Transduction efficiency-corrected reprogramming rates of fetal LPCs were 275-fold higher, compared with unsorted fetal liver cells, when 3 reprogramming factors were transduced. The increased reprogramming efficiency of LPCs, compared with differentiated liver cells, occurred independently of proliferation rates, but was associated with endogenous expression of reprogramming factors (Klf4 and c-Myc) and BAF (Brg1/Brm associated factor)-complex members Baf155 and Brg1, which mediate epigenetic changes during reprogramming. Knockdown of BAF complex members negated the increased reprogramming efficiency of LPCs, compared with non-LPCs. CONCLUSIONS LPCs have intrinsic, cell proliferation-independent characteristics resulting in an increased reprogramming capacity compared to differentiated liver cells.
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Affiliation(s)
- Alexander Kleger
- Institute of Molecular Medicine and Max-Planck-Research Department on Stem Cell Aging, Ulm University, Ulm, Germany.
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Huth J, Buchholz M, Kraus JM, Mølhave K, Gradinaru C, v Wichert G, Gress TM, Neumann H, Kestler HA. TimeLapseAnalyzer: multi-target analysis for live-cell imaging and time-lapse microscopy. Comput Methods Programs Biomed 2011; 104:227-234. [PMID: 21705106 DOI: 10.1016/j.cmpb.2011.06.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Revised: 05/30/2011] [Accepted: 06/02/2011] [Indexed: 05/31/2023]
Abstract
The direct observation of cells over time using time-lapse microscopy can provide deep insights into many important biological processes. Reliable analyses of motility, proliferation, invasive potential or mortality of cells are essential to many studies involving live cell imaging and can aid in biomarker discovery and diagnostic decisions. Given the vast amount of image- and time-series data produced by modern microscopes, automated analysis is a key feature to capitalize the potential of time-lapse imaging devices. To provide fast and reproducible analyses of multiple aspects of cell behaviour, we developed TimeLapseAnalyzer. Apart from general purpose image enhancements and segmentation procedures, this extensible, self-contained, modular cross-platform package provides dedicated modalities for fast and reliable analysis of multi-target cell tracking, scratch wound healing analysis, cell counting and tube formation analysis in high throughput screening of live-cell experiments. TimeLapseAnalyzer is freely available (MATLAB, Open Source) at http://www.informatik.uni-ulm.de/ni/mitarbeiter/HKestler/tla.
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Affiliation(s)
- Johannes Huth
- Department of Gastroenterology and Endocrinology, University Hospital of Marburg, Germany
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Song Z, von Figura G, Liu Y, Kraus JM, Torrice C, Dillon P, Rudolph-Watabe M, Ju Z, Kestler HA, Sanoff H, Lenhard Rudolph K. Lifestyle impacts on the aging-associated expression of biomarkers of DNA damage and telomere dysfunction in human blood. Aging Cell 2010; 9:607-15. [PMID: 20560902 DOI: 10.1111/j.1474-9726.2010.00583.x] [Citation(s) in RCA: 117] [Impact Index Per Article: 8.4] [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] [Indexed: 12/19/2022] Open
Abstract
Cellular aging is characterized by telomere shortening, which can lead to uncapping of chromosome ends (telomere dysfunction) and activation of DNA damage responses. There is some evidence that DNA damage accumulates during human aging and that lifestyle factors contribute to the accumulation of DNA damage. Recent studies have identified a set of serum markers that are induced by telomere dysfunction and DNA damage, and these markers showed an increased expression in blood during human aging. Here, we investigated the influence of lifestyle factors (such as exercise, smoking, body mass) on the aging-associated expression of serum markers of DNA damage (CRAMP, EF-1alpha, stathmin, n-acetyl-glucosaminidase and chitinase) in comparison with other described markers of cellular aging (p16(INK4a) upregulation and telomere shortening) in human peripheral blood. The study shows that lifestyle factors have an age-independent impact on the expression level of biomarkers of DNA damage. Smoking and increased body mass indices were associated with elevated levels of biomarkers of DNA damage independent of the age of the individuals. In contrast, exercise was associated with an age-independent reduction in the expression of biomarkers of DNA damage in human blood. The expression of biomarkers of DNA damage correlated positively with p16(INK4a) expression and negatively with telomere length in peripheral blood T-lymphocytes. Together, these data provide experimental evidence that both aging and lifestyle impact on the accumulation of DNA damage during human aging.
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Affiliation(s)
- Zhangfa Song
- Max-Planck Research Group on Stem Cell Aging, University of Ulm, Ulm, Germany
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Huth J, Buchholz M, Kraus JM, Schmucker M, von Wichert G, Krndija D, Seufferlein T, Gress TM, Kestler HA. Significantly improved precision of cell migration analysis in time-lapse video microscopy through use of a fully automated tracking system. BMC Cell Biol 2010; 11:24. [PMID: 20377897 PMCID: PMC2858025 DOI: 10.1186/1471-2121-11-24] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Accepted: 04/08/2010] [Indexed: 11/30/2022] Open
Abstract
Background Cell motility is a critical parameter in many physiological as well as pathophysiological processes. In time-lapse video microscopy, manual cell tracking remains the most common method of analyzing migratory behavior of cell populations. In addition to being labor-intensive, this method is susceptible to user-dependent errors regarding the selection of "representative" subsets of cells and manual determination of precise cell positions. Results We have quantitatively analyzed these error sources, demonstrating that manual cell tracking of pancreatic cancer cells lead to mis-calculation of migration rates of up to 410%. In order to provide for objective measurements of cell migration rates, we have employed multi-target tracking technologies commonly used in radar applications to develop fully automated cell identification and tracking system suitable for high throughput screening of video sequences of unstained living cells. Conclusion We demonstrate that our automatic multi target tracking system identifies cell objects, follows individual cells and computes migration rates with high precision, clearly outperforming manual procedures.
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Affiliation(s)
- Johannes Huth
- Research group of Bioinformatics and Systems Biology, Institute of Neural Information Processing, Ulm University, Albert-Einstein-Allee 11, D-89081 Ulm, Germany
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Kraus JM, Kestler HA. A highly efficient multi-core algorithm for clustering extremely large datasets. BMC Bioinformatics 2010; 11:169. [PMID: 20370922 PMCID: PMC2865495 DOI: 10.1186/1471-2105-11-169] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Accepted: 04/06/2010] [Indexed: 11/24/2022] Open
Abstract
Background In recent years, the demand for computational power in computational biology has increased due to rapidly growing data sets from microarray and other high-throughput technologies. This demand is likely to increase. Standard algorithms for analyzing data, such as cluster algorithms, need to be parallelized for fast processing. Unfortunately, most approaches for parallelizing algorithms largely rely on network communication protocols connecting and requiring multiple computers. One answer to this problem is to utilize the intrinsic capabilities in current multi-core hardware to distribute the tasks among the different cores of one computer. Results We introduce a multi-core parallelization of the k-means and k-modes cluster algorithms based on the design principles of transactional memory for clustering gene expression microarray type data and categorial SNP data. Our new shared memory parallel algorithms show to be highly efficient. We demonstrate their computational power and show their utility in cluster stability and sensitivity analysis employing repeated runs with slightly changed parameters. Computation speed of our Java based algorithm was increased by a factor of 10 for large data sets while preserving computational accuracy compared to single-core implementations and a recently published network based parallelization. Conclusions Most desktop computers and even notebooks provide at least dual-core processors. Our multi-core algorithms show that using modern algorithmic concepts, parallelization makes it possible to perform even such laborious tasks as cluster sensitivity and cluster number estimation on the laboratory computer.
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Affiliation(s)
- Johann M Kraus
- Institute of Neural Information Processing, University of Ulm, 89069 Ulm, Germany
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Hombach V, Merkle N, Torzewski J, Kraus JM, Kunze M, Zimmermann O, Kestler HA, Wöhrle J. Electrocardiographic and cardiac magnetic resonance imaging parameters as predictors of a worse outcome in patients with idiopathic dilated cardiomyopathy. Eur Heart J 2009; 30:2011-8. [PMID: 19633015 PMCID: PMC2726960 DOI: 10.1093/eurheartj/ehp293] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Aims Clinical parameters are weak predictors of outcome in patients with idiopathic dilated cardiomyopathy (IDC). We assessed the prognostic value of cardiac magnetic resonance (CMR) parameters in addition to conventional clinical and electrocardiographic characteristics. Methods and results One hundred and forty-one IDC patients were studied. QRS and QTc intervals were measured in 12-lead surface electrocardiogram. Patients were followed for median 1339 days, including 483 patient-years. The primary endpoint—cardiac death or sudden death—occurred in 25 (18%) patients, including 16 patients with cardiac death, 3 patients with sudden cardiac death (SCD), and 6 patients with ICD shock. Late gadolinium enhancement (LGE) was detected in 36 patients (26%). Kaplan–Meier survival analysis displayed QRS >110 ms (P = 0.010), the presence of LGE (P = 0.037), and diabetes mellitus (P < 0.001) as significant parameters for a worse outcome. Multivariable analysis revealed cardiac index (P < 0.001), right ventricular end-diastolic volume index (RVEDVI) (P = 0.006) derived from CMR imaging, the presence of diabetes mellitus (P = 0.006), and QRS >110 ms (P = 0.045) as significant predictors for the primary endpoint. Conclusion Cardiac index and RVEDVI derived from CMR imaging in addition to QRS duration >110 ms from conventional surface ECG and diabetes mellitus provide prognostic impact for cardiac death and SCD in patients with IDC.
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Affiliation(s)
- Vinzenz Hombach
- Clinic of Internal Medicine II, University Hospital Ulm, Albert-Einstein-Allee 23, Ulm 89081, Germany.
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Kestler HA, Müller A, Kraus JM, Buchholz M, Gress TM, Liu H, Kane DW, Zeeberg BR, Weinstein JN. VennMaster: area-proportional Euler diagrams for functional GO analysis of microarrays. BMC Bioinformatics 2008; 9:67. [PMID: 18230172 PMCID: PMC2335321 DOI: 10.1186/1471-2105-9-67] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2007] [Accepted: 01/29/2008] [Indexed: 11/10/2022] Open
Abstract
Background Microarray experiments generate vast amounts of data. The functional context of differentially expressed genes can be assessed by querying the Gene Ontology (GO) database via GoMiner. Directed acyclic graph representations, which are used to depict GO categories enriched with differentially expressed genes, are difficult to interpret and, depending on the particular analysis, may not be well suited for formulating new hypotheses. Additional graphical methods are therefore needed to augment the GO graphical representation. Results We present an alternative visualization approach, area-proportional Euler diagrams, showing set relationships with semi-quantitative size information in a single diagram to support biological hypothesis formulation. The cardinalities of sets and intersection sets are represented by area-proportional Euler diagrams and their corresponding graphical (circular or polygonal) intersection areas. Optimally proportional representations are obtained using swarm and evolutionary optimization algorithms. Conclusion VennMaster's area-proportional Euler diagrams effectively structure and visualize the results of a GO analysis by indicating to what extent flagged genes are shared by different categories. In addition to reducing the complexity of the output, the visualizations facilitate generation of novel hypotheses from the analysis of seemingly unrelated categories that share differentially expressed genes.
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Affiliation(s)
- Hans A Kestler
- Neural Information Processing, University of Ulm, Germany.
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Kestler HA, Kraus JM, Palm G, Schwenker F. On the Effects of Constraints in Semi-supervised Hierarchical Clustering. Artificial Neural Networks in Pattern Recognition 2006. [DOI: 10.1007/11829898_6] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Falor WH, Chang B, White HA, Kraus JM, Taylor B, Hansel JR, Kraus FC. Twenty-four hour esophageal pH monitoring by telemetry. Cost-effective use in outpatients. Am J Surg 1981; 142:514-6. [PMID: 6792938 DOI: 10.1016/0002-9610(81)90387-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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