1
|
Kubiniok P, Marcu A, Bichmann L, Kuchenbecker L, Schuster H, Hamelin DJ, Duquette JD, Kovalchik KA, Wessling L, Kohlbacher O, Rammensee HG, Neidert MC, Sirois I, Caron E. Understanding the constitutive presentation of MHC class I immunopeptidomes in primary tissues. iScience 2022; 25:103768. [PMID: 35141507 PMCID: PMC8810409 DOI: 10.1016/j.isci.2022.103768] [Citation(s) in RCA: 3] [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: 11/10/2020] [Revised: 06/15/2021] [Accepted: 01/11/2022] [Indexed: 12/20/2022] Open
Abstract
Understanding the molecular principles that govern the composition of the MHC-I immunopeptidome across different primary tissues is fundamentally important to predict how T cells respond in different contexts in vivo. Here, we performed a global analysis of the MHC-I immunopeptidome from 29 to 19 primary human and mouse tissues, respectively. First, we observed that different HLA-A, HLA-B, and HLA-C allotypes do not contribute evenly to the global composition of the MHC-I immunopeptidome across multiple human tissues. Second, we found that tissue-specific and housekeeping MHC-I peptides share very distinct properties. Third, we discovered that proteins that are evolutionarily hyperconserved represent the primary source of the MHC-I immunopeptidome at the organism-wide scale. Fourth, we uncovered new components of the antigen processing and presentation network, including the carboxypeptidases CPE, CNDP1/2, and CPVL. Together, this study opens up new avenues toward a system-wide understanding of antigen presentation in vivo across mammalian species. Tissue-specific and housekeeping MHC class I peptides share distinct properties HLA-A, HLA-B, and HLA-C allotypes contribute very unevenly to the pool of class I peptides MHC-I immunopeptidomes are represented by evolutionarily conserved proteins An extended antigen processing and presentation pathway is uncovered
Collapse
Affiliation(s)
- Peter Kubiniok
- CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada
| | - Ana Marcu
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Baden-Württemberg, Germany
- Cluster of Excellence iFIT (EXC 2180), “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, 72076 Tübingen, Baden-Württemberg, Germany
| | - Leon Bichmann
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Baden-Württemberg, Germany
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, 72074 Tübingen, Baden-Württemberg, Germany
| | - Leon Kuchenbecker
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, 72074 Tübingen, Baden-Württemberg, Germany
| | - Heiko Schuster
- Immatics Biotechnologies GmbH, 72076 Tübingen, Baden-Württemberg, Germany
| | - David J. Hamelin
- CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada
| | | | | | - Laura Wessling
- CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada
| | - Oliver Kohlbacher
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, 72074 Tübingen, Baden-Württemberg, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, 72076 Tübingen, Baden-Württemberg, Germany
- Biomolecular Interactions, Max Planck Institute for Developmental Biology, 72076 Tübingen, Baden-Württemberg, Germany
- Cluster of Excellence Machine Learning in the Sciences (EXC 2064), University of Tübingen, 72074 Tübingen, Baden-Württemberg, Germany
- Translational Bioinformatics, University Hospital Tübingen, 72076 Tübingen, Baden-Württemberg, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, 72076 Tübingen, Baden-Württemberg, Germany
- Cluster of Excellence iFIT (EXC 2180), “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, 72076 Tübingen, Baden-Württemberg, Germany
- DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), 72076 Tübingen, Baden-Württemberg, Germany
| | - Marian C. Neidert
- Clinical Neuroscience Center and Department of Neurosurgery, University Hospital and University of Zürich, 8057&8091 Zürich, Switzerland
| | - Isabelle Sirois
- CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada
| | - Etienne Caron
- CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada
- Department of Pathology and Cellular Biology, Faculty of Medicine, Université de Montréal, QC H3T 1J4, Canada
- Corresponding author
| |
Collapse
|
2
|
Bichmann L, Gupta S, Rosenberger G, Kuchenbecker L, Sachsenberg T, Ewels P, Alka O, Pfeuffer J, Kohlbacher O, Röst H. DIAproteomics: A Multifunctional Data Analysis Pipeline for Data-Independent Acquisition Proteomics and Peptidomics. J Proteome Res 2021; 20:3758-3766. [PMID: 34153189 DOI: 10.1021/acs.jproteome.1c00123] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Data-independent acquisition (DIA) is becoming a leading analysis method in biomedical mass spectrometry. The main advantages include greater reproducibility and sensitivity and a greater dynamic range compared with data-dependent acquisition (DDA). However, the data analysis is complex and often requires expert knowledge when dealing with large-scale data sets. Here we present DIAproteomics, a multifunctional, automated, high-throughput pipeline implemented in the Nextflow workflow management system that allows one to easily process proteomics and peptidomics DIA data sets on diverse compute infrastructures. The central components are well-established tools such as the OpenSwathWorkflow for the DIA spectral library search and PyProphet for the false discovery rate assessment. In addition, it provides options to generate spectral libraries from existing DDA data and to carry out the retention time and chromatogram alignment. The output includes annotated tables and diagnostic visualizations from the statistical postprocessing and computation of fold-changes across pairwise conditions, predefined in an experimental design. DIAproteomics is well documented open-source software and is available under a permissive license to the scientific community at https://www.openms.de/diaproteomics/.
Collapse
Affiliation(s)
- Leon Bichmann
- Department of Computer Science, Applied Bioinformatics, University of Tübingen, Tübingen 72076, Germany.,Institute for Cell Biology, Department of Immunology, University of Tübingen, Tübingen 72076, Germany
| | - Shubham Gupta
- Donnelly Center for Biomolecular Research, University of Toronto, Toronto, Ontario ON M5S 3E1, Canada
| | - George Rosenberger
- Department of Systems Biology, Columbia University, New York, New York 10032, United States
| | - Leon Kuchenbecker
- Department of Computer Science, Applied Bioinformatics, University of Tübingen, Tübingen 72076, Germany
| | - Timo Sachsenberg
- Department of Computer Science, Applied Bioinformatics, University of Tübingen, Tübingen 72076, Germany
| | - Phil Ewels
- Science for Life Laboratory (SciLifeLab), Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Oliver Alka
- Department of Computer Science, Applied Bioinformatics, University of Tübingen, Tübingen 72076, Germany
| | - Julianus Pfeuffer
- Department of Computer Science, Applied Bioinformatics, University of Tübingen, Tübingen 72076, Germany.,Institute for Informatics, Freie Universität Berlin, Berlin 14195, Germany.,Zuse Institute Berlin, Berlin 14195, Germany
| | - Oliver Kohlbacher
- Department of Computer Science, Applied Bioinformatics, University of Tübingen, Tübingen 72076, Germany.,Institute for Biological and Medical Informatics, University of Tübingen, Tübingen 72076, Germany.,Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen 72076, Germany
| | - Hannes Röst
- Donnelly Center for Biomolecular Research, University of Toronto, Toronto, Ontario ON M5S 3E1, Canada
| |
Collapse
|
3
|
Marcu A, Bichmann L, Kuchenbecker L, Kowalewski DJ, Freudenmann LK, Backert L, Mühlenbruch L, Szolek A, Lübke M, Wagner P, Engler T, Matovina S, Wang J, Hauri-Hohl M, Martin R, Kapolou K, Walz JS, Velz J, Moch H, Regli L, Silginer M, Weller M, Löffler MW, Erhard F, Schlosser A, Kohlbacher O, Stevanović S, Rammensee HG, Neidert MC. HLA Ligand Atlas: a benign reference of HLA-presented peptides to improve T-cell-based cancer immunotherapy. J Immunother Cancer 2021; 9:e002071. [PMID: 33858848 PMCID: PMC8054196 DOI: 10.1136/jitc-2020-002071] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [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] [Accepted: 02/25/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The human leucocyte antigen (HLA) complex controls adaptive immunity by presenting defined fractions of the intracellular and extracellular protein content to immune cells. Understanding the benign HLA ligand repertoire is a prerequisite to define safe T-cell-based immunotherapies against cancer. Due to the poor availability of benign tissues, if available, normal tissue adjacent to the tumor has been used as a benign surrogate when defining tumor-associated antigens. However, this comparison has proven to be insufficient and even resulted in lethal outcomes. In order to match the tumor immunopeptidome with an equivalent counterpart, we created the HLA Ligand Atlas, the first extensive collection of paired HLA-I and HLA-II immunopeptidomes from 227 benign human tissue samples. This dataset facilitates a balanced comparison between tumor and benign tissues on HLA ligand level. METHODS Human tissue samples were obtained from 16 subjects at autopsy, five thymus samples and two ovary samples originating from living donors. HLA ligands were isolated via immunoaffinity purification and analyzed in over 1200 liquid chromatography mass spectrometry runs. Experimentally and computationally reproducible protocols were employed for data acquisition and processing. RESULTS The initial release covers 51 HLA-I and 86 HLA-II allotypes presenting 90,428 HLA-I- and 142,625 HLA-II ligands. The HLA allotypes are representative for the world population. We observe that immunopeptidomes differ considerably between tissues and individuals on source protein and HLA-ligand level. Moreover, we discover 1407 HLA-I ligands from non-canonical genomic regions. Such peptides were previously described in tumors, peripheral blood mononuclear cells (PBMCs), healthy lung tissues and cell lines. In a case study in glioblastoma, we show that potential on-target off-tumor adverse events in immunotherapy can be avoided by comparing tumor immunopeptidomes to the provided multi-tissue reference. CONCLUSION Given that T-cell-based immunotherapies, such as CAR-T cells, affinity-enhanced T cell transfer, cancer vaccines and immune checkpoint inhibition, have significant side effects, the HLA Ligand Atlas is the first step toward defining tumor-associated targets with an improved safety profile. The resource provides insights into basic and applied immune-associated questions in the context of cancer immunotherapy, infection, transplantation, allergy and autoimmunity. It is publicly available and can be browsed in an easy-to-use web interface at https://hla-ligand-atlas.org .
Collapse
Affiliation(s)
- Ana Marcu
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Leon Bichmann
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Leon Kuchenbecker
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Daniel Johannes Kowalewski
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Lena Katharina Freudenmann
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
| | - Linus Backert
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Lena Mühlenbruch
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
| | - András Szolek
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Maren Lübke
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Philipp Wagner
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Department of Obstetrics and Gynecology, University Hospital of Tübingen, Tübingen, Germany
| | - Tobias Engler
- Department of Obstetrics and Gynecology, University Hospital of Tübingen, Tübingen, Germany
| | - Sabine Matovina
- Department of Obstetrics and Gynecology, University Hospital of Tübingen, Tübingen, Germany
| | - Jian Wang
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Mathias Hauri-Hohl
- Pediatric Stem Cell Transplantation, University Children's Hospital Zurich, Zurich, Switzerland
| | - Roland Martin
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Konstantina Kapolou
- Clinical Neuroscience Center and Department of Neurosurgery, University Hospital and University of Zurich, Zurich, Switzerland
| | - Juliane Sarah Walz
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), University Hospital of Tübingen, Tübingen, Germany
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology (IKP) and Robert Bosch Center for Tumor Diseases (RBCT), Stuttgart, Germany
| | - Julia Velz
- Clinical Neuroscience Center and Department of Neurosurgery, University Hospital and University of Zurich, Zurich, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Luca Regli
- Clinical Neuroscience Center and Department of Neurosurgery, University Hospital and University of Zurich, Zurich, Switzerland
| | - Manuela Silginer
- Clinical Neuroscience Center and Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Michael Weller
- Clinical Neuroscience Center and Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Markus W Löffler
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
- Department of General, Visceral and Transplant Surgery, University Hospital of Tübingen, Tübingen, Germany
- Department of Clinical Pharmacology, University of Hospital Tübingen, Tübingen, Germany
| | - Florian Erhard
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Bayern, Germany
| | - Andreas Schlosser
- Rudolf Virchow Center - Center for Integrative and Translational Bioimaging, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Oliver Kohlbacher
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, Germany
- DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
- Quantitative Biology Center (QBiC), University of Tübingen, Tübingen, Germany
- Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, Germany
- Cluster of Excellence Machine Learning in the Sciences (EXC 2064), University of Tübingen, Tübingen, Germany
- Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany
| | - Stefan Stevanović
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
- DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany
| | - Marian Christoph Neidert
- Clinical Neuroscience Center and Department of Neurosurgery, University Hospital and University of Zurich, Zurich, Switzerland
- Department of Neurosurgery, Cantonal Hospital St.Gallen, St.Gallen, Switzerland
- Neuroscience Center Zurich (ZNZ), University of Zurich and ETH Zurich, Zurich, Switzerland
| |
Collapse
|
4
|
Sbierski-Kind J, Mai K, Kath J, Jurisch A, Streitz M, Kuchenbecker L, Babel N, Nienen M, Jürchott K, Spranger L, Jumpertz von Schwartzenberg R, Decker AM, Krüger U, Volk HD, Spranger J. Association between Subcutaneous Adipose Tissue Inflammation, Insulin Resistance, and Calorie Restriction in Obese Females. J Immunol 2020; 205:45-55. [PMID: 32482712 DOI: 10.4049/jimmunol.2000108] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/21/2020] [Indexed: 01/30/2023]
Abstract
The worldwide epidemic of overweight and obesity has led to an increase in associated metabolic comorbidities. Obesity induces chronic low-grade inflammation in white adipose tissue (WAT). However, the function and regulation of both innate and adaptive immune cells in human WAT under conditions of obesity and calorie restriction (CR) is not fully understood yet. Using a randomized interventional design, we investigated postmenopausal overweight or obese female subjects who either underwent CR for 3 mo followed by a 4-wk phase of weight maintenance or had to maintain a stable weight over the whole study period. A comprehensive immune phenotyping protocol was conducted using validated multiparameter flow cytometry analysis in blood and s.c. WAT (SAT). The TCR repertoire was analyzed by next-generation sequencing and cytokine levels were determined in SAT. Metabolic parameters were determined by hyperinsulinemic-euglycemic clamp. We found that insulin resistance correlates significantly with a shift toward the memory T cell compartment in SAT. TCR analysis revealed a diverse repertoire in SAT of overweight or obese individuals. Additionally, whereas weight loss improved systemic insulin sensitivity in the intervention group, SAT displayed no significant improvement of inflammatory parameters (cytokine levels and leukocyte subpopulations) compared with the control group. Our data demonstrate the accumulation of effector memory T cells in obese SAT and an association between systemic glucose homeostasis and inflammatory parameters in obese females. The long-standing effect of obesity-induced changes in SAT was demonstrated by preserved immune cell composition after short-term CR-induced weight loss.
Collapse
Affiliation(s)
- Julia Sbierski-Kind
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Department of Endocrinology and Metabolism, Berlin Institute of Health, 10178 Berlin, Germany; .,Berlin Institute of Health, 10178 Berlin, Germany.,Berlin Institute of Health Center for Regenerative Therapies, Charité University Medicine Berlin, 10117 Berlin, Germany.,Institute for Medical Immunology, Charité University Medicine Berlin, 10117 Berlin, Germany
| | - Knut Mai
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Department of Endocrinology and Metabolism, Berlin Institute of Health, 10178 Berlin, Germany.,Berlin Institute of Health, 10178 Berlin, Germany.,Charité - Center for Cardiovascular Research, 10117 Berlin, Germany
| | - Jonas Kath
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Department of Endocrinology and Metabolism, Berlin Institute of Health, 10178 Berlin, Germany.,Berlin Institute of Health Center for Regenerative Therapies, Charité University Medicine Berlin, 10117 Berlin, Germany
| | - Anke Jurisch
- Berlin Institute of Health Center for Regenerative Therapies, Charité University Medicine Berlin, 10117 Berlin, Germany.,Institute for Medical Immunology, Charité University Medicine Berlin, 10117 Berlin, Germany
| | - Mathias Streitz
- Berlin Institute of Health Center for Regenerative Therapies, Charité University Medicine Berlin, 10117 Berlin, Germany.,Institute for Medical Immunology, Charité University Medicine Berlin, 10117 Berlin, Germany
| | - Leon Kuchenbecker
- Berlin Institute of Health Center for Regenerative Therapies, Charité University Medicine Berlin, 10117 Berlin, Germany.,Institute for Medical Immunology, Charité University Medicine Berlin, 10117 Berlin, Germany
| | - Nina Babel
- Berlin Institute of Health Center for Regenerative Therapies, Charité University Medicine Berlin, 10117 Berlin, Germany.,Center for Translational Medicine, Department of Internal Medicine I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, 44625 Bochum, Germany
| | - Mikalai Nienen
- Berlin Institute of Health, 10178 Berlin, Germany.,Berlin Institute of Health Center for Regenerative Therapies, Charité University Medicine Berlin, 10117 Berlin, Germany.,Center for Translational Medicine, Department of Internal Medicine I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, 44625 Bochum, Germany
| | - Karsten Jürchott
- Berlin Institute of Health Center for Regenerative Therapies, Charité University Medicine Berlin, 10117 Berlin, Germany.,Institute for Medical Immunology, Charité University Medicine Berlin, 10117 Berlin, Germany
| | - Leonard Spranger
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Department of Endocrinology and Metabolism, Berlin Institute of Health, 10178 Berlin, Germany.,Charité - Center for Cardiovascular Research, 10117 Berlin, Germany
| | - Reiner Jumpertz von Schwartzenberg
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Department of Endocrinology and Metabolism, Berlin Institute of Health, 10178 Berlin, Germany.,Berlin Institute of Health, 10178 Berlin, Germany.,Charité - Center for Cardiovascular Research, 10117 Berlin, Germany.,German Center for Cardiovascular Research, partner site Berlin, 13353 Berlin, Germany; and
| | - Anne-Marie Decker
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Department of Endocrinology and Metabolism, Berlin Institute of Health, 10178 Berlin, Germany.,Berlin Institute of Health, 10178 Berlin, Germany
| | - Ulrike Krüger
- Berlin Institute of Health Center for Regenerative Therapies, Charité University Medicine Berlin, 10117 Berlin, Germany.,Institute for Medical Immunology, Charité University Medicine Berlin, 10117 Berlin, Germany
| | - Hans-Dieter Volk
- Berlin Institute of Health Center for Regenerative Therapies, Charité University Medicine Berlin, 10117 Berlin, Germany.,Institute for Medical Immunology, Charité University Medicine Berlin, 10117 Berlin, Germany.,Berlin Center for Advanced Therapies, Charité University Medicine Berlin, 10117 Berlin, Germany
| | - Joachim Spranger
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Department of Endocrinology and Metabolism, Berlin Institute of Health, 10178 Berlin, Germany.,Berlin Institute of Health, 10178 Berlin, Germany.,Charité - Center for Cardiovascular Research, 10117 Berlin, Germany.,German Center for Cardiovascular Research, partner site Berlin, 13353 Berlin, Germany; and
| |
Collapse
|
5
|
Marcu A, Bichmann L, Kuchenbecker L, Backert L, Kowalewski DJ, Freudenmann LK, Löffler MW, Lübke M, Walz J, Velz J, Moch H, Regli L, Silginer M, Weller M, Schlosser A, Kohlbacher O, Stevanovic S, Rammensee HG, Neidert MC. The HLA Ligand Atlas: A novel immuno-oncology resource for T-cell antigen discovery. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.3128] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
3128 Background: The human leukocyte antigen (HLA) complex regulates the adaptive immune response by showcasing the intracellular and extracellular protein content to the immune system, which is the basis for T cell-dependent tumor rejection. Therefore, a comprehensive map of the entirety of both HLA class I- and class II-presented peptides from various benign tissues is a highly sought after resource, as it enables the definition of tumor-association on the immunologically pivotal level of the HLA ligandome. Methods: Human tissue samples were snap frozen post mortem during autopsy. The study was approved by the local IRB. HLA ligands were immunopurified and characterized using an Orbitrap Fusion Lumos mass spectrometer coupled to an Ultimate 3000 RSLC Nano UHPLC System. Data acquisition was performed as technical triplicates in data-dependent mode, and data were analyzed using the containerized, computational pipeline MHCquant. Results: In this work, we describe the HLA Ligand Atlas, a comprehensive collection of matched HLA class I and class II ligandomes from 29 non-malignant tissues and 13 human subjects (208 samples in total), covering 38 HLA class I, and 17 HLA*DRB alleles and comprising 48,381 HLA class I and 16,146 HLA class II peptides. Nearly 50% of HLA ligands have not been previously described. The HLA Ligand Atlas is publicly available as a raw data resource, but also in the form of a user-friendly web interface that allows users to quickly formulate complex queries against the data set. Both downloadable data and the query interface are available at www.hla-ligand-atlas.org. Conclusions: This data set provides a valuable tool for research in diverse fields such as systems biology, general immunology, autoimmune disease and organ transplantation. Most importantly, the HLA Ligand Atlas provides essential information for translational applications in immuno-oncology. The knowledge of HLA ligands from benign tissues strongly supports the informed design of proteogenomic HLA-dependent target discovery approaches.
Collapse
Affiliation(s)
- Ana Marcu
- University of Tübingen, Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", Tübingen, Germany
| | - Leon Bichmann
- University of Tübingen, Applied Bioinformatics, Center for Bioinformatics, Tübingen, Germany., Tübingen, Germany
| | - Leon Kuchenbecker
- University of Tübingen, Applied Bioinformatics, Center for Bioinformatics, Tübingen, Germany., Tübingen, Germany
| | - Linus Backert
- University of Tübingen, Applied Bioinformatics, Center for Bioinformatics, Tübingen, Germany., Tübingen, Germany
| | - Daniel J Kowalewski
- University of Tübingen, Interfaculty Institute for Cell Biology, Department of Immunology, Tübingen, Germany
| | | | - Markus W. Löffler
- University Hospital Tübingen, Department of Clinical Pharmacology, Tübingen, Germany
| | - Maren Lübke
- University of Tübingen, Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", Tübingen, Germany
| | - Juliane Walz
- University of Tübingen, Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", Tübingen, Germany
| | - Julia Velz
- University Hospital and University of Zurich, Clinical Neuroscience Center and Department of Neurosurgery, Zurich, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Luca Regli
- University Hospital and University of Zürich, Clinical Neuroscience Center and Department of Neurosurgery, Zürich, Switzerland
| | - Manuela Silginer
- University Hospital and University of Zurich, Clinical Neuroscience Center and Department of Neurology, Zurich, Switzerland
| | - Michael Weller
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, and Neuroscience Center Zürich, University Hospital and University of Zürich, Zürich, Switzerland
| | - Andreas Schlosser
- Julius-Maximilians-University Würzburg, Rudolf Virchow Center for Experimental Biomedicine, Würzburg, Germany
| | - Oliver Kohlbacher
- University of Tübingen, Cluster of Excellence Machine Learning in the Sciences (EXC 2064), Tübingen, Germany
| | - Stefan Stevanovic
- DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany., Tübingen, Germany
| | - Hans-Georg Rammensee
- DKFZ Partner Site Tübingen, German Cancer Consortium (DKTK), Tübingen, Germany., Tübingen, Germany
| | - Marian Christoph Neidert
- University Hospital and University of Zurich, Clinical Neuroscience Center and Department of Neurosurgery, Zurich, Switzerland
| |
Collapse
|
6
|
Bichmann L, Nelde A, Ghosh M, Heumos L, Mohr C, Peltzer A, Kuchenbecker L, Sachsenberg T, Walz JS, Stevanović S, Rammensee HG, Kohlbacher O. MHCquant: Automated and Reproducible Data Analysis for Immunopeptidomics. J Proteome Res 2019; 18:3876-3884. [DOI: 10.1021/acs.jproteome.9b00313] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Stefan Stevanović
- German Cancer Consortium (DKTK), DKFZ Partner Site, Tübingen 72076, Germany
| | | | - Oliver Kohlbacher
- Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| |
Collapse
|
7
|
Stervbo U, Nienen M, Weist BJD, Kuchenbecker L, Hecht J, Wehler P, Westhoff TH, Reinke P, Babel N. BKV Clearance Time Correlates With Exhaustion State and T-Cell Receptor Repertoire Shape of BKV-Specific T-Cells in Renal Transplant Patients. Front Immunol 2019; 10:767. [PMID: 31024575 PMCID: PMC6468491 DOI: 10.3389/fimmu.2019.00767] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 03/22/2019] [Indexed: 01/08/2023] Open
Abstract
Reactivation of the BK polyomavirus is known to lead to severe complications in kidney transplant patients. The current treatment strategy relies on decreasing the immunosuppression to allow the immune system to clear the virus. Recently, we demonstrated a clear association between the resolution of BKV reactivation and reconstitution of BKV-specific CD4+ T-cells. However, which factors determine the duration of viral infection clearance remains so far unclear. Here we apply a combination of in-depth multi-parametric flow cytometry and NGS-based CDR3 beta chain receptor repertoire analysis of BKV-specific T-cells to a cohort of 7 kidney transplant patients during the clinical course of BKV reactivation. This way we followed TCR repertoires at single clone levels and functional activity of BKV-specific T-cells during the resolution of BKV infection. The duration of BKV clearance did not depend on the number of peripheral blood BKV-specific T-cells nor on a few immunodominant BKV-specific T-cell clones. Rather, the T-cell receptor repertoire diversity and exhaustion status of BKV-specific T-cells affected the duration of viral clearance: high clonotype diversity and lack of PD1 and TIM3 exhaustion markers on BKV-specific T-cells was associated with short clearance time. Our data thus demonstrate how the diversity and the exhaustion state of the T-cells can determine the clinical course of BKV infection.
Collapse
Affiliation(s)
- Ulrik Stervbo
- Center for Translational Medicine, Medical Clinic I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany.,Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Mikalai Nienen
- Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Institute for Medical Immunology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Labor Berlin-Charité Vivantes GmbH, Berlin, Germany
| | - Benjamin J D Weist
- Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Leon Kuchenbecker
- Applied Bioinformatics, Center for Bioinformatics Tübingen, University of Tübingen, Tübingen, Germany
| | - Jochen Hecht
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Patrizia Wehler
- Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Timm H Westhoff
- Center for Translational Medicine, Medical Clinic I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany
| | - Petra Reinke
- Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Berlin Center for Advanced Therapies, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Nina Babel
- Center for Translational Medicine, Medical Clinic I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany.,Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| |
Collapse
|
8
|
Nienen M, Stervbo U, Mölder F, Kaliszczyk S, Kuchenbecker L, Gayova L, Schweiger B, Jürchott K, Hecht J, Neumann AU, Rahmann S, Westhoff T, Reinke P, Thiel A, Babel N. The Role of Pre-existing Cross-Reactive Central Memory CD4 T-Cells in Vaccination With Previously Unseen Influenza Strains. Front Immunol 2019; 10:593. [PMID: 31019503 PMCID: PMC6458262 DOI: 10.3389/fimmu.2019.00593] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 03/05/2019] [Indexed: 11/13/2022] Open
Abstract
Influenza vaccination is a common approach to prevent seasonal and pandemic influenza. Pre-existing antibodies against close viral strains might impair antibody formation against previously unseen strains-a process called original antigenic sin. The role of this pre-existing cellular immunity in this process is, despite some hints from animal models, not clear. Here, we analyzed cellular and humoral immunity in healthy individuals before and after vaccination with seasonal influenza vaccine. Based on influenza-specific hemagglutination inhibiting (HI) titers, vaccinees were grouped into HI-negative and -positive cohorts followed by in-depth cytometric and TCR repertoire analysis. Both serological groups revealed cross-reactive T-cell memory to the vaccine strains at baseline that gave rise to the majority of vaccine-specific T-cells post vaccination. On the contrary, very limited number of vaccine-specific T-cell clones was recruited from the naive pool. Furthermore, baseline quantity of vaccine-specific central memory helper T-cells and clonotype richness of this population directly correlated with the vaccination efficacy. Our findings suggest that the deliberate recruitment of pre-existing cross-reactive cellular memory might help to improve vaccination outcome.
Collapse
Affiliation(s)
- Mikalai Nienen
- Institute for Medical Immunology, Charité University Medicine Berlin, Berlin, Germany.,Berlin-Brandenburg Center for Regenerative Therapies, Charité University Medicine Berlin, Berlin, Germany.,Labor Berlin-Charité Vivantes GmbH, Berlin, Germany
| | - Ulrik Stervbo
- Center for Translational Medicine, Immunology and Transplantation, Marien Hospital Herne, Ruhr University Bochum, Herne, Germany
| | - Felix Mölder
- Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Sviatlana Kaliszczyk
- Center for Translational Medicine, Immunology and Transplantation, Marien Hospital Herne, Ruhr University Bochum, Herne, Germany
| | | | | | | | - Karsten Jürchott
- Berlin-Brandenburg Center for Regenerative Therapies, Charité University Medicine Berlin, Berlin, Germany
| | - Jochen Hecht
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Avidan U Neumann
- Institute of Environmental Medicine, German Research Center for Environmental Health, Helmholtz Zentrum München, Augsburg, Germany
| | - Sven Rahmann
- Genome Informatics, Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Timm Westhoff
- Department of Internal Medicine, Marien Hospital Herne, Ruhr University Bochum, Herne, Germany
| | - Petra Reinke
- Berlin-Brandenburg Center for Regenerative Therapies, Charité University Medicine Berlin, Berlin, Germany.,Department of Nephrology and Intensive Care, Charité University Medicine Berlin, Berlin, Germany
| | - Andreas Thiel
- Berlin-Brandenburg Center for Regenerative Therapies, Charité University Medicine Berlin, Berlin, Germany
| | - Nina Babel
- Berlin-Brandenburg Center for Regenerative Therapies, Charité University Medicine Berlin, Berlin, Germany.,Center for Translational Medicine, Immunology and Transplantation, Marien Hospital Herne, Ruhr University Bochum, Herne, Germany.,Department of Nephrology and Intensive Care, Charité University Medicine Berlin, Berlin, Germany
| |
Collapse
|
9
|
Winter S, Jahn K, Wehner S, Kuchenbecker L, Marz M, Stoye J, Böcker S. Finding approximate gene clusters with Gecko 3. Nucleic Acids Res 2016; 44:9600-9610. [PMID: 27679480 PMCID: PMC5175365 DOI: 10.1093/nar/gkw843] [Citation(s) in RCA: 13] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 09/06/2016] [Accepted: 09/12/2016] [Indexed: 12/15/2022] Open
Abstract
Gene-order-based comparison of multiple genomes provides signals for functional analysis of genes and the evolutionary process of genome organization. Gene clusters are regions of co-localized genes on genomes of different species. The rapid increase in sequenced genomes necessitates bioinformatics tools for finding gene clusters in hundreds of genomes. Existing tools are often restricted to few (in many cases, only two) genomes, and often make restrictive assumptions such as short perfect conservation, conserved gene order or monophyletic gene clusters. We present Gecko 3, an open-source software for finding gene clusters in hundreds of bacterial genomes, that comes with an easy-to-use graphical user interface. The underlying gene cluster model is intuitive, can cope with low degrees of conservation as well as misannotations and is complemented by a sound statistical evaluation. To evaluate the biological benefit of Gecko 3 and to exemplify our method, we search for gene clusters in a dataset of 678 bacterial genomes using Synechocystis sp. PCC 6803 as a reference. We confirm detected gene clusters reviewing the literature and comparing them to a database of operons; we detect two novel clusters, which were confirmed by publicly available experimental RNA-Seq data. The computational analysis is carried out on a laptop computer in <40 min.
Collapse
Affiliation(s)
- Sascha Winter
- Chair for Bioinformatics, Institute for Computer Science, Friedrich-Schiller-University Jena, Jena, Germany
| | - Katharina Jahn
- Genome Informatics, Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
- Computational Biology Group, Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
- SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Stefanie Wehner
- RNA Bioinformatics and High Throughput Analysis, Institute for Computer Science, Friedrich-Schiller-University Jena, Jena, Germany
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, FK9LA, Scotland, UK
| | - Leon Kuchenbecker
- Genome Informatics, Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
- Berlin-Brandenburg Center for Regenerative Therapies, Charité University Medicine Berlin, Berlin, Germany
| | - Manja Marz
- RNA Bioinformatics and High Throughput Analysis, Institute for Computer Science, Friedrich-Schiller-University Jena, Jena, Germany
- Leibniz Institute for Age Research-Fritz Lipmann Institute (FLI), Jena, Germany
| | - Jens Stoye
- Genome Informatics, Faculty of Technology and Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Sebastian Böcker
- Chair for Bioinformatics, Institute for Computer Science, Friedrich-Schiller-University Jena, Jena, Germany
| |
Collapse
|
10
|
Gorochov G, Larsen M, Parizot C, Brisson H, Nienen M, Kuchenbecker L, Babel N, Neumann AU. Comment on "Tracking donor-reactive T cells: Evidence for clonal deletion in tolerant kidney transplant patients". Sci Transl Med 2015. [PMID: 26203079 DOI: 10.1126/scitranslmed.aab1994] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Guy Gorochov
- Sorbonne Universités, Université Pierre et Marie Curie Univ Paris 06, Unité Mixte de Recherche de Santé CR7, Centre d'Immunologie et des Maladies Infectieuses (CIMI), F-75013 Paris, France. INSERM, Unité 1135, CIMI, F-75013 Paris, France. Assistance Publique-Hôpitaux de Paris (AP-HP), Départment d'Immunologie, Hôpital Pitié-Salpêtrière, F-75013 Paris, France.
| | | | - Christophe Parizot
- Assistance Publique-Hôpitaux de Paris (AP-HP), Départment d'Immunologie, Hôpital Pitié-Salpêtrière, F-75013 Paris, France
| | | | - Mikalai Nienen
- Berlin-Brandenburger Centrum für Regenerative Therapien, Charité University Hospital, Berlin 13353, Germany. Marien Hospital Herne, Ruhr University, Bochum 44625, Germany
| | - Leon Kuchenbecker
- Berlin-Brandenburger Centrum für Regenerative Therapien, Charité University Hospital, Berlin 13353, Germany
| | - Nina Babel
- Berlin-Brandenburger Centrum für Regenerative Therapien, Charité University Hospital, Berlin 13353, Germany. Marien Hospital Herne, Ruhr University, Bochum 44625, Germany
| | - Avidan U Neumann
- Berlin-Brandenburger Centrum für Regenerative Therapien, Charité University Hospital, Berlin 13353, Germany. Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel. Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, 7270 Davos, Switzerland
| |
Collapse
|
11
|
Lei H, Kuchenbecker L, Streitz M, Sawitzki B, Vogt K, Landwehr-Kenzel S, Millward J, Juelke K, Babel N, Neumann A, Reinke P, Volk HD. Human CD45RA(-) FoxP3(hi) Memory-Type Regulatory T Cells Show Distinct TCR Repertoires With Conventional T Cells and Play an Important Role in Controlling Early Immune Activation. Am J Transplant 2015; 15:2625-35. [PMID: 25988290 DOI: 10.1111/ajt.13315] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 03/10/2015] [Accepted: 03/15/2015] [Indexed: 01/25/2023]
Abstract
Adoptive immunotherapy with regulatory T cells (Treg) is a new option to promote immune tolerance following solid organ transplantation (SOT). However, Treg from elderly patients awaiting transplantation are dominated by the CD45RA(-) CD62L(+) central memory type Treg subset (TregCM), and the yield of well-characterized and stable naïve Treg (TregN) is low. It is, therefore, important to determine whether these TregCM are derived from the thymus and express high stability, suppressive capacity and a broad antigen repertoire like TregN. In this study, we showed that TregCM use a different T cell receptor (TCR) repertoire from conventional T cells (Tconv), using next-generation sequencing of all 24 Vβ families, with an average depth of 534 677 sequences. This showed almost no contamination with induced Treg. Furthermore, TregCM showed enhanced suppressive activity on Tconv at early checkpoints of immune activation controlling activation markers expression and cytokine secretion, but comparable inhibition of proliferation. Following in vitro expansion under mTOR inhibition, TregCM expanded equally as well as TregN without losing their function. Despite relatively limited TCR repertoire, TregCM also showed specific alloresponse, although slightly reduced compared to TregN. These results support the therapeutic usefulness of manufacturing Treg products from CD45RA(-) CD62L(+) Treg-enriched starting material to be applied for adoptive Treg therapy.
Collapse
Affiliation(s)
- H Lei
- Berlin-Brandenburg Center for Regenerative Therapies, Charité University Medicine Berlin, Berlin, Germany.,Institute of Medical Immunology, Charité University Medicine Berlin, Berlin, Germany.,Berlin-Brandenburg School for Regenerative Therapies, Charité University Medicine Berlin, Berlin, Germany
| | - L Kuchenbecker
- Berlin-Brandenburg Center for Regenerative Therapies, Charité University Medicine Berlin, Berlin, Germany.,International Max Planck Research School for Computational Biology and Scientific Computing, Berlin, Germany
| | - M Streitz
- Berlin-Brandenburg Center for Regenerative Therapies, Charité University Medicine Berlin, Berlin, Germany.,Institute of Medical Immunology, Charité University Medicine Berlin, Berlin, Germany
| | - B Sawitzki
- Berlin-Brandenburg Center for Regenerative Therapies, Charité University Medicine Berlin, Berlin, Germany.,Institute of Medical Immunology, Charité University Medicine Berlin, Berlin, Germany.,Berlin-Brandenburg School for Regenerative Therapies, Charité University Medicine Berlin, Berlin, Germany
| | - K Vogt
- Institute of Medical Immunology, Charité University Medicine Berlin, Berlin, Germany
| | - S Landwehr-Kenzel
- Berlin-Brandenburg Center for Regenerative Therapies, Charité University Medicine Berlin, Berlin, Germany.,Berlin-Brandenburg School for Regenerative Therapies, Charité University Medicine Berlin, Berlin, Germany.,Department of Pediatric Pulmonology and Immunology, Charité University Medicine Berlin, Berlin, Germany
| | - J Millward
- Institute of Medical Immunology, Charité University Medicine Berlin, Berlin, Germany.,Experimental and Clinical Research Center (ECRC), MDC and Charité University Medicine, Berlin, Germany
| | - K Juelke
- Berlin-Brandenburg Center for Regenerative Therapies, Charité University Medicine Berlin, Berlin, Germany.,Institute of Medical Immunology, Charité University Medicine Berlin, Berlin, Germany
| | - N Babel
- Berlin-Brandenburg Center for Regenerative Therapies, Charité University Medicine Berlin, Berlin, Germany.,Berlin-Brandenburg School for Regenerative Therapies, Charité University Medicine Berlin, Berlin, Germany.,Department of Nephrology and Intensive Care, Charité University Medicine Berlin, Berlin, Germany
| | - A Neumann
- Berlin-Brandenburg Center for Regenerative Therapies, Charité University Medicine Berlin, Berlin, Germany.,Goodman Faculty of Life Sciences, Bar Ilan University, Ramat-Gan, Israel.,Institute for Theoretical Biology, Humboldt University, Berlin, Germany
| | - P Reinke
- Berlin-Brandenburg Center for Regenerative Therapies, Charité University Medicine Berlin, Berlin, Germany.,Berlin-Brandenburg School for Regenerative Therapies, Charité University Medicine Berlin, Berlin, Germany.,Department of Nephrology and Intensive Care, Charité University Medicine Berlin, Berlin, Germany
| | - H-D Volk
- Berlin-Brandenburg Center for Regenerative Therapies, Charité University Medicine Berlin, Berlin, Germany.,Institute of Medical Immunology, Charité University Medicine Berlin, Berlin, Germany.,Berlin-Brandenburg School for Regenerative Therapies, Charité University Medicine Berlin, Berlin, Germany
| |
Collapse
|
12
|
Kuchenbecker L, Nienen M, Hecht J, Neumann AU, Babel N, Reinert K, Robinson PN. IMSEQ—a fast and error aware approach to immunogenetic sequence analysis. Bioinformatics 2015; 31:2963-71. [DOI: 10.1093/bioinformatics/btv309] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 05/11/2015] [Indexed: 01/08/2023] Open
|
13
|
Holtgrewe M, Kuchenbecker L, Reinert K. Methods for the detection and assembly of novel sequence in high-throughput sequencing data. Bioinformatics 2015; 31:1904-12. [PMID: 25649620 DOI: 10.1093/bioinformatics/btv051] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 01/26/2015] [Indexed: 01/04/2023] Open
Abstract
MOTIVATION Large insertions of novel sequence are an important type of structural variants. Previous studies used traditional de novo assemblers for assembling non-mapping high-throughput sequencing (HTS) or capillary reads and then tried to anchor them in the reference using paired read information. RESULTS We present approaches for detecting insertion breakpoints and targeted assembly of large insertions from HTS paired data: BASIL and ANISE. On near identity repeats that are hard for assemblers, ANISE employs a repeat resolution step. This results in far better reconstructions than obtained by the compared methods. On simulated data, we found our insert assembler to be competitive with the de novo assemblers ABYSS and SGA while yielding already anchored inserted sequence as opposed to unanchored contigs as from ABYSS/SGA. On real-world data, we detected novel sequence in a human individual and thoroughly validated the assembled sequence. ANISE was found to be superior to the competing tool MindTheGap on both simulated and real-world data. AVAILABILITY AND IMPLEMENTATION ANISE and BASIL are available for download at http://www.seqan.de/projects/herbarium under a permissive open source license.
Collapse
Affiliation(s)
- Manuel Holtgrewe
- Department of Computer Science, Freie Universität Berlin and Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Leon Kuchenbecker
- Department of Computer Science, Freie Universität Berlin and Max Planck Institute for Molecular Genetics, Berlin, Germany Department of Computer Science, Freie Universität Berlin and Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Knut Reinert
- Department of Computer Science, Freie Universität Berlin and Max Planck Institute for Molecular Genetics, Berlin, Germany
| |
Collapse
|
14
|
Dziubianau M, Hecht J, Kuchenbecker L, Sattler A, Stervbo U, Rödelsperger C, Nickel P, Neumann AU, Robinson PN, Mundlos S, Volk HD, Thiel A, Reinke P, Babel N. TCR repertoire analysis by next generation sequencing allows complex differential diagnosis of T cell-related pathology. Am J Transplant 2013; 13:2842-54. [PMID: 24020931 DOI: 10.1111/ajt.12431] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 06/19/2013] [Accepted: 07/08/2013] [Indexed: 01/25/2023]
Abstract
Clonotype analysis is essential for complete characterization of antigen-specific T cells. Moreover, knowledge on clonal identity allows tracking of antigen-specific T cells in whole blood and tissue infiltrates and can provide information on antigenic specificity. Here, we developed a next generation sequencing (NGS)-based platform for the highly quantitative clonotype characterization of T cells and determined requirements for the unbiased characterization of the input material (DNA, RNA, ex vivo derived or cell culture expanded T cells). Thereafter we performed T cell receptor (TCR) repertoire analysis of various specimens in clinical settings including cytomegalovirus (CMV), polyomavirus BK (BKV) reactivation and acute cellular allograft rejection. Our results revealed dynamic nature of virus-specific T cell clonotypes; CMV reactivation was linked to appearance of new highly abundant antigen-specific clonalities. Moreover, analysis of clonotype overlap between BKV-, alloantigen-specific T cell-, kidney allograft- and urine-derived lymphocytes provided hints for the differential diagnosis of allograft dysfunction and enabled appropriate therapy adjustment. We believe that the established approach will provide insights into the regulation of virus-specific/anti-tumor immunity and has high diagnostic potential in the clinical routine.
Collapse
Affiliation(s)
- M Dziubianau
- Berlin-Brandenburg Center for Regenerative Therapies, Charité University Medicine Berlin, Berlin, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|