1
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Hanssen F, Garcia MU, Folkersen L, Pedersen A, Lescai F, Jodoin S, Miller E, Seybold M, Wacker O, Smith N, Gabernet G, Nahnsen S. Scalable and efficient DNA sequencing analysis on different compute infrastructures aiding variant discovery. NAR Genom Bioinform 2024; 6:lqae031. [PMID: 38666213 PMCID: PMC11044436 DOI: 10.1093/nargab/lqae031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 03/23/2024] [Indexed: 04/28/2024] Open
Abstract
DNA variation analysis has become indispensable in many aspects of modern biomedicine, most prominently in the comparison of normal and tumor samples. Thousands of samples are collected in local sequencing efforts and public databases requiring highly scalable, portable, and automated workflows for streamlined processing. Here, we present nf-core/sarek 3, a well-established, comprehensive variant calling and annotation pipeline for germline and somatic samples. It is suitable for any genome with a known reference. We present a full rewrite of the original pipeline showing a significant reduction of storage requirements by using the CRAM format and runtime by increasing intra-sample parallelization. Both are leading to a 70% cost reduction in commercial clouds enabling users to do large-scale and cross-platform data analysis while keeping costs and CO2 emissions low. The code is available at https://nf-co.re/sarek.
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Affiliation(s)
- Friederike Hanssen
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Otfried-Müller Str. 37, Tübingen 72076, Baden-Württemberg, Germany
- Department of Computer Science, Eberhard-Karls University of Tübingen, 72076 Baden-Württemberg, Germany
- M3 Research Center, University Hospital, Otfried-Müller Str. 37, Tübingen 72076, Baden-Württemberg, Germany
- Cluster of Excellence iFIT (EXC 2180) ‘Image-Guided and Functionally Instructed Tumor Therapies’, Eberhard-Karls University of Tübingen, Tübingen 72076, Baden-Württemberg, Germany
| | - Maxime U Garcia
- Seqera Labs, Carrer de Marià Aguilò, 28, Barcelona 08005, Spain
- Barntumörbanken, Department of Oncology-Pathology, Karolinska Institutet, BioClinicum, Visionsgatan 4, Solna 17164, Sweden
- National Genomics Infrastructure, SciLifeLab, SciLifeLab, Tomtebodavägen 23, Solna 17165, Sweden
| | | | | | - Francesco Lescai
- Department of Biology and Biotechnology ”L. Spallanzani”, University of Pavia, via Ferrata, 9, Pavia, 27100 PV, Italy
| | - Susanne Jodoin
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Otfried-Müller Str. 37, Tübingen 72076, Baden-Württemberg, Germany
- M3 Research Center, University Hospital, Otfried-Müller Str. 37, Tübingen 72076, Baden-Württemberg, Germany
| | - Edmund Miller
- Department of Biological Sciences and Center for Systems Biology, University of Texas at Dallas, 800 W Campbell Rd, Richardson, TX 75080, USA
| | - Matthias Seybold
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Otfried-Müller Str. 37, Tübingen 72076, Baden-Württemberg, Germany
| | - Oskar Wacker
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Otfried-Müller Str. 37, Tübingen 72076, Baden-Württemberg, Germany
- M3 Research Center, University Hospital, Otfried-Müller Str. 37, Tübingen 72076, Baden-Württemberg, Germany
| | - Nicholas Smith
- Department of Informatics, Technical University of Munich, Boltzmannstr. 3, Garching, 85748 Bavaria, Germany
| | - Gisela Gabernet
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Otfried-Müller Str. 37, Tübingen 72076, Baden-Württemberg, Germany
- Department of Pathology, Yale School of Medicine, 300 George, New Haven, CT 06510, USA
| | - Sven Nahnsen
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Otfried-Müller Str. 37, Tübingen 72076, Baden-Württemberg, Germany
- Department of Computer Science, Eberhard-Karls University of Tübingen, 72076 Baden-Württemberg, Germany
- M3 Research Center, University Hospital, Otfried-Müller Str. 37, Tübingen 72076, Baden-Württemberg, Germany
- Cluster of Excellence iFIT (EXC 2180) ‘Image-Guided and Functionally Instructed Tumor Therapies’, Eberhard-Karls University of Tübingen, Tübingen 72076, Baden-Württemberg, Germany
- Institute for Bioinformatics and Medical Informatics (IBMI), Eberhard-Karls University of Tübingen, Tübingen 72076, Baden-Württemberg, Germany
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2
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Perelo LW, Gabernet G, Straub D, Nahnsen S. How tool combinations in different pipeline versions affect the outcome in RNA-seq analysis. NAR Genom Bioinform 2024; 6:lqae020. [PMID: 38456178 PMCID: PMC10919883 DOI: 10.1093/nargab/lqae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/07/2024] [Accepted: 02/12/2024] [Indexed: 03/09/2024] Open
Abstract
Data analysis tools are continuously changed and improved over time. In order to test how these changes influence the comparability between analyses, the output of different workflow options of the nf-core/rnaseq pipeline were compared. Five different pipeline settings (STAR+Salmon, STAR+RSEM, STAR+featureCounts, HISAT2+featureCounts, pseudoaligner Salmon) were run on three datasets (human, Arabidopsis, zebrafish) containing spike-ins of the External RNA Control Consortium (ERCC). Fold change ratios and differential expression of genes and spike-ins were used for comparative analyses of the different tools and versions settings of the pipeline. An overlap of 85% for differential gene classification between pipelines could be shown. Genes interpreted with a bias were mostly those present at lower concentration. Also, the number of isoforms and exons per gene were determinants. Previous pipeline versions using featureCounts showed a higher sensitivity to detect one-isoform genes like ERCC. To ensure data comparability in long-term analysis series it would be recommendable to either stay with the pipeline version the series was initialized with or to run both versions during a transition time in order to ensure that the target genes are addressed the same way.
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Affiliation(s)
- Louisa Wessels Perelo
- Quantitative Biology Center (QBiC), University of Tübingen, Otfried-Müller-Str. 37, 72076 Tübingen, Baden-Württemberg, 72076, Germany
| | - Gisela Gabernet
- Quantitative Biology Center (QBiC), University of Tübingen, Otfried-Müller-Str. 37, 72076 Tübingen, Baden-Württemberg, 72076, Germany
| | - Daniel Straub
- Quantitative Biology Center (QBiC), University of Tübingen, Otfried-Müller-Str. 37, 72076 Tübingen, Baden-Württemberg, 72076, Germany
| | - Sven Nahnsen
- Quantitative Biology Center (QBiC), University of Tübingen, Otfried-Müller-Str. 37, 72076 Tübingen, Baden-Württemberg, 72076, Germany
- M3 Research Center, Faculty of Medicine, University of Tübingen, Otfried-Müller-Str. 37, 72076 Tübingen, Baden-Württemberg, 72076, Germany
- Department of Computer Science, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Otfried-Müller-Str. 37, 72076 Tübingen, Baden-Württemberg, 72076, Germany
- Cluster of Excellence iFIT (EXC 2180), Image-Guided and Functionally Instructed Tumor Therapies, University of Tübingen, Otfried-Müller-Str. 37, 72076 Tübingen, Baden-Württemberg, 72076, Germany
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3
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Gabernet G, Marquez S, Bjornson R, Peltzer A, Meng H, Aron E, Lee NY, Jensen C, Ladd D, Hanssen F, Heumos S, Yaari G, Kowarik MC, Nahnsen S, Kleinstein SH. nf-core/airrflow: an adaptive immune receptor repertoire analysis workflow employing the Immcantation framework. bioRxiv 2024:2024.01.18.576147. [PMID: 38293151 PMCID: PMC10827190 DOI: 10.1101/2024.01.18.576147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) is a valuable experimental tool to study the immune state in health and following immune challenges such as infectious diseases, (auto)immune diseases, and cancer. Several tools have been developed to reconstruct B cell and T cell receptor sequences from AIRR-seq data and infer B and T cell clonal relationships. However, currently available tools offer limited parallelization across samples, scalability or portability to high-performance computing infrastructures. To address this need, we developed nf-core/airrflow, an end-to-end bulk and single-cell AIRR-seq processing workflow which integrates the Immcantation Framework following BCR and TCR sequencing data analysis best practices. The Immcantation Framework is a comprehensive toolset, which allows the processing of bulk and single-cell AIRR-seq data from raw read processing to clonal inference. nf-core/airrflow is written in Nextflow and is part of the nf-core project, which collects community contributed and curated Nextflow workflows for a wide variety of analysis tasks. We assessed the performance of nf-core/airrflow on simulated sequencing data with sequencing errors and show example results with real datasets. To demonstrate the applicability of nf-core/airrflow to the high-throughput processing of large AIRR-seq datasets, we validated and extended previously reported findings of convergent antibody responses to SARS-CoV-2 by analyzing 97 COVID-19 infected individuals and 99 healthy controls, including a mixture of bulk and single-cell sequencing datasets. Using this dataset, we extended the convergence findings to 20 additional subjects, highlighting the applicability of nf-core/airrflow to validate findings in small in-house cohorts with reanalysis of large publicly available AIRR datasets. nf-core/airrflow is available free of charge, under the MIT license on GitHub (https://github.com/nf-core/airrflow). Detailed documentation and example results are available on the nf-core website at (https://nf-co.re/airrflow).
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4
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Heumos L, Ehmele P, Kuhn Cuellar L, Menden K, Miller E, Lemke S, Gabernet G, Nahnsen S. mlf-core: a framework for deterministic machine learning. Bioinformatics 2023; 39:7099608. [PMID: 37004171 PMCID: PMC10089676 DOI: 10.1093/bioinformatics/btad164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 01/24/2023] [Accepted: 02/27/2023] [Indexed: 04/03/2023]
Abstract
MOTIVATION Machine learning has shown extensive growth in recent years and is now routinely applied to sensitive areas. To allow appropriate verification of predictive models before deployment, models must be deterministic. Solely fixing all random seeds is not sufficient for deterministic machine learning, as major machine learning libraries default to the usage of non-deterministic algorithms based on atomic operations. RESULTS Various machine learning libraries released deterministic counterparts to the non-deterministic algorithms. We evaluated the effect of these algorithms on determinism and runtime. Based on these results, we formulated a set of requirements for deterministic machine learning and developed a new software solution, the mlf-core ecosystem, which aids machine learning projects to meet and keep these requirements. We applied mlf-core to develop deterministic models in various biomedical fields including a single cell autoencoder with TensorFlow, a PyTorch-based U-Net model for liver-tumor segmentation in CT scans, and a liver cancer classifier based on gene expression profiles with XGBoost. AVAILABILITY The complete data together with the implementations of the mlf-core ecosystem and use case models are available at https://github.com/mlf-core. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Lukas Heumos
- Quantitative Biology Center (QBiC), Eberhard Karls University of Tübingen, Tübingen, Germany
- Institute of Computational Biology, Helmholtz Zentrum München, Munich, Germany
- Institute of Lung Biology and Disease and Comprehensive Pneumology Center, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
- TUM school of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Philipp Ehmele
- Department of Informatics, University of Hamburg, Hamburg
| | - Luis Kuhn Cuellar
- Quantitative Biology Center (QBiC), Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Kevin Menden
- Quantitative Biology Center (QBiC), Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Edmund Miller
- Department of Biological Sciences and Center for Systems Biology, The University of Texas at Dallas, Richardson, Texas, USA
| | - Steffen Lemke
- Quantitative Biology Center (QBiC), Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Gisela Gabernet
- Quantitative Biology Center (QBiC), Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Sven Nahnsen
- Quantitative Biology Center (QBiC), Eberhard Karls University of Tübingen, Tübingen, Germany
- Biomedical Data Science, Department for Computer Science, Eberhard Karls University of Tübingen, Tübingen, Germany
- Institute of Bioinformatics and Medical Informatics, Eberhard Karls University of Tübingen, Tübingen, Germany
- Faculty of Medicine, Eberhard Karls University of Tübingen, Tübingen, Germany
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5
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Renovanz M, Kurz SC, Rieger J, Walter B, Becker H, Hille H, Bombach P, Rieger D, Grosse L, Häusser L, Skardelly M, Merk DJ, Paulsen F, Hoffmann E, Gani C, Neumann M, Beschorner R, Rieß O, Roggia C, Schroeder C, Ossowski S, Armeanu-Ebinger S, Gschwind A, Biskup S, Schulze M, Fend F, Singer S, Zender L, Lengerke C, Brucker SY, Engler T, Forschner A, Stenzl A, Kohlbacher O, Nahnsen S, Gabernet G, Fillinger S, Bender B, Ernemann U, Öner Ö, Beha J, Malek HS, Möller Y, Ruhm K, Tatagiba M, Schittenhelm J, Bitzer M, Malek N, Zips D, Tabatabai G. Clinical outcome of biomarker-guided therapies in adult patients with tumors of the nervous system. Neurooncol Adv 2023; 5:vdad012. [PMID: 36915613 PMCID: PMC10007909 DOI: 10.1093/noajnl/vdad012] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023] Open
Abstract
Background The clinical utility of molecular profiling and targeted therapies for neuro-oncology patients outside of clinical trials is not established. We aimed at investigating feasibility and clinical utility of molecular profiling and targeted therapy in adult patients with advanced tumors in the nervous system within a prospective observational study. Methods molecular tumor board (MTB)@ZPM (NCT03503149) is a prospective observational precision medicine study for patients with advanced tumors. After inclusion of patients, we performed comprehensive molecular profiling, formulated ranked biomarker-guided therapy recommendations based on consensus by the MTB, and collected prospective clinical outcome data. Results Here, we present initial data of 661 adult patients with tumors of the nervous system enrolled by December 31, 2021. Of these, 408 patients were presented at the MTB. Molecular-instructed therapy recommendations could be made in 380/408 (93.1%) cases and were prioritized by evidence levels. Therapies were initiated in 86/380 (22.6%) cases until data cutoff. We observed a progression-free survival ratio >1.3 in 31.3% of patients. Conclusions Our study supports the clinical utility of biomarker-guided therapies for neuro-oncology patients and indicates clinical benefit in a subset of patients. Our data might inform future clinical trials, translational studies, and even clinical care.
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Affiliation(s)
- Mirjam Renovanz
- Department of Neurology and Interdisciplinary Neuro-Oncology, Hertie Institute for Clinical Brain Research, Eberhard Karls University Tübingen, Germany.,Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Germany.,Department of Neurosurgery, Eberhard Karls University Tübingen, Germany
| | - Sylvia C Kurz
- Department of Neurology and Interdisciplinary Neuro-Oncology, Hertie Institute for Clinical Brain Research, Eberhard Karls University Tübingen, Germany.,Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Germany
| | - Johannes Rieger
- Department of Neurology and Interdisciplinary Neuro-Oncology, Hertie Institute for Clinical Brain Research, Eberhard Karls University Tübingen, Germany.,Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Germany
| | - Bianca Walter
- Department of Neurology and Interdisciplinary Neuro-Oncology, Hertie Institute for Clinical Brain Research, Eberhard Karls University Tübingen, Germany
| | - Hannes Becker
- Department of Neurology and Interdisciplinary Neuro-Oncology, Hertie Institute for Clinical Brain Research, Eberhard Karls University Tübingen, Germany.,Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Germany.,Department of Neurosurgery, Eberhard Karls University Tübingen, Germany
| | - Hanni Hille
- Department of Neurology and Interdisciplinary Neuro-Oncology, Hertie Institute for Clinical Brain Research, Eberhard Karls University Tübingen, Germany
| | - Paula Bombach
- Department of Neurology and Interdisciplinary Neuro-Oncology, Hertie Institute for Clinical Brain Research, Eberhard Karls University Tübingen, Germany.,Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Germany.,Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany
| | - David Rieger
- Department of Neurology and Interdisciplinary Neuro-Oncology, Hertie Institute for Clinical Brain Research, Eberhard Karls University Tübingen, Germany.,Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Germany
| | - Lucia Grosse
- Department of Neurology and Interdisciplinary Neuro-Oncology, Hertie Institute for Clinical Brain Research, Eberhard Karls University Tübingen, Germany.,Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Germany
| | - Lara Häusser
- Department of Neurology and Interdisciplinary Neuro-Oncology, Hertie Institute for Clinical Brain Research, Eberhard Karls University Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University of Tübingen, Germany
| | - Marco Skardelly
- Department of Neurology and Interdisciplinary Neuro-Oncology, Hertie Institute for Clinical Brain Research, Eberhard Karls University Tübingen, Germany.,Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Germany
| | - Daniel J Merk
- Department of Neurology and Interdisciplinary Neuro-Oncology, Hertie Institute for Clinical Brain Research, Eberhard Karls University Tübingen, Germany
| | - Frank Paulsen
- Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Germany.,Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Department of Radiation Oncology, Eberhard Karls University Tübingen, Germany
| | - Elgin Hoffmann
- Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Germany.,Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Department of Radiation Oncology, Eberhard Karls University Tübingen, Germany
| | - Cihan Gani
- Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Germany.,Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Department of Radiation Oncology, Eberhard Karls University Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University of Tübingen, Germany
| | - Manuela Neumann
- Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Germany.,Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Institute of Pathology and Neuropathology, Department of Neuropathology, Eberhard Karls University Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University of Tübingen, Germany
| | - Rudi Beschorner
- Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Germany.,Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Institute of Pathology and Neuropathology, Department of Neuropathology, Eberhard Karls University Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University of Tübingen, Germany
| | - Olaf Rieß
- Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Institute of Medical Genetics and Applied Genomics, Eberhard Karls University Tübingen, Germany.,Cluster of Excellence (EXC 2180) "Image Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University of Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University of Tübingen, Germany
| | - Cristiana Roggia
- Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Institute of Medical Genetics and Applied Genomics, Eberhard Karls University Tübingen, Germany
| | - Christopher Schroeder
- Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Institute of Medical Genetics and Applied Genomics, Eberhard Karls University Tübingen, Germany
| | - Stephan Ossowski
- Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Institute of Medical Genetics and Applied Genomics, Eberhard Karls University Tübingen, Germany
| | - Sorin Armeanu-Ebinger
- Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Institute of Medical Genetics and Applied Genomics, Eberhard Karls University Tübingen, Germany
| | - Axel Gschwind
- Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Institute of Medical Genetics and Applied Genomics, Eberhard Karls University Tübingen, Germany
| | - Saskia Biskup
- Center for Genomics and Transcriptomics (CeGaT) & Center for Human Genetics Tübingen, Germany.,Cluster of Excellence (EXC 2180) "Image Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University of Tübingen, Germany
| | - Martin Schulze
- Center for Genomics and Transcriptomics (CeGaT) & Center for Human Genetics Tübingen, Germany
| | - Falko Fend
- Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Department of Pathology and Neuropathology, Institute of Pathology and Molecular Pathology, Eberhard Karls University Tübingen, Germany.,Cluster of Excellence (EXC 2180) "Image Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University of Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University of Tübingen, Germany
| | - Stephan Singer
- Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Department of Pathology and Neuropathology, Institute of Pathology and Molecular Pathology, Eberhard Karls University Tübingen, Germany.,Cluster of Excellence (EXC 2180) "Image Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University of Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University of Tübingen, Germany
| | - Lars Zender
- Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Department of Medical Oncology and Pneumology (Internal Medicine VIII), Eberhard Karls University Tübingen, Germany.,Cluster of Excellence (EXC 2180) "Image Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University of Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University of Tübingen, Germany
| | - Claudia Lengerke
- Department of Internal Medicine II, Eberhard Karls University Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University of Tübingen, Germany
| | - Sara Yvonne Brucker
- Department of Gynecology and Obstetrics, Eberhard Karls University Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University of Tübingen, Germany
| | - Tobias Engler
- Department of Gynecology and Obstetrics, Eberhard Karls University Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University of Tübingen, Germany
| | - Andrea Forschner
- Department of Dermatology and Center for Dermato-Oncology, Eberhard Karls University Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University of Tübingen, Germany
| | - Arnulf Stenzl
- Department of Urology, Eberhard Karls University Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University of Tübingen, Germany
| | - Oliver Kohlbacher
- Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Institute for Translational Bioinformatics, Eberhard Karls University Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University of Tübingen, Germany
| | - Sven Nahnsen
- Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Quantitative Biology Center (QBiC), Eberhard Karls University Tübingen, Germany.,Department of Medical Oncology and Pneumology (Internal Medicine VIII), Eberhard Karls University Tübingen, Germany.,Cluster of Excellence (EXC 2180) "Image Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University of Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University of Tübingen, Germany
| | - Gisela Gabernet
- Quantitative Biology Center (QBiC), Eberhard Karls University Tübingen, Germany
| | - Sven Fillinger
- Quantitative Biology Center (QBiC), Eberhard Karls University Tübingen, Germany
| | - Benjamin Bender
- Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Germany.,Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Department of Diagnostic and Interventional Neuroradiology, Department of Radiology, Eberhard Karls University Tübingen, Germany
| | - Ulrike Ernemann
- Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Germany.,Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Department of Diagnostic and Interventional Neuroradiology, Department of Radiology, Eberhard Karls University Tübingen, Germany
| | - Öznur Öner
- Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany
| | - Janina Beha
- Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany
| | - Holly Sundberg Malek
- Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany
| | - Yvonne Möller
- Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany
| | - Kristina Ruhm
- Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany
| | - Marcos Tatagiba
- Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Germany.,Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Department of Neurosurgery, Eberhard Karls University Tübingen, Germany
| | - Jens Schittenhelm
- Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Germany.,Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Institute of Pathology and Neuropathology, Department of Neuropathology, Eberhard Karls University Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University of Tübingen, Germany
| | - Michael Bitzer
- Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Department of Internal Medicine I, Eberhard Karls University Tübingen, Germany.,Cluster of Excellence (EXC 2180) "Image Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University of Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University of Tübingen, Germany
| | - Nisar Malek
- Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Department of Internal Medicine I, Eberhard Karls University Tübingen, Germany.,Cluster of Excellence (EXC 2180) "Image Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University of Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University of Tübingen, Germany
| | - Daniel Zips
- Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Germany.,Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Department of Radiation Oncology, Eberhard Karls University Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University of Tübingen, Germany
| | - Ghazaleh Tabatabai
- Department of Neurology and Interdisciplinary Neuro-Oncology, Hertie Institute for Clinical Brain Research, Eberhard Karls University Tübingen, Germany.,Center for Neuro-Oncology, Comprehensive Cancer Center Tübingen-Stuttgart, University Hospital Tübingen, Germany.,Center for Personalized Medicine Tübingen, Eberhard Karls University Tübingen, Germany.,Cluster of Excellence (EXC 2180) "Image Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University of Tübingen, Germany.,German Cancer Consortium (DKTK), DKFZ partner site Tübingen, Eberhard Karls University of Tübingen, Germany
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6
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Ruschil C, Gabernet G, Kemmerer CL, Jarboui MA, Klose F, Poli S, Ziemann U, Nahnsen S, Kowarik MC. Cladribine treatment specifically affects peripheral blood memory B cell clones and clonal expansion in multiple sclerosis patients. Front Immunol 2023; 14:1133967. [PMID: 36960053 PMCID: PMC10028280 DOI: 10.3389/fimmu.2023.1133967] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Accepted: 02/13/2023] [Indexed: 03/09/2023] Open
Abstract
Introduction B cells are acknowledged as crucial players in the pathogenesis of multiple sclerosis (MS). Several disease modifying drugs including cladribine have been shown to exert differential effects on peripheral blood B cell subsets. However, little is known regarding functional changes within the peripheral B cell populations. In this study, we obtained a detailed picture of B cell repertoire changes under cladribine treatment on a combined immunoglobulin (Ig) transcriptome and proteome level. Methods We performed next-generation sequencing of Ig heavy chain (IGH) transcripts and Ig mass spectrometry in cladribine-treated patients with relapsing-remitting multiple sclerosis (n = 8) at baseline and after 6 and 12 months of treatment in order to generate Ig transcriptome and Ig peptide libraries. Ig peptides were overlapped with the corresponding IGH transcriptome in order to analyze B cell clones on a combined transcriptome and proteome level. Results The analysis of peripheral blood B cell percentages pointed towards a significant decrease of memory B cells and an increase of naive B cells following cladribine therapy. While basic IGH repertoire parameters (e.g. variable heavy chain family usage and Ig subclasses) were only slightly affected by cladribine treatment, a significantly decreased number of clones and significantly lower diversity in the memory subset was noticeable at 6 months following treatment which was sustained at 12 months. When looking at B-cell clones comprising sequences from the different time-points, clones spanning between all three time-points were significantly more frequent than clones including sequences from two time-points. Furthermore, Ig proteome analyses showed that Ig transcriptome specific peptides could mostly be equally aligned to all three time-points pointing towards a proportion of B-cell clones that are maintained during treatment. Discussion Our findings suggest that peripheral B cell related treatment effects of cladribine tablets might be exerted through a reduction of possibly disease relevant clones in the memory B cell subset without disrupting the overall clonal composition of B cells. Our results -at least partially- might explain the relatively mild side effects regarding infections and the sustained immune response after vaccinations during treatment. However, exact disease driving B cell subsets and their effects remain unknown and should be addressed in future studies.
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Affiliation(s)
- Christoph Ruschil
- Department of Neurology and Stroke, Center for Neurology, Eberhard Karls University of Tübingen, Tübingen, Germany
- Hertie-Institute for Clinical Brain Research, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Gisela Gabernet
- Quantitative Biology Center (QBiC), Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Constanze Louisa Kemmerer
- Hertie-Institute for Clinical Brain Research, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Mohamed Ali Jarboui
- Core Facility for Medical Bioanalytics (CFMB), Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Franziska Klose
- Core Facility for Medical Bioanalytics (CFMB), Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Sven Poli
- Department of Neurology and Stroke, Center for Neurology, Eberhard Karls University of Tübingen, Tübingen, Germany
- Hertie-Institute for Clinical Brain Research, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Ulf Ziemann
- Department of Neurology and Stroke, Center for Neurology, Eberhard Karls University of Tübingen, Tübingen, Germany
- Hertie-Institute for Clinical Brain Research, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Sven Nahnsen
- Quantitative Biology Center (QBiC), Eberhard Karls University of Tübingen, Tübingen, Germany
- Biomedical Data Science, Department of Computer Science, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Markus Christian Kowarik
- Department of Neurology and Stroke, Center for Neurology, Eberhard Karls University of Tübingen, Tübingen, Germany
- Hertie-Institute for Clinical Brain Research, Eberhard Karls University of Tübingen, Tübingen, Germany
- *Correspondence: Markus Christian Kowarik,
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7
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Krakau S, Straub D, Gourlé H, Gabernet G, Nahnsen S. nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning. NAR Genom Bioinform 2022; 4:lqac007. [PMID: 35118380 PMCID: PMC8808542 DOI: 10.1093/nargab/lqac007] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/19/2021] [Accepted: 01/25/2022] [Indexed: 12/18/2022] Open
Abstract
The analysis of shotgun metagenomic data provides valuable insights into microbial communities, while allowing resolution at individual genome level. In absence of complete reference genomes, this requires the reconstruction of metagenome assembled genomes (MAGs) from sequencing reads. We present the nf-core/mag pipeline for metagenome assembly, binning and taxonomic classification. It can optionally combine short and long reads to increase assembly continuity and utilize sample-wise group-information for co-assembly and genome binning. The pipeline is easy to install-all dependencies are provided within containers-portable and reproducible. It is written in Nextflow and developed as part of the nf-core initiative for best-practice pipeline development. All codes are hosted on GitHub under the nf-core organization https://github.com/nf-core/mag and released under the MIT license.
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Affiliation(s)
- Sabrina Krakau
- Quantitative Biology Center (QBiC), University of Tübingen, 72076 Tübingen, Germany
| | - Daniel Straub
- Quantitative Biology Center (QBiC), University of Tübingen, 72076 Tübingen, Germany
| | - Hadrien Gourlé
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, S-75007 Uppsala, Sweden
| | - Gisela Gabernet
- Quantitative Biology Center (QBiC), University of Tübingen, 72076 Tübingen, Germany
| | - Sven Nahnsen
- Quantitative Biology Center (QBiC), University of Tübingen, 72076 Tübingen, Germany
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8
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Reich M, Spomer L, Klindt C, Fuchs K, Stindt J, Deutschmann K, Höhne J, Liaskou E, Hov JR, Karlsen TH, Beuers U, Verheij J, Ferreira-Gonzalez S, Hirschfield G, Forbes SJ, Schramm C, Esposito I, Nierhoff D, Fickert P, Fuchs CD, Trauner M, García-Beccaria M, Gabernet G, Nahnsen S, Mallm JP, Vogel M, Schoonjans K, Lautwein T, Köhrer K, Häussinger D, Luedde T, Heikenwalder M, Keitel V. Downregulation of TGR5 (GPBAR1) in biliary epithelial cells contributes to the pathogenesis of sclerosing cholangitis. J Hepatol 2021; 75:634-646. [PMID: 33872692 DOI: 10.1016/j.jhep.2021.03.029] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND & AIMS Primary sclerosing cholangitis (PSC) is characterized by chronic inflammation and progressive fibrosis of the biliary tree. The bile acid receptor TGR5 (GPBAR1) is found on biliary epithelial cells (BECs), where it promotes secretion, proliferation and tight junction integrity. Thus, we speculated that changes in TGR5-expression in BECs may contribute to PSC pathogenesis. METHODS TGR5-expression and -localization were analyzed in PSC livers and liver tissue, isolated bile ducts and BECs from Abcb4-/-, Abcb4-/-/Tgr5Tg and ursodeoxycholic acid (UDCA)- or 24-norursodeoxycholic acid (norUDCA)-fed Abcb4-/- mice. The effects of IL8/IL8 homologues on TGR5 mRNA and protein levels were studied. BEC gene expression was analyzed by single-cell transcriptomics (scRNA-seq) from distinct mouse models. RESULTS TGR5 mRNA expression and immunofluorescence staining intensity were reduced in BECs of PSC and Abcb4-/- livers, in Abcb4-/- extrahepatic bile ducts, but not in intrahepatic macrophages. No changes in TGR5 BEC fluorescence intensity were detected in liver tissue of other liver diseases, including primary biliary cholangitis. Incubation of BECs with IL8/IL8 homologues, but not with other cytokines, reduced TGR5 mRNA and protein levels. BECs from Abcb4-/- mice had lower levels of phosphorylated Erk and higher expression levels of Icam1, Vcam1 and Tgfβ2. Overexpression of Tgr5 abolished the activated inflammatory phenotype characteristic of Abcb4-/- BECs. NorUDCA-feeding restored TGR5-expression levels in BECs in Abcb4-/- livers. CONCLUSIONS Reduced TGR5 levels in BECs from patients with PSC and Abcb4-/- mice promote development of a reactive BEC phenotype, aggravate biliary injury and thus contribute to the pathogenesis of sclerosing cholangitis. Restoration of biliary TGR5-expression levels represents a previously unknown mechanism of action of norUDCA. LAY SUMMARY Primary sclerosing cholangitis (PSC) is a chronic cholestatic liver disease-associated with progressive inflammation of the bile duct, leading to fibrosis and end-stage liver disease. Bile acid (BA) toxicity may contribute to the development and disease progression of PSC. TGR5 is a membrane-bound receptor for BAs, which is found on bile ducts and protects bile ducts from BA toxicity. In this study, we show that TGR5 levels were reduced in bile ducts from PSC livers and in bile ducts from a genetic mouse model of PSC. Our investigations indicate that lower levels of TGR5 in bile ducts may contribute to PSC development and progression. Furthermore, treatment with norUDCA, a drug currently being tested in a phase III trial for PSC, restored TGR5 levels in biliary epithelial cells.
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Affiliation(s)
- Maria Reich
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Medical Faculty of Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Lina Spomer
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Medical Faculty of Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Caroline Klindt
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Medical Faculty of Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Katharina Fuchs
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Medical Faculty of Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Jan Stindt
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Medical Faculty of Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Kathleen Deutschmann
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Medical Faculty of Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Johanna Höhne
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Medical Faculty of Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Evaggelia Liaskou
- Centre for Liver and Gastrointestinal Research, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK; NIHR Birmingham Biomedical Research Centre, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Johannes R Hov
- Norwegian PSC Research Centre and Section of Gastroenterology at the Department of Transplantation Medicine, and Research Institute of Internal Medicine, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Tom H Karlsen
- Norwegian PSC Research Centre and Section of Gastroenterology at the Department of Transplantation Medicine, and Research Institute of Internal Medicine, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ulrich Beuers
- Department of Gastroenterology and Hepatology and Tytgat Institute for Liver and Intestinal Research and Department of Pathology, Amsterdam University Medical Centers, Location AMC, AGEM Amsterdam, The Netherlands
| | - Joanne Verheij
- Department of Gastroenterology and Hepatology and Tytgat Institute for Liver and Intestinal Research and Department of Pathology, Amsterdam University Medical Centers, Location AMC, AGEM Amsterdam, The Netherlands
| | | | - Gideon Hirschfield
- Toronto Centre for Liver Disease, Toronto General Hospital, Toronto, Canada
| | - Stuart J Forbes
- Centre for Regenerative Medicine, University of Edinburgh, UK
| | - Christoph Schramm
- I. Department of Medicine and Martin Zeitz Centre for Rare Diseases, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Irene Esposito
- Institute of Pathology, University Hospital Düsseldorf, Medical Faculty of Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Dirk Nierhoff
- Department of Gastroenterology and Hepatology, University of Cologne, Cologne, Germany
| | - Peter Fickert
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Claudia Daniela Fuchs
- Hans Popper Laboratory of Molecular Hepatology, Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - Michael Trauner
- Hans Popper Laboratory of Molecular Hepatology, Division of Gastroenterology and Hepatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
| | - María García-Beccaria
- Division of Chronic Inflammation and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany
| | - Gisela Gabernet
- Quantitative Biology Center (QBiC), Eberhard-Karls University of Tübingen, Tübingen, Germany
| | - Sven Nahnsen
- Quantitative Biology Center (QBiC), Eberhard-Karls University of Tübingen, Tübingen, Germany
| | - Jan-Philipp Mallm
- Single Cell Open Lab, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany
| | - Marina Vogel
- DKFZ Genomics and Proteomics Core Facility, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany
| | - Kristina Schoonjans
- Laboratory of Metabolic Signaling, Institute of Bioengineering, School of Life Sciences and School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Tobias Lautwein
- Genomics and Transcriptomics Laboratory, Biologisch-Medizinisches-Forschungszentrum (BMFZ), Heinrich Heine University Düsseldorf, Germany
| | - Karl Köhrer
- Genomics and Transcriptomics Laboratory, Biologisch-Medizinisches-Forschungszentrum (BMFZ), Heinrich Heine University Düsseldorf, Germany
| | - Dieter Häussinger
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Medical Faculty of Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Tom Luedde
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Medical Faculty of Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Mathias Heikenwalder
- Division of Chronic Inflammation and Cancer, German Cancer Research Center Heidelberg (DKFZ), Heidelberg, Germany
| | - Verena Keitel
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Düsseldorf, Medical Faculty of Heinrich Heine University Düsseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany.
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9
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Ruschil C, Gabernet G, Lepennetier G, Heumos S, Kaminski M, Hracsko Z, Irmler M, Beckers J, Ziemann U, Nahnsen S, Owens GP, Bennett JL, Hemmer B, Kowarik MC. Specific Induction of Double Negative B Cells During Protective and Pathogenic Immune Responses. Front Immunol 2020; 11:606338. [PMID: 33391273 PMCID: PMC7775384 DOI: 10.3389/fimmu.2020.606338] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/17/2020] [Indexed: 01/12/2023] Open
Abstract
Double negative (DN) (CD19+CD20lowCD27-IgD-) B cells are expanded in patients with autoimmune and infectious diseases; however their role in the humoral immune response remains unclear. Using systematic flow cytometric analyses of peripheral blood B cell subsets, we observed an inflated DN B cell population in patients with variety of active inflammatory conditions: myasthenia gravis, Guillain-Barré syndrome, neuromyelitis optica spectrum disorder, meningitis/encephalitis, and rheumatic disorders. Furthermore, we were able to induce DN B cells in healthy subjects following vaccination against influenza and tick borne encephalitis virus. Transcriptome analysis revealed a gene expression profile in DN B cells that clustered with naïve B cells, memory B cells, and plasmablasts. Immunoglobulin VH transcriptome sequencing and analysis of recombinant antibodies revealed clonal expansion of DN B cells that were targeted against the vaccine antigen. Our study suggests that DN B cells are expanded in multiple inflammatory neurologic diseases and represent an inducible B cell population that responds to antigenic stimulation, possibly through an extra-follicular maturation pathway.
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Affiliation(s)
- Christoph Ruschil
- Department of Neurology and Stroke, Eberhard-Karls University, Tübingen, Germany
- Hertie Institute for Clinical Brain Research, Eberhard-Karls University, Tübingen, Germany
| | - Gisela Gabernet
- Quantitative Biology Center (QBiC), Eberhard-Karls University of Tübingen, Tübingen, Germany
| | - Gildas Lepennetier
- Department of Neurology, Technische Universität München, Munich, Germany
| | - Simon Heumos
- Quantitative Biology Center (QBiC), Eberhard-Karls University of Tübingen, Tübingen, Germany
| | - Miriam Kaminski
- Department of Psychiatry and Psychotherapy, Charite Universitätsmedizin, Berlin, Germany
| | - Zsuzsanna Hracsko
- Department of Internal Medicine 1, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Martin Irmler
- Institute of Experimental Genetics, Helmholtz Zentrum München GmbH, Neuherberg, Germany
| | - Johannes Beckers
- Institute of Experimental Genetics, Helmholtz Zentrum München GmbH, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Chair of Experimental Genetics, Technische Universität München, Freising, Germany
| | - Ulf Ziemann
- Department of Neurology and Stroke, Eberhard-Karls University, Tübingen, Germany
- Hertie Institute for Clinical Brain Research, Eberhard-Karls University, Tübingen, Germany
| | - Sven Nahnsen
- Quantitative Biology Center (QBiC), Eberhard-Karls University of Tübingen, Tübingen, Germany
| | - Gregory P. Owens
- Department of Biochemistry and Molecular Genetics, University of Colorado, Aurora, CO, United States
| | - Jeffrey L. Bennett
- Department of Neurology, Programs in Neuroscience and Immunology University of Colorado School of Medicine, Aurora, CO, United States
- Department of Ophthalmology, Programs in Neuroscience and Immunology University of Colorado School of Medicine, Aurora, CO, United States
| | - Bernhard Hemmer
- Department of Neurology, Technische Universität München, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Markus C. Kowarik
- Department of Neurology and Stroke, Eberhard-Karls University, Tübingen, Germany
- Hertie Institute for Clinical Brain Research, Eberhard-Karls University, Tübingen, Germany
- Department of Neurology, Technische Universität München, Munich, Germany
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10
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Müller AT, Posselt G, Gabernet G, Neuhaus C, Bachler S, Blatter M, Pfeiffer B, Hiss JA, Dittrich PS, Altmann KH, Wessler S, Schneider G. Morphing of Amphipathic Helices to Explore the Activity and Selectivity of Membranolytic Antimicrobial Peptides. Biochemistry 2020; 59:3772-3781. [PMID: 32936629 PMCID: PMC7547863 DOI: 10.1021/acs.biochem.0c00565] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/07/2020] [Indexed: 01/17/2023]
Abstract
Naturally occurring membranolytic antimicrobial peptides (AMPs) are rarely cell-type selective and highly potent at the same time. Template-based peptide design can be used to generate AMPs with improved properties de novo. Following this approach, 18 linear peptides were obtained by computationally morphing the natural AMP Aurein 2.2d2 GLFDIVKKVVGALG into the synthetic model AMP KLLKLLKKLLKLLK. Eleven of the 18 chimeric designs inhibited the growth of Staphylococcus aureus, and six peptides were tested and found to be active against one resistant pathogenic strain or more. One of the peptides was broadly active against bacterial and fungal pathogens without exhibiting toxicity to certain human cell lines. Solution nuclear magnetic resonance and molecular dynamics simulation suggested an oblique-oriented membrane insertion mechanism of this helical de novo peptide. Temperature-resolved circular dichroism spectroscopy pointed to conformational flexibility as an essential feature of cell-type selective AMPs.
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Affiliation(s)
- Alex T. Müller
- Department
of Chemistry and Applied Biosciences, ETH
Zurich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Gernot Posselt
- Department
of Biosciences, Division of Microbiology, Paris Lodron University of Salzburg, Billrothstrasse 11, 5020 Salzburg, Austria
| | - Gisela Gabernet
- Department
of Chemistry and Applied Biosciences, ETH
Zurich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Claudia Neuhaus
- Department
of Chemistry and Applied Biosciences, ETH
Zurich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Simon Bachler
- Department
of Biosystems Science and Engineering, ETH
Zurich, Mattenstrasse
26, 4058 Basel, Switzerland
| | - Markus Blatter
- Novartis
Institutes for BioMedical Research, Novartis
Pharma AG, Novartis Campus, 4002 Basel, Switzerland
| | - Bernhard Pfeiffer
- Department
of Chemistry and Applied Biosciences, ETH
Zurich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Jan A. Hiss
- Department
of Chemistry and Applied Biosciences, ETH
Zurich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Petra S. Dittrich
- Department
of Biosystems Science and Engineering, ETH
Zurich, Mattenstrasse
26, 4058 Basel, Switzerland
| | - Karl-Heinz Altmann
- Department
of Chemistry and Applied Biosciences, ETH
Zurich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
| | - Silja Wessler
- Department
of Biosciences, Division of Microbiology, Paris Lodron University of Salzburg, Billrothstrasse 11, 5020 Salzburg, Austria
| | - Gisbert Schneider
- Department
of Chemistry and Applied Biosciences, ETH
Zurich, Vladimir-Prelog-Weg 4, 8093 Zürich, Switzerland
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11
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Lam WLM, Gabernet G, Poth T, De Ponti A, Saborowski A, Nahnsen S, Schneller D, Angel P. Abstract 5728: Liver progenitor cells induces fibrosis via RAGE signaling upon liver injury. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-5728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Liver fibrosis is characterized by hepatic stellate cell activation and extracellular matrix deposition upon persistent injury and inflammation, which can impair hepatic function and its ability to regenerate. The origin and physiological role of facultative liver progenitor cells (LPCs) have been a controversial issue as it was found to be a major player to regenerate the damaged liver, but it is also associated with fibrosis, disease progression or tumor initiation.
The receptor for advanced glycation end products (RAGE) signaling axis is often associated with chronic inflammation-associated tissue damage and plays an essential role in modulating the tumor microenvironment. Our previous data suggested that RAGE mediates LPC expansion, onset of liver fibrosis and HCC formation (Pusterla et al. Hepatology. 2013.) Hence, in this study, we seek to delineate the functional role and underlying mechanism of RAGE activity in LPC activation in response to inflammation-associated liver injury.
R26TomHnf1β-CreER transgenic mice were crossed with Rage flox/flox (Ragefl/fl) mice to generate tamoxifen-inducible LPC-specific RAGE knockout mice (RAGEΔLPC). They were exposed to a choline-deficient ethionine-supplemented (CDE) diet for three weeks to induce liver damage. Ablation of RAGE in LPCs strongly impairs LPC expanding capacities in CDE diet-treated mice. Strikingly, this is accompanied by reduction of activated hepatic stellate cells and bridging fibrosis. This demonstrated that RAGE signaling in LPCs is a mediator of liver fibrosis in vivo.
Necroinflammation is known to be associated with liver fibrosis. To investigate the role of RAGE in LPCs in the context of necroinflammation in vitro, primary LPCs were isolated from CDE-treated Ragefl/fl C57BL/6 mouse. Wildtype and knockout Rage cell lines were established. LPCs were stimulated with supernatants from necrotic hepatocytes followed by whole transcriptome sequencing to identify downstream targets of RAGE-dependent pathways. Stress response, inflammatory and pro-fibrotic pathways were enriched in LPCs upon treatment with necrotic medium. Most interestingly, signaling pathways that regulate organ size, tissue homeostasis and cell survival were found to be RAGE-dependent. Moreover, clusters of stem cell renewal-related genes were deregulated upon ablation of RAGE. In line with the whole transcriptome profile, we demonstrated that ablation of RAGE attenuates LPCs organoid-forming ability, implying that RAGE regulates stemness properties of LPCs.
Our recent results demonstrated that RAGE is required for LPCs activation and proliferation, as well as the crosstalk with stellate cells in supporting fibrogenesis. Taken together, our data uncovers a potential mechanistic insight on the role of RAGE in LPCs in association with fibrosis upon chronic liver injury.
Citation Format: Wai Ling Macrina Lam, Gisela Gabernet, Tanja Poth, Aurora De Ponti, Anna Saborowski, Sven Nahnsen, Doris Schneller, Peter Angel. Liver progenitor cells induces fibrosis via RAGE signaling upon liver injury [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5728.
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Affiliation(s)
| | | | - Tanja Poth
- 3University Hospital Heidelberg, Heidelberg, Germany
| | | | | | - Sven Nahnsen
- 2Eberhard Karls University of Tübingen, Tübingen, Germany
| | | | - Peter Angel
- 1German Cancer Research Center, Heidelberg, Germany
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12
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Gabernet G, Gautschi D, Müller AT, Neuhaus CS, Armbrecht L, Dittrich PS, Hiss JA, Schneider G. In silico design and optimization of selective membranolytic anticancer peptides. Sci Rep 2019; 9:11282. [PMID: 31375699 PMCID: PMC6677754 DOI: 10.1038/s41598-019-47568-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [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: 12/20/2018] [Accepted: 06/17/2019] [Indexed: 12/31/2022] Open
Abstract
Membranolytic anticancer peptides represent a potential strategy in the fight against cancer. However, our understanding of the underlying structure-activity relationships and the mechanisms driving their cell selectivity is still limited. We developed a computational approach as a step towards the rational design of potent and selective anticancer peptides. This machine learning model distinguishes between peptides with and without anticancer activity. This classifier was experimentally validated by synthesizing and testing a selection of 12 computationally generated peptides. In total, 83% of these predictions were correct. We then utilized an evolutionary molecular design algorithm to improve the peptide selectivity for cancer cells. This simulated molecular evolution process led to a five-fold selectivity increase with regard to human dermal microvascular endothelial cells and more than ten-fold improvement towards human erythrocytes. The results of the present study advocate for the applicability of machine learning models and evolutionary algorithms to design and optimize novel synthetic anticancer peptides with reduced hemolytic liability and increased cell-type selectivity.
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Affiliation(s)
- Gisela Gabernet
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Damian Gautschi
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Alex T Müller
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Claudia S Neuhaus
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Lucas Armbrecht
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Petra S Dittrich
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Jan A Hiss
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland.
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13
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Grisoni F, Neuhaus CS, Hishinuma M, Gabernet G, Hiss JA, Kotera M, Schneider G. De novo design of anticancer peptides by ensemble artificial neural networks. J Mol Model 2019; 25:112. [PMID: 30953170 DOI: 10.1007/s00894-019-4007-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 03/21/2019] [Indexed: 12/17/2022]
Abstract
Membranolytic anticancer peptides (ACPs) are drawing increasing attention as potential future therapeutics against cancer, due to their ability to hinder the development of cellular resistance and their potential to overcome common hurdles of chemotherapy, e.g., side effects and cytotoxicity. In this work, we present an ensemble machine learning model to design potent ACPs. Four counter-propagation artificial neural-networks were trained to identify peptides that kill breast and/or lung cancer cells. For prospective application of the ensemble model, we selected 14 peptides from a total of 1000 de novo designs, for synthesis and testing in vitro on breast cancer (MCF7) and lung cancer (A549) cell lines. Six de novo designs showed anticancer activity in vitro, five of which against both MCF7 and A549 cell lines. The novel active peptides populate uncharted regions of ACP sequence space.
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Affiliation(s)
- Francesca Grisoni
- Department of Chemistry and Applied Biosciences, RETHINK, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland. .,Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126, Milan, Italy.
| | - Claudia S Neuhaus
- Department of Chemistry and Applied Biosciences, RETHINK, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Miyabi Hishinuma
- Department of Chemistry and Applied Biosciences, RETHINK, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland.,Department of Chemical System Engineering, School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,School of Life Science and Technology, Tokyo Institute of Technology, 1-11-5, Midorigaoka, Meguro-ku, Tokyo, 152-0034, Japan
| | - Gisela Gabernet
- Department of Chemistry and Applied Biosciences, RETHINK, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Jan A Hiss
- Department of Chemistry and Applied Biosciences, RETHINK, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Masaaki Kotera
- Department of Chemical System Engineering, School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences, RETHINK, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland.
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14
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Neuhaus CS, Gabernet G, Steuer C, Root K, Hiss JA, Zenobi R, Schneider G. Simulated Molecular Evolution for Anticancer Peptide Design. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201811215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Claudia S. Neuhaus
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH) Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Gisela Gabernet
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH) Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Christian Steuer
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH) Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Katharina Root
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH) Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Jan A. Hiss
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH) Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH) Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Gisbert Schneider
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH) Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
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15
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Neuhaus CS, Gabernet G, Steuer C, Root K, Hiss JA, Zenobi R, Schneider G. Simulated Molecular Evolution for Anticancer Peptide Design. Angew Chem Int Ed Engl 2019; 58:1674-1678. [DOI: 10.1002/anie.201811215] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 11/01/2018] [Indexed: 02/01/2023]
Affiliation(s)
- Claudia S. Neuhaus
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH) Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Gisela Gabernet
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH) Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Christian Steuer
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH) Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Katharina Root
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH) Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Jan A. Hiss
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH) Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH) Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Gisbert Schneider
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH) Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
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16
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Grisoni F, Neuhaus CS, Gabernet G, Müller AT, Hiss JA, Schneider G. Front Cover: Designing Anticancer Peptides by Constructive Machine Learning (ChemMedChem 13/2018). ChemMedChem 2018. [DOI: 10.1002/cmdc.201800415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Francesca Grisoni
- Swiss Federal Institute of Technology (ETH); Department of Chemistry and Applied Biosciences; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
- University of Milano-Bicocca; Milano Chemometrics & QSAR Research Group; Department of Earth and Environmental Sciences; 20126 Milan Italy
| | - Claudia S. Neuhaus
- Swiss Federal Institute of Technology (ETH); Department of Chemistry and Applied Biosciences; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Gisela Gabernet
- Swiss Federal Institute of Technology (ETH); Department of Chemistry and Applied Biosciences; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Alex T. Müller
- Swiss Federal Institute of Technology (ETH); Department of Chemistry and Applied Biosciences; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Jan A. Hiss
- Swiss Federal Institute of Technology (ETH); Department of Chemistry and Applied Biosciences; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Gisbert Schneider
- Swiss Federal Institute of Technology (ETH); Department of Chemistry and Applied Biosciences; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
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17
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Grisoni F, Neuhaus CS, Gabernet G, Müller AT, Hiss JA, Schneider G. Designing Anticancer Peptides by Constructive Machine Learning. ChemMedChem 2018; 13:1300-1302. [DOI: 10.1002/cmdc.201800204] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Indexed: 11/07/2022]
Affiliation(s)
- Francesca Grisoni
- Swiss Federal Institute of Technology (ETH); Department of Chemistry and Applied Biosciences; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
- University of Milano-Bicocca; Milano Chemometrics & QSAR Research Group; Department of Earth and Environmental Sciences; 20126 Milan Italy
| | - Claudia S. Neuhaus
- Swiss Federal Institute of Technology (ETH); Department of Chemistry and Applied Biosciences; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Gisela Gabernet
- Swiss Federal Institute of Technology (ETH); Department of Chemistry and Applied Biosciences; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Alex T. Müller
- Swiss Federal Institute of Technology (ETH); Department of Chemistry and Applied Biosciences; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Jan A. Hiss
- Swiss Federal Institute of Technology (ETH); Department of Chemistry and Applied Biosciences; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Gisbert Schneider
- Swiss Federal Institute of Technology (ETH); Department of Chemistry and Applied Biosciences; Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
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18
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Armbrecht L, Gabernet G, Kurth F, Hiss JA, Schneider G, Dittrich PS. Characterisation of anticancer peptides at the single-cell level. Lab Chip 2017; 17:2933-2940. [PMID: 28736788 PMCID: PMC6440648 DOI: 10.1039/c7lc00505a] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The development of efficacious anticancer therapeutics is difficult due to the heterogeneity of the cellular response to chemotherapy. Anticancer peptides (ACPs) are promising drug candidates that have been shown to be active against a range of cancer cells. However, few ACP studies focus on tumour single-cell heterogeneities. In order to address this need, we developed a microfluidic device and an imaging procedure that enable the capture, monitoring, and analysis of several hundred single cells for the study of drug response. MCF-7 human breast adenocarcinoma cells were captured in hydrodynamic traps and isolated in individual microchambers of less than 100 pL volume. With pneumatic valves, different sets of microchambers were actuated to expose the cells to various drugs. Here, the effect of three membranolytic ACPs - melittin, aurein 1.2 and aurein 2.2 - was investigated by monitoring the efflux of calcein from single MCF-7 cells. The loss of membrane integrity was observed with two different strategies that allow either focusing on one cell for mechanistic studies or parallel analysis of hundreds of individual cells. In general, the device is applicable to the analysis of the effect of various drugs on a large number of different cell types. The platform will enable us in the future to determine the origin of heterogeneous responses on pharmacological substances like ACPs within cell populations by combining it with other on-chip analytical methods.
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Affiliation(s)
- L Armbrecht
- Department of Biosystems Science and Engineering, ETH Zurich, Switzerland.
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19
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Müller AT, Gabernet G, Hiss JA, Schneider G. modlAMP: Python for antimicrobial peptides. Bioinformatics 2017; 33:2753-2755. [DOI: 10.1093/bioinformatics/btx285] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 04/22/2017] [Indexed: 01/01/2023] Open
Affiliation(s)
- Alex T Müller
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland
| | - Gisela Gabernet
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland
| | - Jan A Hiss
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland
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20
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Müller AT, Kaymaz AC, Gabernet G, Posselt G, Wessler S, Hiss JA, Schneider G. Sparse Neural Network Models of Antimicrobial Peptide-Activity Relationships. Mol Inform 2016; 35:606-614. [DOI: 10.1002/minf.201600029] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 06/13/2016] [Indexed: 01/07/2023]
Affiliation(s)
- Alex T. Müller
- Swiss Federal Institute of Technology (ETH); Department of Chemistry and Applied Biosciences; Vladimir-Prelog-Weg 4 CH-8093 Zurich Switzerland
| | - Aral C. Kaymaz
- Swiss Federal Institute of Technology (ETH); Department of Chemistry and Applied Biosciences; Vladimir-Prelog-Weg 4 CH-8093 Zurich Switzerland
| | - Gisela Gabernet
- Swiss Federal Institute of Technology (ETH); Department of Chemistry and Applied Biosciences; Vladimir-Prelog-Weg 4 CH-8093 Zurich Switzerland
| | - Gernot Posselt
- Department of Molecular Biology, Division of Microbiology, Paris Lodron; University of Salzburg; Billrothstr. 11 A-5020 Salzburg Austria
| | - Silja Wessler
- Department of Molecular Biology, Division of Microbiology, Paris Lodron; University of Salzburg; Billrothstr. 11 A-5020 Salzburg Austria
| | - Jan A. Hiss
- Swiss Federal Institute of Technology (ETH); Department of Chemistry and Applied Biosciences; Vladimir-Prelog-Weg 4 CH-8093 Zurich Switzerland
| | - Gisbert Schneider
- Swiss Federal Institute of Technology (ETH); Department of Chemistry and Applied Biosciences; Vladimir-Prelog-Weg 4 CH-8093 Zurich Switzerland
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21
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Schneider P, Müller AT, Gabernet G, Button AL, Posselt G, Wessler S, Hiss JA, Schneider G. Hybrid Network Model for "Deep Learning" of Chemical Data: Application to Antimicrobial Peptides. Mol Inform 2016; 36. [PMID: 28124834 DOI: 10.1002/minf.201600011] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Accepted: 02/24/2016] [Indexed: 01/26/2023]
Abstract
We present a "deep" network architecture for chemical data analysis and classification together with a prospective proof-of-concept application. The model features a self-organizing map (SOM) as the input layer of a feedforward neural network. The SOM converts molecular descriptors to a two-dimensional image for further processing. We implemented lateral neuron inhibition for contrast enhancement. The model achieved improved classification accuracy and predictive robustness compared to feedforward network classifiers lacking the SOM layer. By nonlinear dimensionality reduction the networks extracted meaningful chemical features from the data and outperformed linear principal component analysis (PCA). The learning machine was trained on the sequence-length independent recognition of antibacterial peptides and correctly predicted the killing activity of a synthetic test peptide against Staphylococcus aureus in an in vitro experiment.
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Affiliation(s)
- Petra Schneider
- Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, CH-8093, Zurich, Switzerland.,inSili.com LLC, Segantinisteig 3, CH-8049, Zurich, Switzerland
| | - Alex T Müller
- Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, CH-8093, Zurich, Switzerland
| | - Gisela Gabernet
- Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, CH-8093, Zurich, Switzerland
| | - Alexander L Button
- Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, CH-8093, Zurich, Switzerland
| | - Gernot Posselt
- Paris-Lodron Universität Salzburg, Division of Microbiology, Billroth Str. 11, A-5020 Salzburg, Austria
| | - Silja Wessler
- Paris-Lodron Universität Salzburg, Division of Microbiology, Billroth Str. 11, A-5020 Salzburg, Austria
| | - Jan A Hiss
- Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, CH-8093, Zurich, Switzerland
| | - Gisbert Schneider
- Swiss Federal Institute of Technology (ETH), Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, CH-8093, Zurich, Switzerland
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22
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Abstract
Understanding the structure–activity relationships and mechanisms of action of membranolytic anticancer peptides could help them advance to therapeutic success.
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Affiliation(s)
- G. Gabernet
- Department of Chemistry and Applied Biosciences
- Swiss Federal Institute of Technology (ETH)
- CH-8093 Zurich
- Switzerland
| | - A. T. Müller
- Department of Chemistry and Applied Biosciences
- Swiss Federal Institute of Technology (ETH)
- CH-8093 Zurich
- Switzerland
| | - J. A. Hiss
- Department of Chemistry and Applied Biosciences
- Swiss Federal Institute of Technology (ETH)
- CH-8093 Zurich
- Switzerland
| | - G. Schneider
- Department of Chemistry and Applied Biosciences
- Swiss Federal Institute of Technology (ETH)
- CH-8093 Zurich
- Switzerland
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23
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Rodrigues T, Reker D, Welin M, Caldera M, Brunner C, Gabernet G, Schneider P, Walse B, Schneider G. De Novo Fragment Design for Drug Discovery and Chemical Biology. Angew Chem Int Ed Engl 2015; 54:15079-83. [DOI: 10.1002/anie.201508055] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Indexed: 01/08/2023]
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24
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Rodrigues T, Reker D, Welin M, Caldera M, Brunner C, Gabernet G, Schneider P, Walse B, Schneider G. De-novo-Fragmententwurf für die Wirkstoffforschung und chemische Biologie. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201508055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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25
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Gang A, Gabernet G, Renner LD, Baraban L, Cuniberti G. A simple two-step silane-based (bio-) receptor molecule immobilization without additional binding site passivation. RSC Adv 2015. [DOI: 10.1039/c5ra04469c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Immobilizing (bio-) receptor molecules via 3-(triethoxysilyl)propylsuccinic anhydride makes subsequent binding site blocking dispensable, while maintaining receptor specificity for target analytes.
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Affiliation(s)
- A. Gang
- Institute for Materials Science and Max Bergmann Center of Biomaterials TU Dresden
- 01062 Dresden
- Germany
- Center for Advancing Electronics Dresden
- TU Dresden
| | - G. Gabernet
- Institute for Materials Science and Max Bergmann Center of Biomaterials TU Dresden
- 01062 Dresden
- Germany
| | - L. D. Renner
- Institute for Materials Science and Max Bergmann Center of Biomaterials TU Dresden
- 01062 Dresden
- Germany
- Leibniz Institute of Polymer Research Dresden and the Max-Bergmann Center of Biomaterials
- 01069 Dresden
| | - L. Baraban
- Institute for Materials Science and Max Bergmann Center of Biomaterials TU Dresden
- 01062 Dresden
- Germany
| | - G. Cuniberti
- Institute for Materials Science and Max Bergmann Center of Biomaterials TU Dresden
- 01062 Dresden
- Germany
- Center for Advancing Electronics Dresden
- TU Dresden
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26
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Iglesias-Guimarais V, Gil-Guiñon E, Gabernet G, García-Belinchón M, Sánchez-Osuna M, Casanelles E, Comella JX, Yuste VJ. Apoptotic DNA degradation into oligonucleosomal fragments, but not apoptotic nuclear morphology, relies on a cytosolic pool of DFF40/CAD endonuclease. J Biol Chem 2012; 287:7766-79. [PMID: 22253444 DOI: 10.1074/jbc.m111.290718] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Apoptotic cell death is characterized by nuclear fragmentation and oligonucleosomal DNA degradation, mediated by the caspase-dependent specific activation of DFF40/CAD endonuclease. Here, we describe how, upon apoptotic stimuli, SK-N-AS human neuroblastoma-derived cells show apoptotic nuclear morphology without displaying concomitant internucleosomal DNA fragmentation. Cytotoxicity afforded after staurosporine treatment is comparable with that obtained in SH-SY5Y cells, which exhibit a complete apoptotic phenotype. SK-N-AS cell death is a caspase-dependent process that can be impaired by the pan-caspase inhibitor q-VD-OPh. The endogenous inhibitor of DFF40/CAD, ICAD, is correctly processed, and dff40/cad cDNA sequence does not reveal mutations altering its amino acid composition. Biochemical approaches show that both SH-SY5Y and SK-N-AS resting cells express comparable levels of DFF40/CAD. However, the endonuclease is poorly expressed in the cytosolic fraction of healthy SK-N-AS cells. Despite this differential subcellular distribution of DFF40/CAD, we find no differences in the subcellular localization of both pro-caspase-3 and ICAD between the analyzed cell lines. After staurosporine treatment, the preferential processing of ICAD in the cytosolic fraction allows the translocation of DFF40/CAD from this fraction to a chromatin-enriched one. Therefore, the low levels of cytosolic DFF40/CAD detected in SK-N-AS cells determine the absence of DNA laddering after staurosporine treatment. In these cells DFF40/CAD cytosolic levels can be restored by the overexpression of their own endonuclease, which is sufficient to make them proficient at degrading their chromatin into oligonucleosome-size fragments after staurosporine treatment. Altogether, the cytosolic levels of DFF40/CAD are determinants in achieving a complete apoptotic phenotype, including oligonucleosomal DNA degradation.
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Affiliation(s)
- Victoria Iglesias-Guimarais
- Cell Death, Senescence, and Survival Group, Departament de Bioquimica i Biologia Molecular and Institut de Neurociencies, Facultat de Medicina, Universitat Autonoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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