1
|
Shingai M, Iida S, Kawai N, Kawahara M, Sekiya T, Ohno M, Nomura N, Handabile C, Kawakita T, Omori R, Yamagishi J, Sano K, Ainai A, Suzuki T, Ohnishi K, Ito K, Kida H. Extraction of the CDRH3 sequence of the mouse antibody repertoire selected upon influenza virus infection by subtraction of the background antibody repertoire. J Virol 2024; 98:e0199523. [PMID: 38323813 PMCID: PMC10949447 DOI: 10.1128/jvi.01995-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 01/14/2024] [Indexed: 02/08/2024] Open
Abstract
Historically, antibody reactivity to pathogens and vaccine antigens has been evaluated using serological measurements of antigen-specific antibodies. However, it is difficult to evaluate all antibodies that contribute to various functions in a single assay, such as the measurement of the neutralizing antibody titer. Bulk antibody repertoire analysis using next-generation sequencing is a comprehensive method for analyzing the overall antibody response; however, it is unreliable for estimating antigen-specific antibodies due to individual variation. To address this issue, we propose a method to subtract the background signal from the repertoire of data of interest. In this study, we analyzed changes in antibody diversity and inferred the heavy-chain complementarity-determining region 3 (CDRH3) sequences of antibody clones that were selected upon influenza virus infection in a mouse model using bulk repertoire analysis. A decrease in the diversity of the antibody repertoire was observed upon viral infection, along with an increase in neutralizing antibody titers. Using kernel density estimation of sequences in a high-dimensional sequence space with background signal subtraction, we identified several clusters of CDRH3 sequences induced upon influenza virus infection. Most of these repertoires were detected more frequently in infected mice than in uninfected control mice, suggesting that infection-specific antibody sequences can be extracted using this method. Such an accurate extraction of antigen- or infection-specific repertoire information will be a useful tool for vaccine evaluation in the future. IMPORTANCE As specific interactions between antigens and cell-surface antibodies trigger the proliferation of B-cell clones, the frequency of each antibody sequence in the samples reflects the size of each clonal population. Nevertheless, it is extremely difficult to extract antigen-specific antibody sequences from the comprehensive bulk antibody sequences obtained from blood samples due to repertoire bias influenced by exposure to dietary antigens and other infectious agents. This issue can be addressed by subtracting the background noise from the post-immunization or post-infection repertoire data. In the present study, we propose a method to quantify repertoire data from comprehensive repertoire data. This method allowed subtraction of the background repertoire, resulting in more accurate extraction of expanded antibody repertoires upon influenza virus infection. This accurate extraction of antigen- or infection-specific repertoire information is a useful tool for vaccine evaluation.
Collapse
Affiliation(s)
- Masashi Shingai
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- Division of Vaccine Immunology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Sayaka Iida
- Division of Bioinformatics, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Naoko Kawai
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Mamiko Kawahara
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Toshiki Sekiya
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Marumi Ohno
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Naoki Nomura
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
| | - Chimuka Handabile
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
| | - Tomomi Kawakita
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- Division of Vaccine Immunology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Ryosuke Omori
- Division of Bioinformatics, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Junya Yamagishi
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Kaori Sano
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Akira Ainai
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kazuo Ohnishi
- Department of Immunology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kimihito Ito
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Division of Bioinformatics, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Hiroshi Kida
- Division of Biologics Development, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| |
Collapse
|
2
|
Chang YW, Hsiao HW, Chen JP, Tzeng SF, Tsai CH, Wu CY, Hsieh HH, Carmona SJ, Andreatta M, Di Conza G, Su MT, Koni PA, Ho PC, Chen HK, Yang MH. A CSF-1R-blocking antibody/IL-10 fusion protein increases anti-tumor immunity by effectuating tumor-resident CD8 + T cells. Cell Rep Med 2023; 4:101154. [PMID: 37586318 PMCID: PMC10439276 DOI: 10.1016/j.xcrm.2023.101154] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 06/04/2023] [Accepted: 07/18/2023] [Indexed: 08/18/2023]
Abstract
Strategies to increase intratumoral concentrations of an anticancer agent are desirable to optimize its therapeutic potential when said agent is efficacious primarily within a tumor but also have significant systemic side effects. Here, we generate a bifunctional protein by fusing interleukin-10 (IL-10) to a colony-stimulating factor-1 receptor (CSF-1R)-blocking antibody. The fusion protein demonstrates significant antitumor activity in multiple cancer models, especially head and neck cancer. Moreover, this bifunctional protein not only leads to the anticipated reduction in tumor-associated macrophages but also triggers proliferation, activation, and metabolic reprogramming of CD8+ T cells. Furthermore, it extends the clonotype diversity of tumor-infiltrated T cells and shifts the tumor microenvironment (TME) to an immune-active state. This study suggests an efficient strategy for designing immunotherapeutic agents by fusing a potent immunostimulatory molecule to an antibody targeting TME-enriched factors.
Collapse
Affiliation(s)
- Yao-Wen Chang
- Cancer and Immunology Research Center, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | | | - Ju-Pei Chen
- Cancer and Immunology Research Center, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Sheue-Fen Tzeng
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 11221, Taiwan
| | - Chin-Hsien Tsai
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 11221, Taiwan
| | - Chun-Yi Wu
- Department of Biomedical Imaging and Radiological Sciences, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Hsin-Hua Hsieh
- Department of Biomedical Imaging and Radiological Sciences, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Santiago J Carmona
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research at University of Lausanne, Lausanne, Switzerland
| | - Massimo Andreatta
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research at University of Lausanne, Lausanne, Switzerland
| | - Giusy Di Conza
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research at University of Lausanne, Lausanne, Switzerland
| | - Mei-Tzu Su
- Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | | | - Ping-Chih Ho
- Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute for Cancer Research at University of Lausanne, Lausanne, Switzerland
| | - Hung-Kai Chen
- Elixiron Immunotherapeutics (Hong Kong) Ltd., Hong Kong.
| | - Muh-Hwa Yang
- Cancer and Immunology Research Center, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan; Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan; Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan; Department of Oncology, Taipei Veterans General Hospital, Taipei 11217, Taiwan; Department of Teaching and Research, Taipei City Hospital, Taipei, Taiwan.
| |
Collapse
|
3
|
Peng K, Nowicki TS, Campbell K, Vahed M, Peng D, Meng Y, Nagareddy A, Huang YN, Karlsberg A, Miller Z, Brito J, Nadel B, Pak VM, Abedalthagafi MS, Burkhardt AM, Alachkar H, Ribas A, Mangul S. Rigorous benchmarking of T-cell receptor repertoire profiling methods for cancer RNA sequencing. Brief Bioinform 2023; 24:bbad220. [PMID: 37291798 PMCID: PMC10359085 DOI: 10.1093/bib/bbad220] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/02/2023] [Accepted: 05/24/2023] [Indexed: 06/10/2023] Open
Abstract
The ability to identify and track T-cell receptor (TCR) sequences from patient samples is becoming central to the field of cancer research and immunotherapy. Tracking genetically engineered T cells expressing TCRs that target specific tumor antigens is important to determine the persistence of these cells and quantify tumor responses. The available high-throughput method to profile TCR repertoires is generally referred to as TCR sequencing (TCR-Seq). However, the available TCR-Seq data are limited compared with RNA sequencing (RNA-Seq). In this paper, we have benchmarked the ability of RNA-Seq-based methods to profile TCR repertoires by examining 19 bulk RNA-Seq samples across 4 cancer cohorts including both T-cell-rich and T-cell-poor tissue types. We have performed a comprehensive evaluation of the existing RNA-Seq-based repertoire profiling methods using targeted TCR-Seq as the gold standard. We also highlighted scenarios under which the RNA-Seq approach is suitable and can provide comparable accuracy to the TCR-Seq approach. Our results show that RNA-Seq-based methods are able to effectively capture the clonotypes and estimate the diversity of TCR repertoires, as well as provide relative frequencies of clonotypes in T-cell-rich tissues and low-diversity repertoires. However, RNA-Seq-based TCR profiling methods have limited power in T-cell-poor tissues, especially in highly diverse repertoires of T-cell-poor tissues. The results of our benchmarking provide an additional appealing argument to incorporate RNA-Seq into the immune repertoire screening of cancer patients as it offers broader knowledge into the transcriptomic changes that exceed the limited information provided by TCR-Seq.
Collapse
Affiliation(s)
- Kerui Peng
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Theodore S Nowicki
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, University of California, Los Angeles, CA, USA
- Department of Microbiology, Immunology, & Molecular Genetics, University of California, Los Angeles, CA, USA
| | - Katie Campbell
- Department of Medicine, Division of Hematology-Oncology, University of California, Los Angeles, CA, USA
| | - Mohammad Vahed
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Dandan Peng
- Department of Quantitative and Computational Biology, USC Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, USA
| | - Yiting Meng
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Anish Nagareddy
- Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA
| | - Yu-Ning Huang
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Aaron Karlsberg
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Zachary Miller
- Department of Pharmaceutical Sciences, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Jaqueline Brito
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Brian Nadel
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Victoria M Pak
- Emory Nell Hodgson School of Nursing, Emory University, Atlanta, GA, USA
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Malak S Abedalthagafi
- Department of Pathology & Laboratory Medicine, Emory University Hospital, Atlanta, GA, USA
- King Salman Center for Disability Research, Riyadh, Saudi Arabia
| | - Amanda M Burkhardt
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Houda Alachkar
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Antoni Ribas
- Departments of Medicine (Hematology-Oncology), Surgery (Surgical Oncology) and Molecular & Medical Pharmacology, University of California, Los Angeles, CA, USA
| | - Serghei Mangul
- Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
- Department of Quantitative and Computational Biology, USC Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, USA
| |
Collapse
|
4
|
Zong F, Long C, Hu W, Chen S, Dai W, Xiao ZX, Cao Y. Abalign: a comprehensive multiple sequence alignment platform for B-cell receptor immune repertoires. Nucleic Acids Res 2023:7173809. [PMID: 37207341 DOI: 10.1093/nar/gkad400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 04/23/2023] [Accepted: 05/08/2023] [Indexed: 05/21/2023] Open
Abstract
The utilization of high-throughput sequencing (HTS) for B-cell receptor (BCR) immune repertoire analysis has become widespread in the fields of adaptive immunity and antibody drug development. However, the sheer volume of sequences generated by these experiments presents a challenge in data processing. Specifically, multiple sequence alignment (MSA), a critical aspect of BCR analysis, remains inadequate for handling massive BCR sequencing data and lacks the ability to provide immunoglobulin-specific information. To address this gap, we introduce Abalign, a standalone program specifically designed for ultrafast MSA of BCR/antibody sequences. Benchmark tests demonstrate that Abalign achieves comparable or even better accuracy than state-of-the-art MSA tools, and shows remarkable advantages in terms of speed and memory consumption, reducing the time required for high-throughput analysis from weeks to hours. In addition to its alignment capabilities, Abalign offers a broad range of BCR analysis features, including extracting BCRs, constructing lineage trees, assigning VJ genes, analyzing clonotypes, profiling mutations, and comparing BCR immune repertoires. With its user-friendly graphic interface, Abalign can be easily run on personal computers instead of computing clusters. Overall, Abalign is an easy-to-use and effective tool that enables researchers to analyze massive BCR/antibody sequences, leading to new discoveries in the field of immunoinformatics. The software is freely available at http://cao.labshare.cn/abalign/.
Collapse
Affiliation(s)
- Fanjie Zong
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, Chengdu, China
| | - Chenyu Long
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, Chengdu, China
| | - Wanxin Hu
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, Chengdu, China
| | - Shuang Chen
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Wentao Dai
- NHC Key Laboratory of Reproduction Regulation & Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Zhi-Xiong Xiao
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yang Cao
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, Chengdu, China
| |
Collapse
|
5
|
Schwarz C, Eschenhagen P, Schmidt H, Hohnstein T, Iwert C, Grehn C, Roehmel J, Steinke E, Stahl M, Lozza L, Tikhonova E, Rosati E, Stervbo U, Babel N, Mainz JG, Wisplinghoff H, Ebel F, Jia LJ, Blango MG, Hortschansky P, Brunke S, Hube B, Brakhage AA, Kniemeyer O, Scheffold A, Bacher P. Antigen specificity and cross-reactivity drive functionally diverse anti-Aspergillus fumigatus T cell responses in cystic fibrosis. J Clin Invest 2023; 133:161593. [PMID: 36701198 PMCID: PMC9974102 DOI: 10.1172/jci161593] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 01/19/2023] [Indexed: 01/27/2023] Open
Abstract
BACKGROUNDThe fungus Aspergillus fumigatus causes a variety of clinical phenotypes in patients with cystic fibrosis (pwCF). Th cells orchestrate immune responses against fungi, but the types of A. fumigatus-specific Th cells in pwCF and their contribution to protective immunity or inflammation remain poorly characterized.METHODSWe used antigen-reactive T cell enrichment (ARTE) to investigate fungus-reactive Th cells in peripheral blood of pwCF and healthy controls.RESULTSWe show that clonally expanded, high-avidity A. fumigatus-specific effector Th cells, which were absent in healthy donors, developed in pwCF. Individual patients were characterized by distinct Th1-, Th2-, or Th17-dominated responses that remained stable over several years. These different Th subsets target different A. fumigatus proteins, indicating that differential antigen uptake and presentation directs Th cell subset development. Patients with allergic bronchopulmonary aspergillosis (ABPA) are characterized by high frequencies of Th2 cells that cross-recognize various filamentous fungi.CONCLUSIONOur data highlight the development of heterogenous Th responses targeting different protein fractions of a single fungal pathogen and identify the development of multispecies cross-reactive Th2 cells as a potential risk factor for ABPA.FUNDINGGerman Research Foundation (DFG), under Germany's Excellence Strategy (EXC 2167-390884018 "Precision Medicine in Chronic Inflammation" and EXC 2051-390713860 "Balance of the Microverse"); Oskar Helene Heim Stiftung; Christiane Herzog Stiftung; Mukoviszidose Institut gGmb; German Cystic Fibrosis Association Mukoviszidose e.V; German Federal Ministry of Education and Science (BMBF) InfectControl 2020 Projects AnDiPath (BMBF 03ZZ0838A+B).
Collapse
Affiliation(s)
- Carsten Schwarz
- Klinikum Westbrandenburg, Campus Potsdam, Cystic Fibrosis Section, Potsdam, Germany
| | - Patience Eschenhagen
- Klinikum Westbrandenburg, Campus Potsdam, Cystic Fibrosis Section, Potsdam, Germany
| | - Henrijette Schmidt
- Institute of Clinical Molecular Biology, Christian-Albrecht University of Kiel, Kiel, Germany.,Institute of Immunology, Christian-Albrecht University of Kiel and UKSH Schleswig-Holstein, Kiel, Germany
| | - Thordis Hohnstein
- Department of Microbiology, Infectious Diseases and Immunology, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Christina Iwert
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Translational Immunology, Berlin, Germany
| | - Claudia Grehn
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Jobst Roehmel
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt – Universität zu Berlin, Berlin, Germany
| | - Eva Steinke
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany.,Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt – Universität zu Berlin, Berlin, Germany.,German Center for Lung Research (DZL), associated partner site, Berlin, Germany
| | - Mirjam Stahl
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany.,Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt – Universität zu Berlin, Berlin, Germany.,German Center for Lung Research (DZL), associated partner site, Berlin, Germany
| | - Laura Lozza
- Cell Biology Laboratory, Precision for Medicine GmbH, Berlin, Germany
| | - Ekaterina Tikhonova
- Institute of Clinical Molecular Biology, Christian-Albrecht University of Kiel, Kiel, Germany.,Institute of Immunology, Christian-Albrecht University of Kiel and UKSH Schleswig-Holstein, Kiel, Germany
| | - Elisa Rosati
- Institute of Clinical Molecular Biology, Christian-Albrecht University of Kiel, Kiel, Germany.,Institute of Immunology, Christian-Albrecht University of Kiel and UKSH Schleswig-Holstein, Kiel, Germany
| | - Ulrik Stervbo
- Center for Translational Medicine and Immune Diagnostics Laboratory, Marien Hospital Herne, University Hospital of the Ruhr University Bochum, Herne, Germany
| | - Nina Babel
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany.,Center for Translational Medicine and Immune Diagnostics Laboratory, Marien Hospital Herne, University Hospital of the Ruhr University Bochum, Herne, Germany
| | - Jochen G. Mainz
- Brandenburg Medical School/Medizinische Hochschule Brandenburg (MHB), University, Pediatric Pulmonology/Cystic Fibrosis, Klinikum Westbrandenburg, Brandenburg an der Havel, Germany
| | - Hilmar Wisplinghoff
- Labor Dr. Wisplinghoff, Cologne, Germany.,Institute for Virology and Microbiology, Witten/Herdecke University, Witten, Germany
| | - Frank Ebel
- Institute for Infectious Diseases and Zoonoses, LMU, Munich, Germany
| | - Lei-Jie Jia
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), Jena, Germany
| | - Matthew G. Blango
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), Jena, Germany
| | - Peter Hortschansky
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), Jena, Germany
| | - Sascha Brunke
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), Jena, Germany
| | - Bernhard Hube
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), Jena, Germany.,Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Axel A. Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), Jena, Germany.,Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Olaf Kniemeyer
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), Jena, Germany
| | - Alexander Scheffold
- Institute of Immunology, Christian-Albrecht University of Kiel and UKSH Schleswig-Holstein, Kiel, Germany
| | - Petra Bacher
- Institute of Clinical Molecular Biology, Christian-Albrecht University of Kiel, Kiel, Germany.,Institute of Immunology, Christian-Albrecht University of Kiel and UKSH Schleswig-Holstein, Kiel, Germany
| |
Collapse
|
6
|
Obermayer B, Keilholz L, Conrad T, Frentsch M, Blau IW, Vuong L, Lesch S, Movasshagi K, Tietze-Stolley C, Loyal L, Henze L, Penack O, Stervbo U, Babel N, Haas S, Beule D, Bullinger L, Wittenbecher F, Na IK. Single-cell clonal tracking of persistent T-cells in allogeneic hematopoietic stem cell transplantation. Front Immunol 2023; 14:1114368. [PMID: 36860867 PMCID: PMC9969884 DOI: 10.3389/fimmu.2023.1114368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 01/23/2023] [Indexed: 02/17/2023] Open
Abstract
The critical balance between intended and adverse effects in allogeneic hematopoietic stem cell transplantation (alloHSCT) depends on the fate of individual donor T-cells. To this end, we tracked αβT-cell clonotypes during stem cell mobilization treatment with granulocyte-colony stimulating factor (G-CSF) in healthy donors and for six months during immune reconstitution after transfer to transplant recipients. More than 250 αβT-cell clonotypes were tracked from donor to recipient. These clonotypes consisted almost exclusively of CD8+ effector memory T cells (CD8TEM), which exhibited a different transcriptional signature with enhanced effector and cytotoxic functions compared to other CD8TEM. Importantly, these distinct and persisting clonotypes could already be delineated in the donor. We confirmed these phenotypes on the protein level and their potential for selection from the graft. Thus, we identified a transcriptional signature associated with persistence and expansion of donor T-cell clonotypes after alloHSCT that may be exploited for personalized graft manipulation strategies in future studies.
Collapse
Affiliation(s)
- Benedikt Obermayer
- Core Unit Bioinformatics (CUBI), Berlin Institute of Health at Charite – Universitätsmedizin Berlin, Berlin, Germany
| | - Luisa Keilholz
- Department of Hematology, Oncology, and Tumor Immunology, Charite – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany,BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charite – Universitätsmedizin Berlin, Berlin, Germany
| | - Thomas Conrad
- Core Unit Genomics, Berlin Institute of Health at Charite – Universitätsmedizin Berlin, Berlin, Germany,Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Marco Frentsch
- Department of Hematology, Oncology, and Tumor Immunology, Charite – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany,BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charite – Universitätsmedizin Berlin, Berlin, Germany
| | - Igor-Wolfgang Blau
- Department of Hematology, Oncology, and Tumor Immunology, Charite – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Lam Vuong
- Department of Hematology, Oncology, and Tumor Immunology, Charite – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany,Stem Cell Facility, Charite - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Stella Lesch
- Department of Hematology, Oncology, and Tumor Immunology, Charite – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany,BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charite – Universitätsmedizin Berlin, Berlin, Germany
| | - Kamran Movasshagi
- Department of Hematology, Oncology, and Tumor Immunology, Charite – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany,Stem Cell Facility, Charite - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Carola Tietze-Stolley
- Department of Hematology, Oncology, and Tumor Immunology, Charite – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany,Stem Cell Facility, Charite - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Lucie Loyal
- BIH Center for Exploratory Diagnostic Sciences (EDS), Berlin Institute of Health at Charite – Universitätsmedizin Berlin, Berlin, Germany,Si-M/”Der Simulierte Mensch” a science framework of Technische Universität Berlin and Charite - Universitätsmedizin Berlin, Berlin, Germany,Immunomics - Regenerative Immunology and Aging, Berlin Institute of Health at Charite – Universitätsmedizin Berlin, Berlin, Germany
| | - Larissa Henze
- BIH Center for Exploratory Diagnostic Sciences (EDS), Berlin Institute of Health at Charite – Universitätsmedizin Berlin, Berlin, Germany,Si-M/”Der Simulierte Mensch” a science framework of Technische Universität Berlin and Charite - Universitätsmedizin Berlin, Berlin, Germany,Immunomics - Regenerative Immunology and Aging, Berlin Institute of Health at Charite – Universitätsmedizin Berlin, Berlin, Germany
| | - Olaf Penack
- Department of Hematology, Oncology, and Tumor Immunology, Charite – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany,BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charite – Universitätsmedizin Berlin, Berlin, Germany
| | - Ulrik Stervbo
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charite – Universitätsmedizin Berlin, Berlin, Germany,Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany
| | - Nina Babel
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charite – Universitätsmedizin Berlin, Berlin, Germany,Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany
| | - Simon Haas
- Department of Hematology, Oncology, and Tumor Immunology, Charite – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany,BIH Center for Exploratory Diagnostic Sciences (EDS), Berlin Institute of Health at Charite – Universitätsmedizin Berlin, Berlin, Germany,German Cancer Consortium (DKTK), Charite - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Dieter Beule
- Core Unit Bioinformatics (CUBI), Berlin Institute of Health at Charite – Universitätsmedizin Berlin, Berlin, Germany
| | - Lars Bullinger
- Department of Hematology, Oncology, and Tumor Immunology, Charite – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany,German Cancer Consortium (DKTK), Charite - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany,ECRC Experimental and Clinical Research Center, Charite – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
| | - Friedrich Wittenbecher
- Department of Hematology, Oncology, and Tumor Immunology, Charite – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany,BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charite – Universitätsmedizin Berlin, Berlin, Germany
| | - Il-Kang Na
- Department of Hematology, Oncology, and Tumor Immunology, Charite – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany,BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charite – Universitätsmedizin Berlin, Berlin, Germany,Si-M/”Der Simulierte Mensch” a science framework of Technische Universität Berlin and Charite - Universitätsmedizin Berlin, Berlin, Germany,German Cancer Consortium (DKTK), Charite - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany,ECRC Experimental and Clinical Research Center, Charite – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany,*Correspondence: Il-Kang Na,
| |
Collapse
|
7
|
Swan SL, Mehta N, Ilich E, Shen SH, Wilkinson DS, Anderson AR, Segura T, Sanchez-Perez L, Sampson JH, Bellamkonda RV. IL7 and IL7 Flt3L co-expressing CAR T cells improve therapeutic efficacy in mouse EGFRvIII heterogeneous glioblastoma. Front Immunol 2023; 14:1085547. [PMID: 36817432 PMCID: PMC9936235 DOI: 10.3389/fimmu.2023.1085547] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/04/2023] [Indexed: 02/05/2023] Open
Abstract
Chimeric antigen receptor (CAR) T cell therapy in glioblastoma faces many challenges including insufficient CAR T cell abundance and antigen-negative tumor cells evading targeting. Unfortunately, preclinical studies evaluating CAR T cells in glioblastoma focus on tumor models that express a single antigen, use immunocompromised animals, and/or pre-treat with lymphodepleting agents. While lymphodepletion enhances CAR T cell efficacy, it diminishes the endogenous immune system that has the potential for tumor eradication. Here, we engineered CAR T cells to express IL7 and/or Flt3L in 50% EGFRvIII-positive and -negative orthotopic tumors pre-conditioned with non-lymphodepleting irradiation. IL7 and IL7 Flt3L CAR T cells increased intratumoral CAR T cell abundance seven days after treatment. IL7 co-expression with Flt3L modestly increased conventional dendritic cells as well as the CD103+XCR1+ population known to have migratory and antigen cross-presenting capabilities. Treatment with IL7 or IL7 Flt3L CAR T cells improved overall survival to 67% and 50%, respectively, compared to 9% survival with conventional or Flt3L CAR T cells. We concluded that CAR T cells modified to express IL7 enhanced CAR T cell abundance and improved overall survival in EGFRvIII heterogeneous tumors pre-conditioned with non-lymphodepleting irradiation. Potentially IL7 or IL7 Flt3L CAR T cells can provide new opportunities to combine CAR T cells with other immunotherapies for the treatment of glioblastoma.
Collapse
Affiliation(s)
- Sheridan L Swan
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, United States
| | - Nalini Mehta
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, United States
| | - Ekaterina Ilich
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, United States
| | - Steven H Shen
- Duke Brain Tumor Immunotherapy Program, Department of Neurosurgery, Duke University Medical Center, Durham, NC, United States.,The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, United States.,Department of Pathology, Duke University Medical Center, Durham, NC, United States
| | - Daniel S Wilkinson
- Duke Brain Tumor Immunotherapy Program, Department of Neurosurgery, Duke University Medical Center, Durham, NC, United States
| | - Alexa R Anderson
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, United States
| | - Tatiana Segura
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, United States.,Clinical Science Departments of Neurology and Dermatology, Duke University, Durham, NC, United States
| | - Luis Sanchez-Perez
- Duke Brain Tumor Immunotherapy Program, Department of Neurosurgery, Duke University Medical Center, Durham, NC, United States.,The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, United States.,Department of Neurosurgery, Duke University Medical Center, Durham, NC, United States
| | - John H Sampson
- Duke Brain Tumor Immunotherapy Program, Department of Neurosurgery, Duke University Medical Center, Durham, NC, United States.,The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center, Durham, NC, United States.,Department of Pathology, Duke University Medical Center, Durham, NC, United States.,Department of Neurosurgery, Duke University Medical Center, Durham, NC, United States
| | - Ravi V Bellamkonda
- Department of Biology, Emory University, Atlanta, GA, United States.,Wallace H. Coulter Department of Biomedical Engineering, Emory University, Atlanta, GA, United States
| |
Collapse
|
8
|
Porciello N, Franzese O, D’Ambrosio L, Palermo B, Nisticò P. T-cell repertoire diversity: friend or foe for protective antitumor response? JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2022; 41:356. [PMID: 36550555 PMCID: PMC9773533 DOI: 10.1186/s13046-022-02566-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022]
Abstract
Profiling the T-Cell Receptor (TCR) repertoire is establishing as a potent approach to investigate autologous and treatment-induced antitumor immune response. Technical and computational breakthroughs, including high throughput next-generation sequencing (NGS) approaches and spatial transcriptomics, are providing unprecedented insight into the mechanisms underlying antitumor immunity. A precise spatiotemporal variation of T-cell repertoire, which dynamically mirrors the functional state of the evolving host-cancer interaction, allows the tracking of the T-cell populations at play, and may identify the key cells responsible for tumor eradication, the evaluation of minimal residual disease and the identification of biomarkers of response to immunotherapy. In this review we will discuss the relationship between global metrics characterizing the TCR repertoire such as T-cell clonality and diversity and the resultant functional responses. In particular, we will explore how specific TCR repertoires in cancer patients can be predictive of prognosis or response to therapy and in particular how a given TCR re-arrangement, following immunotherapy, can predict a specific clinical outcome. Finally, we will examine current improvements in terms of T-cell sequencing, discussing advantages and challenges of current methodologies.
Collapse
Affiliation(s)
- Nicla Porciello
- grid.417520.50000 0004 1760 5276Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
| | - Ornella Franzese
- grid.6530.00000 0001 2300 0941Department of Systems Medicine, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy
| | - Lorenzo D’Ambrosio
- grid.417520.50000 0004 1760 5276Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
| | - Belinda Palermo
- grid.417520.50000 0004 1760 5276Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
| | - Paola Nisticò
- grid.417520.50000 0004 1760 5276Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
| |
Collapse
|
9
|
Thieme CJ, Schulz M, Wehler P, Anft M, Amini L, Blàzquez-Navarro A, Stervbo U, Hecht J, Nienen M, Stittrich AB, Choi M, Zgoura P, Viebahn R, Schmueck-Henneresse M, Reinke P, Westhoff TH, Roch T, Babel N. In vitro and in vivo evidence that the switch from calcineurin to mTOR inhibitors may be a strategy for immunosuppression in Epstein-Barr virus-associated post-transplant lymphoproliferative disorder. Kidney Int 2022; 102:1392-1408. [PMID: 36103953 DOI: 10.1016/j.kint.2022.08.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 08/02/2022] [Accepted: 08/12/2022] [Indexed: 01/12/2023]
Abstract
Post-transplant lymphoproliferative disorder is a life-threatening complication of immunosuppression following transplantation mediated by failure of T cells to control Epstein-Barr virus (EBV)-infected and transformed B cells. Typically, a modification or reduction of immunosuppression is recommended, but insufficiently defined thus far. In order to help delineate this, we characterized EBV-antigen-specific T cells and lymphoblastoid cell lines from healthy donors and in patients with a kidney transplant in the absence or presence of the standard immunosuppressants tacrolimus, cyclosporin A, prednisolone, rapamycin, and mycophenolic acid. Phenotypes of lymphoblastoid cell-lines and T cells, T cell-receptor-repertoire diversity, and T-cell reactivity upon co-culture with autologous lymphoblastoid cell lines were analyzed. Rapamycin and mycophenolic acid inhibited lymphoblastoid cell-line proliferation. T cells treated with prednisolone and rapamycin showed nearly normal cytokine production. Proliferation and the viability of T cells were decreased by mycophenolic acid, while tacrolimus and cyclosporin A were strong suppressors of T-cell function including their killing activity. Overall, our study provides a basis for the clinical decision for the modification and reduction of immunosuppression and adds information to the complex balance of maintaining anti-viral immunity while preventing acute rejection. Thus, an immunosuppressive regime based on mTOR inhibition and reduced or withdrawn calcineurin inhibitors could be a promising strategy for patients with increased risk of or manifested EBV-associated post-transplant lymphoproliferative disorder.
Collapse
Affiliation(s)
- Constantin J Thieme
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany; Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Malissa Schulz
- Hochschule für Technik und Wirtschaft Berlin (HTW), Berlin, Germany
| | - Patrizia Wehler
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Moritz Anft
- Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, Ruhr-University Bochum, Herne, Germany
| | - Leila Amini
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany; Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Arturo Blàzquez-Navarro
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany; Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, Ruhr-University Bochum, Herne, Germany
| | - Ulrik Stervbo
- Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, Ruhr-University Bochum, Herne, Germany
| | - Jochen Hecht
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain; Experimental and Health Sciences Department, Universitat Pompeu Fabra, Barcelona, Spain
| | - Mikalai Nienen
- Institute of Medical Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | | | - Mira Choi
- Department of Nephrology and Medical Intensive Care, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Panagiota Zgoura
- Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, Ruhr-University Bochum, Herne, Germany
| | - Richard Viebahn
- Department of Surgery, University Hospital Knappschaftskrankenhaus Bochum, Ruhr-University Bochum, Bochum, Germany
| | - Michael Schmueck-Henneresse
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany; Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Petra Reinke
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany; Berlin Center for Advanced Therapies (BeCAT), 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 and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, Ruhr-University Bochum, Herne, Germany
| | - Toralf Roch
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany; Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, Ruhr-University Bochum, Herne, Germany
| | - Nina Babel
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany; Center for Translational Medicine and Immune Diagnostics Laboratory, Medical Department I, Marien Hospital Herne, Ruhr-University Bochum, Herne, Germany.
| |
Collapse
|
10
|
Galigalidou C, Zaragoza-Infante L, Chatzidimitriou A, Stamatopoulos K, Psomopoulos F, Agathangelidis A. Purpose-Built Immunoinformatics for BcR IG/TR Repertoire Data Analysis. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2453:585-603. [PMID: 35622343 DOI: 10.1007/978-1-0716-2115-8_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The study of antigen receptor gene repertoires using next-generation sequencing (NGS) technologies has disclosed an unprecedented depth of complexity, requiring novel computational and analytical solutions. Several bioinformatics workflows have been developed to this end, including the T-cell receptor/immunoglobulin profiler (TRIP), a web application implemented in R shiny, specifically designed for the purposes of comprehensive repertoire analysis, which is the focus of this chapter. TRIP has the potential to perform robust immunoprofiling analysis through the extraction and processing of the IMGT/HighV-Quest output, via a series of functions, ensuring the analysis of high-quality, biologically relevant data through a multilevel process of data filtering. Subsequently, it provides in-depth analysis of antigen receptor gene rearrangements, including (a) clonality assessment; (b) extraction of variable (V), diversity (D), and joining (J) gene repertoires; (c) CDR3 characterization at both the nucleotide and amino acid level; and (d) somatic hypermutation analysis, in the case of immunoglobulin gene rearrangements. Relevant to mention, TRIP enables a high level of customization through the integration of various options in key aspects of the analysis, such as clonotype definition and computation, hence allowing for flexibility without compromising on accuracy.
Collapse
Affiliation(s)
- Chrysi Galigalidou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece.,Department of Molecular Biology and Genetics (MBG), Democritus University of Thrace, Alexandroupolis, Greece
| | - Laura Zaragoza-Infante
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece.,First Department of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Anastasia Chatzidimitriou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece.,Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece. .,Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden.
| | - Fotis Psomopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece.,Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Andreas Agathangelidis
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece.,Department of Biology, School of Science, National and Kapodistrian University of Athens, Athens, Greece
| |
Collapse
|
11
|
Adaptive Immune Receptor Repertoire (AIRR) Community Guide to TR and IG Gene Annotation. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2453:279-296. [PMID: 35622332 DOI: 10.1007/978-1-0716-2115-8_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
High-throughput sequencing of adaptive immune receptor repertoires (AIRR, i.e., IG and TR) has revolutionized the ability to carry out large-scale experiments to study the adaptive immune response. Since the method was first introduced in 2009, AIRR sequencing (AIRR-Seq) has been applied to survey the immune state of individuals, identify antigen-specific or immune-state-associated signatures of immune responses, study the development of the antibody immune response, and guide the development of vaccines and antibody therapies. Recent advancements in the technology include sequencing at the single-cell level and in parallel with gene expression, which allows the introduction of multi-omics approaches to understand in detail the adaptive immune response. Analyzing AIRR-seq data can prove challenging even with high-quality sequencing, in part due to the many steps involved and the need to parameterize each step. In this chapter, we outline key factors to consider when preprocessing raw AIRR-Seq data and annotating the genetic origins of the rearranged receptors. We also highlight a number of common difficulties with common AIRR-seq data processing and provide strategies to address them.
Collapse
|
12
|
Crider J, Quiniou SMA, Felch KL, Showmaker K, Bengtén E, Wilson M. A Comprehensive Annotation of the Channel Catfish ( Ictalurus punctatus) T Cell Receptor Alpha/Delta, Beta, and Gamma Loci. Front Immunol 2021; 12:786402. [PMID: 34899754 PMCID: PMC8656973 DOI: 10.3389/fimmu.2021.786402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/05/2021] [Indexed: 12/28/2022] Open
Abstract
The complete germline repertoires of the channel catfish, Ictalurus punctatus, T cell receptor (TR) loci, TRAD, TRB, and TRG were obtained by analyzing genomic data from PacBio sequencing. The catfish TRB locus spans 214 kb, and contains 112 TRBV genes, a single TRBD gene, 31 TRBJ genes and two TRBC genes. In contrast, the TRAD locus is very large, at 1,285 kb. It consists of four TRDD genes, one TRDJ gene followed by the exons for TRDC, 125 TRAJ genes and the exons encoding the TRAC. Downstream of the TRAC, are 140 TRADV genes, and all of them are in the opposite transcriptional orientation. The catfish TRGC locus spans 151 kb and consists of four diverse V-J-C cassettes. Altogether, this locus contains 15 TRGV genes and 10 TRGJ genes. To place our data into context, we also analyzed the zebrafish TR germline gene repertoires. Overall, our findings demonstrated that catfish possesses a more restricted repertoire compared to the zebrafish. For example, the 140 TRADV genes in catfish form eight subgroups based on members sharing 75% nucleotide identity. However, the 149 TRAD genes in zebrafish form 53 subgroups. This difference in subgroup numbers between catfish and zebrafish is best explained by expansions of catfish TRADV subgroups, which likely occurred through multiple, relatively recent gene duplications. Similarly, 112 catfish TRBV genes form 30 subgroups, while the 51 zebrafish TRBV genes are placed into 36 subgroups. Notably, several catfish and zebrafish TRB subgroups share ancestor nodes. In addition, the complete catfish TR gene annotation was used to compile a TR gene segment database, which was applied in clonotype analysis of an available gynogenetic channel catfish transcriptome. Combined, the TR annotation and clonotype analysis suggested that the expressed TRA, TRB, and TRD repertoires were generated by different mechanisms. The diversity of the TRB repertoire depends on the number of TRBV subgroups and TRBJ genes, while TRA diversity relies on the many different TRAJ genes, which appear to be only minimally trimmed. In contrast, TRD diversity relies on nucleotide additions and the utilization of up to four TRDD segments.
Collapse
Affiliation(s)
- Jonathan Crider
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, United States
| | - Sylvie M A Quiniou
- Warmwater Aquaculture Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Stoneville, MS, United States
| | - Kristianna L Felch
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, United States
| | - Kurt Showmaker
- Department of Pharmacology and Toxicology, University of Mississippi Medical Center, Jackson, MS, United States.,Department of Data Science, John D. Bower School of Population Health, University of Mississippi Medical Center, Jackson, MS, United States
| | - Eva Bengtén
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, United States
| | - Melanie Wilson
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, United States
| |
Collapse
|
13
|
Next Generation Sequencing of Cerebrospinal Fluid B Cell Repertoires in Multiple Sclerosis and Other Neuro-Inflammatory Diseases-A Comprehensive Review. Diagnostics (Basel) 2021; 11:diagnostics11101871. [PMID: 34679570 PMCID: PMC8534365 DOI: 10.3390/diagnostics11101871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/29/2021] [Accepted: 10/05/2021] [Indexed: 11/17/2022] Open
Abstract
During the last few decades, the role of B cells has been well established and redefined in neuro-inflammatory diseases, including multiple sclerosis and autoantibody-associated diseases. In particular, B cell maturation and trafficking across the blood–brain barrier (BBB) has recently been deciphered with the development of next-generation sequencing (NGS) approaches, which allow the assessment of representative cerebrospinal fluid (CSF) and peripheral blood B cell repertoires. In this review, we perform literature research focusing on NGS studies that allow further insights into B cell pathophysiology during neuro-inflammation. Besides the analysis of CSF B cells, the paralleled assessment of peripheral blood B cell repertoire provides deep insights into not only the CSF compartment, but also in B cell trafficking patterns across the BBB. In multiple sclerosis, CSF-specific B cell maturation, in combination with a bidirectional exchange of B cells across the BBB, is consistently detectable. These data suggest that B cells most likely encounter antigen(s) within the CSF and migrate across the BBB, with further maturation also taking place in the periphery. Autoantibody-mediated diseases, such as neuromyelitis optica spectrum disorder and LGI1 / NMDAR encephalitis, also show features of a CSF-specific B cell maturation and clonal connectivity with peripheral blood. In conclusion, these data suggest an intense exchange of B cells across the BBB, possibly feeding autoimmune circuits. Further developments in sequencing technologies will help to dissect the exact pathophysiologic mechanisms of B cells during neuro-inflammation.
Collapse
|
14
|
Zhang Y, Yang X, Zhang Y, Zhang Y, Wang M, Ou JX, Zhu Y, Zeng H, Wu J, Lan C, Zhou HW, Yang W, Zhang Z. Tools for fundamental analysis functions of TCR repertoires: a systematic comparison. Brief Bioinform 2021; 21:1706-1716. [PMID: 31624828 PMCID: PMC7947996 DOI: 10.1093/bib/bbz092] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 07/02/2019] [Accepted: 07/05/2019] [Indexed: 12/30/2022] Open
Abstract
The full set of T cell receptors (TCRs) in an individual is known as his or her TCR repertoire. Defining TCR repertoires under physiological conditions and in response to a disease or vaccine may lead to a better understanding of adaptive immunity and thus has great biological and clinical value. In the past decade, several high-throughput sequencing-based tools have been developed to assign TCRs to germline genes and to extract complementarity-determining region 3 (CDR3) sequences using different algorithms. Although these tools claim to be able to perform the full range of fundamental TCR repertoire analyses, there is no clear consensus of which tool is best suited to particular projects. Here, we present a systematic analysis of 12 available TCR repertoire analysis tools using simulated data, with an emphasis on fundamental analysis functions. Our results shed light on the detailed functions of TCR repertoire analysis tools and may therefore help researchers in the field to choose the right tools for their particular experimental design.
Collapse
Affiliation(s)
- Yanfang Zhang
- State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.,Center for Biomedical Informatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou 510515, China.,Center for Precision Medicine, Shunde Hospital, Southern Medical University, Foshan, Guangdong, 528399, China
| | - Xiujia Yang
- State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.,Center for Biomedical Informatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou 510515, China
| | - Yanxia Zhang
- State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.,Center for Biomedical Informatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yan Zhang
- State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.,Center for Biomedical Informatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Minhui Wang
- State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Jin Xia Ou
- Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Yan Zhu
- State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.,Center for Biomedical Informatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Huikun Zeng
- State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.,Center for Biomedical Informatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jiaqi Wu
- State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.,Center for Biomedical Informatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Chunhong Lan
- State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.,Center for Biomedical Informatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou 510515, China.,Center for Precision Medicine, Shunde Hospital, Southern Medical University, Foshan, Guangdong, 528399, China
| | - Hong-Wei Zhou
- Microbiome Medicine Center, Division of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510282, China
| | - Wei Yang
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, China.,Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Zhenhai Zhang
- State Key Laboratory of Organ Failure Research, National Clinical Research Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.,Center for Biomedical Informatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou 510515, China.,Center for Precision Medicine, Shunde Hospital, Southern Medical University, Foshan, Guangdong, 528399, China
| |
Collapse
|
15
|
Bentham R, Litchfield K, Watkins TBK, Lim EL, Rosenthal R, Martínez-Ruiz C, Hiley CT, Bakir MA, Salgado R, Moore DA, Jamal-Hanjani M, Swanton C, McGranahan N. Using DNA sequencing data to quantify T cell fraction and therapy response. Nature 2021; 597:555-560. [PMID: 34497419 DOI: 10.1038/s41586-021-03894-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 08/10/2021] [Indexed: 02/07/2023]
Abstract
The immune microenvironment influences tumour evolution and can be both prognostic and predict response to immunotherapy1,2. However, measurements of tumour infiltrating lymphocytes (TILs) are limited by a shortage of appropriate data. Whole-exome sequencing (WES) of DNA is frequently performed to calculate tumour mutational burden and identify actionable mutations. Here we develop T cell exome TREC tool (T cell ExTRECT), a method for estimation of T cell fraction from WES samples using a signal from T cell receptor excision circle (TREC) loss during V(D)J recombination of the T cell receptor-α gene (TCRA (also known as TRA)). TCRA T cell fraction correlates with orthogonal TIL estimates and is agnostic to sample type. Blood TCRA T cell fraction is higher in females than in males and correlates with both tumour immune infiltrate and presence of bacterial sequencing reads. Tumour TCRA T cell fraction is prognostic in lung adenocarcinoma. Using a meta-analysis of tumours treated with immunotherapy, we show that tumour TCRA T cell fraction predicts immunotherapy response, providing value beyond measuring tumour mutational burden. Applying T cell ExTRECT to a multi-sample pan-cancer cohort reveals a high diversity of the degree of immune infiltration within tumours. Subclonal loss of 12q24.31-32, encompassing SPPL3, is associated with reduced TCRA T cell fraction. T cell ExTRECT provides a cost-effective technique to characterize immune infiltrate alongside somatic changes.
Collapse
Affiliation(s)
- Robert Bentham
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Kevin Litchfield
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- The Tumour Immunogenomics and Immunosurveillance Lab, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Thomas B K Watkins
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Emilia L Lim
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Rachel Rosenthal
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Carlos Martínez-Ruiz
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Crispin T Hiley
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Maise Al Bakir
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Roberto Salgado
- Department of Pathology, GZA-ZNA, Antwerp, Belgium
- Division of Research, Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia
| | - David A Moore
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Cellular Pathology, University College London Hospitals, London, UK
- Department of Medical Oncology, University College London Hospitals, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Medical Oncology, University College London Hospitals, London, UK
- Cancer Metastasis Lab, University College London Cancer Institute, London, UK
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Department of Medical Oncology, University College London Hospitals, London, UK
| | - Nicholas McGranahan
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
| |
Collapse
|
16
|
Vollmer T, Schlickeiser S, Amini L, Schulenberg S, Wendering DJ, Banday V, Jurisch A, Noster R, Kunkel D, Brindle NR, Savidis I, Akyüz L, Hecht J, Stervbo U, Roch T, Babel N, Reinke P, Winqvist O, Sherif A, Volk HD, Schmueck-Henneresse M. The intratumoral CXCR3 chemokine system is predictive of chemotherapy response in human bladder cancer. Sci Transl Med 2021; 13:13/576/eabb3735. [PMID: 33441425 DOI: 10.1126/scitranslmed.abb3735] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 07/23/2020] [Accepted: 10/14/2020] [Indexed: 12/12/2022]
Abstract
Chemotherapy has direct toxic effects on cancer cells; however, long-term cancer control and complete remission are likely to involve CD8+ T cell immune responses. To study the role of CD8+ T cell infiltration in the success of chemotherapy, we examined patients with muscle invasive bladder cancer (MIBC) who were categorized on the basis of the response to neoadjuvant chemotherapy (NAC). We identified the intratumoral CXCR3 chemokine system (ligands and receptor splice variants) as a critical component for tumor eradication upon NAC in MIBC. Through characterization of CD8+ T cells, we found that stem-like T cell subpopulations with abundant CXCR3alt, a variant form of the CXCL11 receptor, responded to CXCL11 in culture as demonstrated by migration and enhanced effector function. In tumor biopsies of patients with MIBC accessed before treatment, CXCL11 abundance correlated with high numbers of tumor-infiltrating T cells and response to NAC. The presence of CXCR3alt and CXCL11 was associated with improved overall survival in MIBC. Evaluation of both CXCR3alt and CXCL11 enabled discrimination between responder and nonresponder patients with MIBC before treatment. We validated the prognostic role of the CXCR3-CXCL11 chemokine system in an independent cohort of chemotherapy-treated and chemotherapy-naïve patients with MIBC from data in TCGA. In summary, our data revealed stimulatory activity of the CXCR3alt-CXCL11 chemokine system on CD8+ T cells that is predictive of chemotherapy responsiveness in MIBC. This may offer immunotherapeutic options for targeted activation of intratumoral stem-like T cells in solid tumors.
Collapse
Affiliation(s)
- Tino Vollmer
- Institute of Medical Immunology, Charité - Universitätsmedizin Berlin, D-13353 Berlin, Germany.,Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, D-13353 Berlin, Germany.,Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, D-13353 Berlin, Germany
| | - Stephan Schlickeiser
- Institute of Medical Immunology, Charité - Universitätsmedizin Berlin, D-13353 Berlin, Germany.,Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, D-13353 Berlin, Germany
| | - Leila Amini
- Institute of Medical Immunology, Charité - Universitätsmedizin Berlin, D-13353 Berlin, Germany.,Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, D-13353 Berlin, Germany.,Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, D-13353 Berlin, Germany
| | - Sarah Schulenberg
- Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, D-13353 Berlin, Germany
| | - Desiree J Wendering
- Institute of Medical Immunology, Charité - Universitätsmedizin Berlin, D-13353 Berlin, Germany.,Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, D-13353 Berlin, Germany.,Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, D-13353 Berlin, Germany
| | - Viqar Banday
- Department of Surgical and Perioperative Sciences, Urology and Andrology, Umea University, 901 85 Umea, Sweden.,Department of Clinical Microbiology, Immunology, Umea University, 901 85 Umea, Sweden
| | - Anke Jurisch
- Institute of Medical Immunology, Charité - Universitätsmedizin Berlin, D-13353 Berlin, Germany.,Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, D-13353 Berlin, Germany.,Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, D-13353 Berlin, Germany
| | - Rebecca Noster
- Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, D-13353 Berlin, Germany
| | - Desiree Kunkel
- Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, D-13353 Berlin, Germany
| | - Nicola R Brindle
- Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, D-13353 Berlin, Germany
| | - Ioannis Savidis
- Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, D-13353 Berlin, Germany
| | - Levent Akyüz
- Institute of Medical Immunology, Charité - Universitätsmedizin Berlin, D-13353 Berlin, Germany.,Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, D-13353 Berlin, Germany
| | - Jochen Hecht
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Ulrik Stervbo
- Center for Translational Medicine, Medical Clinic I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, D-44623 Herne, Germany
| | - Toralf Roch
- Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, D-13353 Berlin, Germany.,Center for Translational Medicine, Medical Clinic I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, D-44623 Herne, Germany
| | - Nina Babel
- Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, D-13353 Berlin, Germany.,Center for Translational Medicine, Medical Clinic I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, D-44623 Herne, Germany
| | - Petra Reinke
- Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, D-13353 Berlin, Germany.,Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, D-13353 Berlin, Germany
| | - Ola Winqvist
- Department of Clinical Immunology, Karolinska University Hospital, 17 176 Stockholm, Sweden
| | - Amir Sherif
- Department of Surgical and Perioperative Sciences, Urology and Andrology, Umea University, 901 85 Umea, Sweden
| | - Hans-Dieter Volk
- Institute of Medical Immunology, Charité - Universitätsmedizin Berlin, D-13353 Berlin, Germany.,Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, D-13353 Berlin, Germany
| | - Michael Schmueck-Henneresse
- Institute of Medical Immunology, Charité - Universitätsmedizin Berlin, D-13353 Berlin, Germany. .,Berlin Institute of Health Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, D-13353 Berlin, Germany.,Berlin Center for Advanced Therapies (BeCAT), Charité - Universitätsmedizin Berlin, D-13353 Berlin, Germany
| |
Collapse
|
17
|
Dréno B, Khammari A, Fortun A, Vignard V, Saiagh S, Beauvais T, Jouand N, Bercegay S, Simon S, Lang F, Labarrière N. Phase I/II clinical trial of adoptive cell transfer of sorted specific T cells for metastatic melanoma patients. Cancer Immunol Immunother 2021; 70:3015-3030. [PMID: 34120214 PMCID: PMC8423703 DOI: 10.1007/s00262-021-02961-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 05/06/2021] [Indexed: 02/06/2023]
Abstract
Adoptive cell transfer (ACT) of tumor-specific T lymphocytes represents a relevant therapeutic strategy to treat metastatic melanoma patients. Ideal T-cells should combine tumor specificity and reactivity with survival in vivo, while avoiding autoimmune side effects. Here we report results from a Phase I/II clinical trial (NCT02424916, performed between 2015 and 2018) in which 6 metastatic HLA-A2 melanoma patients received autologous antigen-specific T-cells produced from PBMC, after peptide stimulation in vitro, followed by sorting with HLA-peptide multimers and amplification. Each patient received a combination of Melan-A and MELOE-1 polyclonal specific T-cells, whose specificity and anti-tumor reactivity were checked prior to injection, with subcutaneous IL-2. Transferred T-cells were also characterized in terms of functional avidity, diversity and phenotype and their blood persistence was evaluated. An increase in specific T-cells was detected in the blood of all patients at day 1 and progressively disappeared from day 7 onwards. No serious adverse events occurred after this ACT. Clinically, five patients progressed and one patient experienced a partial response following therapy. Melan-A and MELOE-1 specific T-cells infused to this patient were diverse, of high avidity, with a high proportion of T lymphocytes co-expressing PD-1 and TIGIT but few other exhaustion markers. In conclusion, we demonstrated the feasibility and safety of ACT with multimer-sorted Melan-A and MELOE-1 specific T cells to metastatic melanoma patients. The clinical efficacy of such therapeutic strategy could be further enhanced by the selection of highly reactive T-cells, based on PD-1 and TIGIT co-expression, and a combination with ICI, such as anti-PD-1.
Collapse
Affiliation(s)
- Brigitte Dréno
- Dermato-Cancerology Department, CIC 1413, CHU Nantes, Nantes, France.,UTCG, CHU Nantes, Nantes, France.,CRCINA, Inserm, Université de Nantes, 44000, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France.,CHU Nantes, Nantes, France
| | - Amir Khammari
- Dermato-Cancerology Department, CIC 1413, CHU Nantes, Nantes, France.,CRCINA, Inserm, Université de Nantes, 44000, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France.,CHU Nantes, Nantes, France
| | - Agnès Fortun
- CRCINA, Inserm, Université de Nantes, 44000, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France
| | - Virginie Vignard
- CRCINA, Inserm, Université de Nantes, 44000, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France.,CHU Nantes, Nantes, France
| | | | - Tiffany Beauvais
- CRCINA, Inserm, Université de Nantes, 44000, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France.,CHU Nantes, Nantes, France
| | - Nicolas Jouand
- LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France.,SFR Santé, CNRS, Inserm, Inserm UMS 016, CNRS UMS 3556, Université de Nantes, CHU Nantes, 44000, Nantes, France
| | | | - Sylvain Simon
- CRCINA, Inserm, Université de Nantes, 44000, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France
| | - François Lang
- CRCINA, Inserm, Université de Nantes, 44000, Nantes, France. .,LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France.
| | - Nathalie Labarrière
- CRCINA, Inserm, Université de Nantes, 44000, Nantes, France. .,LabEx IGO "Immunotherapy, Graft, Oncology", Nantes, France. .,SFR Santé, CNRS, Inserm, Inserm UMS 016, CNRS UMS 3556, Université de Nantes, CHU Nantes, 44000, Nantes, France.
| |
Collapse
|
18
|
Mölder F, Stervbo U, Loyal L, Bacher P, Babel N, Rahmann S. Rapid T cell receptor interaction grouping with ting. Bioinformatics 2021; 37:3444-3448. [PMID: 33983394 DOI: 10.1093/bioinformatics/btab361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 01/29/2021] [Accepted: 05/11/2021] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Clustering T cell receptor repertoire (TCRR) sequences according to antigen specificity is challenging. The previously published tool GLIPH needs several days to weeks for clustering large repertoires, making its use impractical in larger studies. In addition, the methodology used in GLIPH suffers from shortcomings, including non-determinism, potential loss of significant antigen-specific sequences or inclusion of too many unspecific sequences. RESULTS We present an algorithm for clustering TCRR sequences that scales efficiently to large repertoires. We clustered 36 real datasets with up to 62 000 unique CDR3β sequences using both an implementation of our method called ting, GLIPH and its successsor GLIPH2. While GLIPH required multiple weeks, ting only needed about one minute for the same task. GLIPH2 is comparably fast, but uses a different grouping paradigm. In addition, we found that in naïve repertoires, where no or very few antigen-specific CDR3 sequences or clusters should exist, our method indeed selects much fewer motifs and produces smaller clusters. AVAILABILITY Our method has been implemented in Python as a tool called ting. It is available from GitHub (https://github.com/FelixMoelder/ting) or PyPI under the MIT license.
Collapse
Affiliation(s)
- Felix Mölder
- Genome Informatics, Institute of Human Genetics, University of Duisburg-Essen, 45147 Essen, Germany.,Institute of Pathology, University of Duisburg-Essen, 45147, Germany
| | - Ulrik Stervbo
- Center for Translational Medicine, Medical Clinic I, Marien Hospital Herne, Ruhr-University Bochum, 44623 Herne, Germany
| | - Lucie Loyal
- Si-M/"Der Simulierte Mensch" a science framework of Technische Universität Berlin and Charité - Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin-Brandenburg Center for Regenerative Therapies, 13353 Berlin, Germany.,Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Petra Bacher
- Institute of Immunology, Christian-Albrechts Universität zu Kiel and Universitätsklinik Schleswig-Holstein, Kiel, Germany.,Institute of Clinical Molecular Biology, Christian-Albrechts Universität zu Kiel, Kiel, Germany
| | - Nina Babel
- Center for Translational Medicine, Medical Clinic I, Marien Hospital Herne, Ruhr-University Bochum, 44623 Herne, Germany.,Berlin Institute of Health, Berlin-Brandenburg Center for Regenerative Therapies, 13353 Berlin, Germany.,Charité Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sven Rahmann
- Genome Informatics, Institute of Human Genetics, University of Duisburg-Essen, 45147 Essen, Germany
| |
Collapse
|
19
|
Hong A, Piva M, Liu S, Hugo W, Lomeli SH, Zoete V, Randolph CE, Yang Z, Wang Y, Lee JJ, Lo SJ, Sun L, Vega-Crespo A, Garcia AJ, Shackelford DB, Dubinett SM, Scumpia PO, Byrum SD, Tackett AJ, Donahue TR, Michielin O, Holmen SL, Ribas A, Moriceau G, Lo RS. Durable Suppression of Acquired MEK Inhibitor Resistance in Cancer by Sequestering MEK from ERK and Promoting Antitumor T-cell Immunity. Cancer Discov 2021; 11:714-735. [PMID: 33318037 PMCID: PMC7933113 DOI: 10.1158/2159-8290.cd-20-0873] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 10/05/2020] [Accepted: 11/23/2020] [Indexed: 12/19/2022]
Abstract
MAPK targeting in cancer often fails due to MAPK reactivation. MEK inhibitor (MEKi) monotherapy provides limited clinical benefits but may serve as a foundation for combination therapies. Here, we showed that combining a type II RAF inhibitor (RAFi) with an allosteric MEKi durably prevents and overcomes acquired resistance among cancers with KRAS, NRAS, NF1, BRAF non-V600, and BRAF V600 mutations. Tumor cell-intrinsically, type II RAFi plus MEKi sequester MEK in RAF complexes, reduce MEK/MEK dimerization, and uncouple MEK from ERK in acquired-resistant tumor subpopulations. Immunologically, this combination expands memory and activated/exhausted CD8+ T cells, and durable tumor regression elicited by this combination requires CD8+ T cells, which can be reinvigorated by anti-PD-L1 therapy. Whereas MEKi reduces dominant intratumoral T-cell clones, type II RAFi cotreatment reverses this effect and promotes T-cell clonotypic expansion. These findings rationalize the clinical development of type II RAFi plus MEKi and their further combination with PD-1/L1-targeted therapy. SIGNIFICANCE: Type I RAFi + MEKi are indicated only in certain BRAF V600MUT cancers. In contrast, type II RAFi + MEKi are durably active against acquired MEKi resistance across broad cancer indications, which reveals exquisite MAPK addiction. Allosteric modulation of MAPK protein/protein interactions and temporal preservation of intratumoral CD8+ T cells are mechanisms that may be further exploited.This article is highlighted in the In This Issue feature, p. 521.
Collapse
MESH Headings
- Animals
- Antineoplastic Combined Chemotherapy Protocols/adverse effects
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Cell Line, Tumor
- Disease Models, Animal
- Dose-Response Relationship, Drug
- Drug Resistance, Neoplasm/drug effects
- Extracellular Signal-Regulated MAP Kinases/antagonists & inhibitors
- GTP Phosphohydrolases/genetics
- GTP Phosphohydrolases/metabolism
- Humans
- Immunity, Cellular/drug effects
- Lymphocytes, Tumor-Infiltrating/drug effects
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- Membrane Proteins/genetics
- Membrane Proteins/metabolism
- Mice
- Mitogen-Activated Protein Kinase Kinases/antagonists & inhibitors
- Mutation
- Neoplasms/drug therapy
- Neoplasms/etiology
- Neoplasms/metabolism
- Neoplasms/pathology
- Protein Binding
- Protein Kinase Inhibitors/pharmacology
- Protein Stability
- T-Lymphocytes/drug effects
- T-Lymphocytes/immunology
- T-Lymphocytes/metabolism
- Treatment Outcome
- Xenograft Model Antitumor Assays
Collapse
Affiliation(s)
- Aayoung Hong
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Marco Piva
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Sixue Liu
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Willy Hugo
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Shirley H Lomeli
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Vincent Zoete
- Department of Fundamental Oncology, Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | | | - Zhentao Yang
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Yan Wang
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Jordan J Lee
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Skylar J Lo
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Lu Sun
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Agustin Vega-Crespo
- Division of Hematology/Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Alejandro J Garcia
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, California
- Division of Hematology/Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California
| | - David B Shackelford
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, California
- Division of Pulmonary and Critical Care, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Steven M Dubinett
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, California
- Division of Pulmonary and Critical Care, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Philip O Scumpia
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, California
- Department of Dermatology, Veteran's Administration Greater Los Angeles Healthcare System, Los Angeles, California
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Alan J Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Timothy R Donahue
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, California
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, California
- Division of Surgical Oncology, Department of Surgery, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Olivier Michielin
- Department of Oncology, Ludwig Center for Cancer Research, University of Lausanne, Lausanne, Switzerland
| | - Sheri L Holmen
- Huntsman Cancer Institute and Department of Surgery, University of Utah Health Sciences Center, Salt Lake City, Utah
| | - Antoni Ribas
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, California
- Division of Hematology/Oncology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, California
- Division of Surgical Oncology, Department of Surgery, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Gatien Moriceau
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California.
| | - Roger S Lo
- Division of Dermatology, Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, California.
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, California
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, California
| |
Collapse
|
20
|
Chen SY, Liu CJ, Zhang Q, Guo AY. An ultra-sensitive T-cell receptor detection method for TCR-Seq and RNA-Seq data. Bioinformatics 2021; 36:4255-4262. [PMID: 32399561 DOI: 10.1093/bioinformatics/btaa432] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 04/14/2020] [Accepted: 05/06/2020] [Indexed: 12/30/2022] Open
Abstract
MOTIVATION T-cell receptors (TCRs) function to recognize antigens and play vital roles in T-cell immunology. Surveying TCR repertoires by characterizing complementarity-determining region 3 (CDR3) is a key issue. Due to the high diversity of CDR3 and technological limitation, accurate characterization of CDR3 repertoires remains a great challenge. RESULTS We propose a computational method named CATT for ultra-sensitive and precise TCR CDR3 sequences detection. CATT can be applied on TCR sequencing, RNA-Seq and single-cell TCR(RNA)-Seq data to characterize CDR3 repertoires. CATT integrated de Bruijn graph-based micro-assembly algorithm, data-driven error correction model and Bayesian inference algorithm, to self-adaptively and ultra-sensitively characterize CDR3 repertoires with high performance. Benchmark results of datasets from in silico and experimental data demonstrated that CATT showed superior recall and precision compared with existing tools, especially for data with short read length and small size and single-cell sequencing data. Thus, CATT will be a useful tool for TCR analysis in researches of cancer and immunology. AVAILABILITY AND IMPLEMENTATION http://bioinfo.life.hust.edu.cn/CATT or https://github.com/GuoBioinfoLab/CATT. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Si-Yi Chen
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Chun-Jie Liu
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Qiong Zhang
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.,Department of Biotechnology, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - An-Yuan Guo
- Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| |
Collapse
|
21
|
Chen SY, Yue T, Lei Q, Guo AY. TCRdb: a comprehensive database for T-cell receptor sequences with powerful search function. Nucleic Acids Res 2021; 49:D468-D474. [PMID: 32990749 PMCID: PMC7778924 DOI: 10.1093/nar/gkaa796] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/02/2020] [Accepted: 09/11/2020] [Indexed: 01/05/2023] Open
Abstract
T cells and the T-cell receptor (TCR) repertoire play pivotal roles in immune response and immunotherapy. TCR sequencing (TCR-Seq) technology has enabled accurate profiling TCR repertoire and currently a large number of TCR-Seq data are available in public. Based on the urgent need to effectively re-use these data, we developed TCRdb, a comprehensive human TCR sequences database, by a uniform pipeline to characterize TCR sequences on TCR-Seq data. TCRdb contains more than 277 million highly reliable TCR sequences from over 8265 TCR-Seq samples across hundreds of tissues/clinical conditions/cell types. The unique features of TCRdb include: (i) comprehensive and reliable sequences for TCR repertoire in different samples generated by a strict and uniform pipeline of TCRdb; (ii) powerful search function, allowing users to identify their interested TCR sequences in different conditions; (iii) categorized sample metadata, enabling comparison of TCRs in different sample types; (iv) interactive data visualization charts, describing the TCR repertoire in TCR diversity, length distribution and V-J gene utilization. The TCRdb database is freely available at http://bioinfo.life.hust.edu.cn/TCRdb/ and will be a useful resource in the research and application community of T cell immunology.
Collapse
Affiliation(s)
- Si-Yi Chen
- Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology; Wuhan, 430074, China
| | - Tao Yue
- Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology; Wuhan, 430074, China
| | - Qian Lei
- Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology; Wuhan, 430074, China
| | - An-Yuan Guo
- Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology; Wuhan, 430074, China
| |
Collapse
|
22
|
Somasundaram R, Connelly T, Choi R, Choi H, Samarkina A, Li L, Gregorio E, Chen Y, Thakur R, Abdel-Mohsen M, Beqiri M, Kiernan M, Perego M, Wang F, Xiao M, Brafford P, Yang X, Xu X, Secreto A, Danet-Desnoyers G, Traum D, Kaestner KH, Huang AC, Hristova D, Wang J, Fukunaga-Kalabis M, Krepler C, Ping-Chen F, Zhou X, Gutierrez A, Rebecca VW, Vonteddu P, Dotiwala F, Bala S, Majumdar S, Dweep H, Wickramasinghe J, Kossenkov AV, Reyes-Arbujas J, Santiago K, Nguyen T, Griss J, Keeney F, Hayden J, Gavin BJ, Weiner D, Montaner LJ, Liu Q, Peiffer L, Becker J, Burton EM, Davies MA, Tetzlaff MT, Muthumani K, Wargo JA, Gabrilovich D, Herlyn M. Tumor-infiltrating mast cells are associated with resistance to anti-PD-1 therapy. Nat Commun 2021; 12:346. [PMID: 33436641 PMCID: PMC7804257 DOI: 10.1038/s41467-020-20600-7] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 12/10/2020] [Indexed: 12/11/2022] Open
Abstract
Anti-PD-1 therapy is used as a front-line treatment for many cancers, but mechanistic insight into this therapy resistance is still lacking. Here we generate a humanized (Hu)-mouse melanoma model by injecting fetal liver-derived CD34+ cells and implanting autologous thymus in immune-deficient NOD-scid IL2Rγnull (NSG) mice. Reconstituted Hu-mice are challenged with HLA-matched melanomas and treated with anti-PD-1, which results in restricted tumor growth but not complete regression. Tumor RNA-seq, multiplexed imaging and immunohistology staining show high expression of chemokines, as well as recruitment of FOXP3+ Treg and mast cells, in selective tumor regions. Reduced HLA-class I expression and CD8+/Granz B+ T cells homeostasis are observed in tumor regions where FOXP3+ Treg and mast cells co-localize, with such features associated with resistance to anti-PD-1 treatment. Combining anti-PD-1 with sunitinib or imatinib results in the depletion of mast cells and complete regression of tumors. Our results thus implicate mast cell depletion for improving the efficacy of anti-PD-1 therapy. Immune checkpoint therapies (ICT) are promising for treating various cancers, but response rates vary. Here the authors show, in mouse models, that tumor-infiltrating mast cells colocalize with regulatory T cells, coincide with local reduction of MHC-I and CD8 T cells, and is associated with resistance to ICT, which can be reversed by c-kit inhibitor treatment.
Collapse
Affiliation(s)
| | | | - Robin Choi
- The Wistar Institute, Philadelphia, PA, USA
| | | | | | - Ling Li
- The Wistar Institute, Philadelphia, PA, USA
| | | | | | - Rohit Thakur
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | | | | | | | | | - Fang Wang
- The Wistar Institute, Philadelphia, PA, USA
| | - Min Xiao
- The Wistar Institute, Philadelphia, PA, USA
| | | | - Xue Yang
- The Wistar Institute, Philadelphia, PA, USA
| | - Xiaowei Xu
- Department of Pathology and Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Anthony Secreto
- Department of Medicine, Stem Cell and Xenograft Core, University of Pennsylvania, Philadelphia, PA, USA
| | - Gwenn Danet-Desnoyers
- Department of Medicine, Stem Cell and Xenograft Core, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel Traum
- Department of Genetics and Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Klaus H Kaestner
- Department of Genetics and Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alexander C Huang
- Department of Pathology and Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Johannes Griss
- Division of Immunology, Allergy and Infectious Diseases (DIAID), Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | | | | | | | | | | | - Qin Liu
- The Wistar Institute, Philadelphia, PA, USA
| | | | | | - Elizabeth M Burton
- Department of Surgical Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Michael A Davies
- Department of Melanoma Medical Oncology, University of California, San Francisco, CA, USA
| | - Michael T Tetzlaff
- Department of Pathology and Dermatology, University of California, San Francisco, CA, USA
| | - Kar Muthumani
- The Wistar Institute, Philadelphia, PA, USA.,GeneOne Life Science Inc., Fort Washington, PA, USA
| | - Jennifer A Wargo
- Department of Surgical Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | | | | |
Collapse
|
23
|
SLAMF7 and IL-6R define distinct cytotoxic versus helper memory CD8 + T cells. Nat Commun 2020; 11:6357. [PMID: 33311473 PMCID: PMC7733515 DOI: 10.1038/s41467-020-19002-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 09/18/2020] [Indexed: 12/17/2022] Open
Abstract
The prevailing ‘division of labor’ concept in cellular immunity is that CD8+ T cells primarily utilize cytotoxic functions to kill target cells, while CD4+ T cells exert helper/inducer functions. Multiple subsets of CD4+ memory T cells have been characterized by distinct chemokine receptor expression. Here, we demonstrate that analogous CD8+ memory T-cell subsets exist, characterized by identical chemokine receptor expression signatures and controlled by similar generic programs. Among them, Tc2, Tc17 and Tc22 cells, in contrast to Tc1 and Tc17 + 1 cells, express IL-6R but not SLAMF7, completely lack cytotoxicity and instead display helper functions including CD40L expression. CD8+ helper T cells exhibit a unique TCR repertoire, express genes related to skin resident memory T cells (TRM) and are altered in the inflammatory skin disease psoriasis. Our findings reveal that the conventional view of CD4+ and CD8+ T cell capabilities and functions in human health and disease needs to be revised. We classically consider the T cell compartment divided into cytotoxic CD8+ T cells and multiple, different helper CD4+ T cell subsets. Here the authors demonstrate that distinct memory CD8+ T cell subsets phenotypically inhabit CD4+ T cell like populations including some with helper-like characteristics.
Collapse
|
24
|
Kotouza MT, Gemenetzi K, Galigalidou C, Vlachonikola E, Pechlivanis N, Agathangelidis A, Sandaltzopoulos R, Mitkas PA, Stamatopoulos K, Chatzidimitriou A, Psomopoulos FE. TRIP - T cell receptor/immunoglobulin profiler. BMC Bioinformatics 2020; 21:422. [PMID: 32993478 PMCID: PMC7525938 DOI: 10.1186/s12859-020-03669-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 07/20/2020] [Indexed: 11/16/2022] Open
Abstract
Background Antigen receptors are characterized by an extreme diversity of specificities, which poses major computational and analytical challenges, particularly in the era of high-throughput immunoprofiling by next generation sequencing (NGS). The T cell Receptor/Immunoglobulin Profiler (TRIP) tool offers the opportunity for an in-depth analysis based on the processing of the output files of the IMGT/HighV-Quest tool, a standard in NGS immunoprofiling, through a number of interoperable modules. These provide detailed information about antigen receptor gene rearrangements, including variable (V), diversity (D) and joining (J) gene usage, CDR3 amino acid and nucleotide composition and clonality of both T cell receptors (TR) and B cell receptor immunoglobulins (BcR IG), and characteristics of the somatic hypermutation within the BcR IG genes. TRIP is a web application implemented in R shiny. Results Two sets of experiments have been performed in order to evaluate the efficiency and performance of the TRIP tool. The first used a number of synthetic datasets, ranging from 250k to 1M sequences, and established the linear response time of the tool (about 6 h for 1M sequences processed through the entire BcR IG data pipeline). The reproducibility of the tool was tested comparing the results produced by the main TRIP workflow with the results from a previous pipeline used on the Galaxy platform. As expected, no significant differences were noted between the two tools; although the preselection process seems to be stricter within the TRIP pipeline, about 0.1% more rearrangements were filtered out, with no impact on the final results. Conclusions TRIP is a software framework that provides analytical services on antigen receptor gene sequence data. It is accurate and contains functions for data wrangling, cleaning, analysis and visualization, enabling the user to build a pipeline tailored to their needs. TRIP is publicly available at https://bio.tools/TRIP_-_T-cell_Receptor_Immunoglobulin_Profiler.
Collapse
Affiliation(s)
- Maria Th Kotouza
- Department of Electrical and Computer Engineering, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
| | - Katerina Gemenetzi
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, 57001, Greece
| | - Chrysi Galigalidou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, 57001, Greece
| | - Elisavet Vlachonikola
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, 57001, Greece
| | - Nikolaos Pechlivanis
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, 57001, Greece
| | - Andreas Agathangelidis
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, 57001, Greece
| | - Raphael Sandaltzopoulos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, 68100, Greece
| | - Pericles A Mitkas
- Department of Electrical and Computer Engineering, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, 57001, Greece
| | - Anastasia Chatzidimitriou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, 57001, Greece
| | - Fotis E Psomopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, 57001, Greece. .,Dept of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.
| | | |
Collapse
|
25
|
Norman RA, Ambrosetti F, Bonvin AMJJ, Colwell LJ, Kelm S, Kumar S, Krawczyk K. Computational approaches to therapeutic antibody design: established methods and emerging trends. Brief Bioinform 2020; 21:1549-1567. [PMID: 31626279 PMCID: PMC7947987 DOI: 10.1093/bib/bbz095] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/07/2019] [Accepted: 07/05/2019] [Indexed: 12/31/2022] Open
Abstract
Antibodies are proteins that recognize the molecular surfaces of potentially noxious molecules to mount an adaptive immune response or, in the case of autoimmune diseases, molecules that are part of healthy cells and tissues. Due to their binding versatility, antibodies are currently the largest class of biotherapeutics, with five monoclonal antibodies ranked in the top 10 blockbuster drugs. Computational advances in protein modelling and design can have a tangible impact on antibody-based therapeutic development. Antibody-specific computational protocols currently benefit from an increasing volume of data provided by next generation sequencing and application to related drug modalities based on traditional antibodies, such as nanobodies. Here we present a structured overview of available databases, methods and emerging trends in computational antibody analysis and contextualize them towards the engineering of candidate antibody therapeutics.
Collapse
|
26
|
Field MA. Detecting pathogenic variants in autoimmune diseases using high-throughput sequencing. Immunol Cell Biol 2020; 99:146-156. [PMID: 32623783 PMCID: PMC7891608 DOI: 10.1111/imcb.12372] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/22/2020] [Accepted: 07/02/2020] [Indexed: 12/12/2022]
Abstract
Sequencing the first human genome in 2003 took 15 years and cost $2.7 billion. Advances in sequencing technologies have since decreased costs to the point where it is now feasible to resequence a whole human genome for $1000 in a single day. These advances have allowed the generation of huge volumes of high‐quality human sequence data used to construct increasingly large catalogs of both population‐level and disease‐causing variation. The existence of such databases, coupled with a high‐quality human reference genome, means we are able to interrogate and annotate all types of genetic variation and identify pathogenic variants for many diseases. Increasingly, sequencing‐based approaches are being used to elucidate the underlying genetic cause of autoimmune diseases, a group of roughly 80 polygenic diseases characterized by abnormal immune responses where healthy tissue is attacked. Although sequence data generation has become routine and affordable, significant challenges remain with no gold‐standard methodology to identify pathogenic variants currently available. This review examines the latest methodologies used to identify pathogenic variants in autoimmune diseases and considers available sequencing options and subsequent bioinformatic methodologies and strategies. The development of reliable and robust sequencing and analytic workflows to detect pathogenic variants is critical to realize the potential of precision medicine programs where patient variant information is used to inform clinical practice.
Collapse
Affiliation(s)
- Matt A Field
- Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia.,John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| |
Collapse
|
27
|
Ni Q, Zhang J, Zheng Z, Chen G, Christian L, Grönholm J, Yu H, Zhou D, Zhuang Y, Li QJ, Wan Y. VisTCR: An Interactive Software for T Cell Repertoire Sequencing Data Analysis. Front Genet 2020; 11:771. [PMID: 32849789 PMCID: PMC7416706 DOI: 10.3389/fgene.2020.00771] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 06/29/2020] [Indexed: 11/13/2022] Open
Abstract
Recent progress in high throughput sequencing technologies has provided an opportunity to probe T cell receptor (TCR) repertoire, bringing about an explosion of TCR sequencing data and analysis tools. For easier and more heuristic analysis TCR sequencing data, we developed a client-based HTML program (VisTCR). It has a data storage module and a data analysis module that integrate multiple cutting-edge analysis algorithms in a hierarchical fashion. Researchers can group and re-group samples for different analysis purposes by customized "Experiment Design File." Moreover, the VisTCR provides a user-friendly interactive interface, by all the TCR analysis methods and visualization results can be accessed and saved as tables or graphs in the process of analysis. The source code is freely available at https://github.com/qingshanni/VisTCR.
Collapse
Affiliation(s)
- Qingshan Ni
- Biomedical Analysis Center, Army Medical University, Chongqing, China.,Chongqing Key Laboratory of Cytomics, Chongqing, China
| | - Jianyang Zhang
- Biomedical Analysis Center, Army Medical University, Chongqing, China.,Chongqing Key Laboratory of Cytomics, Chongqing, China
| | | | - Gang Chen
- Biomedical Analysis Center, Army Medical University, Chongqing, China.,Chongqing Key Laboratory of Cytomics, Chongqing, China
| | - Laura Christian
- Department of Immunology, Duke University Medical Center, Durham, NC, United States
| | - Juha Grönholm
- Molecular Development of the Immune System Section, NIAID Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Haili Yu
- Biomedical Analysis Center, Army Medical University, Chongqing, China.,Chongqing Key Laboratory of Cytomics, Chongqing, China
| | - Daxue Zhou
- Biomedical Analysis Center, Army Medical University, Chongqing, China.,Chongqing Key Laboratory of Cytomics, Chongqing, China
| | - Yuan Zhuang
- Department of Immunology, Duke University Medical Center, Durham, NC, United States
| | - Qi-Jing Li
- Department of Immunology, Duke University Medical Center, Durham, NC, United States
| | - Ying Wan
- Biomedical Analysis Center, Army Medical University, Chongqing, China.,Chongqing Key Laboratory of Cytomics, Chongqing, China
| |
Collapse
|
28
|
Abdirama D, Tesch S, Grießbach AS, von Spee-Mayer C, Humrich JY, Stervbo U, Babel N, Meisel C, Alexander T, Biesen R, Bacher P, Scheffold A, Eckardt KU, Hiepe F, Radbruch A, Burmester GR, Riemekasten G, Enghard P. Nuclear antigen-reactive CD4 + T cells expand in active systemic lupus erythematosus, produce effector cytokines, and invade the kidneys. Kidney Int 2020; 99:238-246. [PMID: 32592813 DOI: 10.1016/j.kint.2020.05.051] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 04/01/2020] [Accepted: 05/21/2020] [Indexed: 10/24/2022]
Abstract
Systemic lupus erythematosus is a systemic and chronic autoimmune disease characterized by loss of tolerance towards nuclear antigens with autoreactive CD4+ T cells implicated in disease pathogenesis. However, very little is known about their receptor specificity since the detection of human autoantigen specific CD4+ T cells has been extremely challenging. Here we present an analysis of CD4+ T cells reactive to nuclear antigens using two complementary methods: T cell libraries and antigen-reactive T cell enrichment. The frequencies of nuclear antigen specific CD4+ T cells correlated with disease severity. These autoreactive T cells produce effector cytokines such as interferon-γ, interleukin-17, and interleukin-10. Compared to blood, these cells were enriched in the urine of patients with active lupus nephritis, suggesting an infiltration of the inflamed kidneys. Thus, these previously unrecognized characteristics support a role for nuclear antigen-specific CD4+ T cells in systemic lupus erythematosus.
Collapse
Affiliation(s)
- Dimas Abdirama
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Deutsches Rheuma-Forschungszentrum, a Leibniz Institute, Berlin, Germany
| | - Sebastian Tesch
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Deutsches Rheuma-Forschungszentrum, a Leibniz Institute, Berlin, Germany
| | - Anna-Sophie Grießbach
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Deutsches Rheuma-Forschungszentrum, a Leibniz Institute, Berlin, Germany
| | - Caroline von Spee-Mayer
- Center for Chronic Immunodeficiency, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jens Y Humrich
- Department of Rheumatology and Clinical Immunology, Universitätsklinikum Schleswig-Holstein, Lübeck, Germany
| | - Ulrik Stervbo
- Berlin-Brandenburg Centrum für Regenerative Therapie, Berlin, Germany; Centre for Translational Medicine, Universitätsklinikum der Ruhr-Universität Bochum, Bochum, Germany
| | - Nina Babel
- Berlin-Brandenburg Centrum für Regenerative Therapie, Berlin, Germany; Centre for Translational Medicine, Universitätsklinikum der Ruhr-Universität Bochum, Bochum, Germany
| | - Christian Meisel
- Institute for Medical Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany; Labor Berlin - Charité Vivantes GmbH, Berlin, Germany
| | - Tobias Alexander
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Robert Biesen
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Petra Bacher
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Deutsches Rheuma-Forschungszentrum, a Leibniz Institute, Berlin, Germany
| | - Alexander Scheffold
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Deutsches Rheuma-Forschungszentrum, a Leibniz Institute, Berlin, Germany
| | - Kai-Uwe Eckardt
- Department of Nephrology and Medical Intensive Care, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Falk Hiepe
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Andreas Radbruch
- Deutsches Rheuma-Forschungszentrum, a Leibniz Institute, Berlin, Germany
| | - Gerd-Rüdiger Burmester
- Department of Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Gabriela Riemekasten
- Department of Rheumatology and Clinical Immunology, Universitätsklinikum Schleswig-Holstein, Lübeck, Germany.
| | - Philipp Enghard
- Department of Nephrology and Medical Intensive Care, Charité - Universitätsmedizin Berlin, Berlin, Germany.
| |
Collapse
|
29
|
Mandric I, Rotman J, Yang HT, Strauli N, Montoya DJ, Van Der Wey W, Ronas JR, Statz B, Yao D, Petrova V, Zelikovsky A, Spreafico R, Shifman S, Zaitlen N, Rossetti M, Ansel KM, Eskin E, Mangul S. Profiling immunoglobulin repertoires across multiple human tissues using RNA sequencing. Nat Commun 2020; 11:3126. [PMID: 32561710 PMCID: PMC7305308 DOI: 10.1038/s41467-020-16857-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 05/24/2020] [Indexed: 11/09/2022] Open
Abstract
Profiling immunoglobulin (Ig) receptor repertoires with specialized assays can be cost-ineffective and time-consuming. Here we report ImReP, a computational method for rapid and accurate profiling of the Ig repertoire, including the complementary-determining region 3 (CDR3), using regular RNA sequencing data such as those from 8,555 samples across 53 tissues types from 544 individuals in the Genotype-Tissue Expression (GTEx v6) project. Using ImReP and GTEx v6 data, we generate a collection of 3.6 million Ig sequences, termed the atlas of immunoglobulin repertoires (TAIR), across a broad range of tissue types that often do not have reported Ig repertoires information. Moreover, the flow of Ig clonotypes and inter-tissue repertoire similarities across immune-related tissues are also evaluated. In summary, TAIR is one of the largest collections of CDR3 sequences and tissue types, and should serve as an important resource for studying immunological diseases. Information on immune receptor repertoire provides important insights on disease progression and therapy development, but can be expensive and time-consuming to obtain. Here the authors report ImReP, a computational method that can extract detailed immune repertoire information from existing tissue-specific RNA sequencing data.
Collapse
Affiliation(s)
- Igor Mandric
- Department of Computer Science, University of California, Los Angeles, 404 Westwood Plaza, Los Angeles, CA, 90095, USA
| | - Jeremy Rotman
- Department of Computer Science, University of California, Los Angeles, 404 Westwood Plaza, Los Angeles, CA, 90095, USA.,Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, 1540 Alcazar Street, Los Angeles, CA, 90033, USA
| | - Harry Taegyun Yang
- Department of Computer Science, University of California, Los Angeles, 404 Westwood Plaza, Los Angeles, CA, 90095, USA.,Bioinformatics Interdepartmental Ph.D. Program, University of California, Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA, 90095-1570, USA
| | - Nicolas Strauli
- Biomedical Sciences Graduate Program, University of California, San Francisco, 1675 Owens Street, Suite 310, San Francisco, CA, 94143-0523, USA
| | - Dennis J Montoya
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, 610 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
| | - William Van Der Wey
- Department of Computer Science, University of California, Los Angeles, 404 Westwood Plaza, Los Angeles, CA, 90095, USA
| | - Jiem R Ronas
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, 609 Charles E. Young Drive East, Los Angeles, CA, 90095, USA
| | - Benjamin Statz
- Department of Computer Science, University of California, Los Angeles, 404 Westwood Plaza, Los Angeles, CA, 90095, USA
| | - Douglas Yao
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, 610 Charles E. Young Drive South, Los Angeles, CA, 90095, USA.,Program in Bioinformatics and Integrative Genomics, Harvard Medical School, 10 Shattuck Street, Suite 514, Boston, MA, 02115, USA
| | - Velislava Petrova
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Alex Zelikovsky
- Department of Computer Science, Georgia State University, 33 Gilmer Street SE, Atlanta, GA, 30303, USA.,The Laboratory of Bioinformatics, I.M. Sechenov First Moscow State Medical University, Moscow, 119991, Russia
| | - Roberto Spreafico
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA, 90095, USA
| | - Sagiv Shifman
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Noah Zaitlen
- Department of Medicine, University of California, San Francisco, 533 Parnassus Avenue, San Francisco, CA, 94143, USA
| | - Maura Rossetti
- Immunogenetics Center, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, 1000 Veteran Avenue, Los Angeles, CA, 90095-1652, USA
| | - K Mark Ansel
- Sandler Asthma Basic Research Center, Department of Microbiology and Immunology, University of California, San Francisco, 513 Parnassus Avenue, San Francisco, CA, 94143-0414, USA
| | - Eleazar Eskin
- Department of Computer Science, University of California, Los Angeles, 404 Westwood Plaza, Los Angeles, CA, 90095, USA.,Department of Human Genetics, David Geffen School of Medicine at UCLA, 695 Charles E. Young Drive South, Box 708822, Los Angeles, CA, 90095, USA.,Department of Computational Medicine, David Geffen School of Medicine at UCLA, 73-235 CHS, Los Angeles, CA, 90095, USA
| | - Serghei Mangul
- Department of Computer Science, University of California, Los Angeles, 404 Westwood Plaza, Los Angeles, CA, 90095, USA. .,Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, 1540 Alcazar Street, Los Angeles, CA, 90033, USA. .,Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA, 90095, USA.
| |
Collapse
|
30
|
The Identity Card of T Cells-Clinical Utility of T-cell Receptor Repertoire Analysis in Transplantation. Transplantation 2020; 103:1544-1555. [PMID: 31033649 DOI: 10.1097/tp.0000000000002776] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
There is a clear medical need to change the current strategy of "one-size-fits-all" immunosuppression for controlling transplant rejection to precision medicine and targeted immune intervention. As T cells play a key role in both undesired graft rejection and protection, a better understanding of the fate and function of both alloreactive graft-deteriorating T cells and those protecting to infections is required. The T-cell receptor (TCR) is the individual identity card of each T cell clone and can help to follow single specificities. In this context, tracking of lymphocytes with certain specificity in blood and tissue in clinical follow up is of especial importance. After overcoming technical limitations of the past, novel molecular technologies opened new avenues of diagnostics. Using advantages of next generation sequencing, a method was established for T-cell tracing by detection of variable TCR region as identifiers of individual lymphocyte clones. The current review describes principles of laboratory and computational methods of TCR repertoire analysis, and gives an overview on applications for the basic understanding of transplant biology and immune monitoring. The review also delineates methodological pitfalls and challenges. With the outlook on prediction of antigens in immune-mediated processes including those of unknown causative pathogens, monitoring the fate and function of individual T cell clones, and the adoptive transfer of protective effector or regulatory T cells, this review highlights the current and future capability of TCR repertoire analysis.
Collapse
|
31
|
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. THE JOURNAL OF IMMUNOLOGY 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] [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
|
32
|
Aversa I, Malanga D, Fiume G, Palmieri C. Molecular T-Cell Repertoire Analysis as Source of Prognostic and Predictive Biomarkers for Checkpoint Blockade Immunotherapy. Int J Mol Sci 2020; 21:ijms21072378. [PMID: 32235561 PMCID: PMC7177412 DOI: 10.3390/ijms21072378] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 03/22/2020] [Accepted: 03/28/2020] [Indexed: 02/08/2023] Open
Abstract
The T cells are key players of the response to checkpoint blockade immunotherapy (CBI) and monitoring the strength and specificity of antitumor T-cell reactivity remains a crucial but elusive component of precision immunotherapy. The entire assembly of T-cell receptor (TCR) sequences accounts for antigen specificity and strength of the T-cell immune response. The TCR repertoire hence represents a “footprint” of the conditions faced by T cells that dynamically evolves according to the challenges that arise for the immune system, such as tumor neo-antigenic load. Hence, TCR repertoire analysis is becoming increasingly important to comprehensively understand the nature of a successful antitumor T-cell response, and to improve the success and safety of current CBI.
Collapse
Affiliation(s)
- Ilenia Aversa
- Research Center of Biochemistry and Advanced Molecular Biology, Department of Experimental and Clinical Medicine, University “Magna Græcia” of Catanzaro, 88100 Catanzaro, Italy;
| | - Donatella Malanga
- Interdepartmental Center of Services (CIS), Department of Experimental and Clinical Medicine, University “Magna Græcia” of Catanzaro, 88100 Catanzaro, Italy;
| | - Giuseppe Fiume
- Department of Experimental and Clinical Medicine, University “Magna Græcia” of Catanzaro, 88100 Catanzaro, Italy;
| | - Camillo Palmieri
- Department of Experimental and Clinical Medicine, University “Magna Græcia” of Catanzaro, 88100 Catanzaro, Italy;
- Correspondence:
| |
Collapse
|
33
|
Adaptive immune receptor repertoires, an overview of this exciting field. Immunol Lett 2020; 221:49-55. [PMID: 32113899 DOI: 10.1016/j.imlet.2020.02.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 02/19/2020] [Accepted: 02/26/2020] [Indexed: 12/30/2022]
Abstract
The adaptive immune response in jawed vertebrates relies on the huge diversity and specificity of the B cell and T cell antigen receptors, the immunoglobulins (IG) or antibodies and the T cell receptors (TR), respectively. The high level of diversity has represented a barrier to a comprehensive analysis of the adaptive immune response before the emergence of high-throughput sequencing (HTS) technologies. The size and complexity of HTS data requires the generation of novel computational and analytical approaches, which are transforming how the adaptive immune responses are deciphered to understand the clonal dynamics and properties of antigen-specific B and T cells in response to different kind of antigens. This exciting and rapidly evolving field is not only impacting human and clinical immunology but also comparative immunology. We are now closer to understanding the evolution of adaptive immune response in jawed vertebrates. This review provides an overview about classical and current strategies developed to assess the IG/TR diversity and their applications in basic and clinical immunology.
Collapse
|
34
|
Minervina A, Pogorelyy M, Mamedov I. T‐cell receptor and B‐cell receptor repertoire profiling in adaptive immunity. Transpl Int 2019; 32:1111-1123. [DOI: 10.1111/tri.13475] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 05/09/2019] [Accepted: 06/25/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Anastasia Minervina
- Department of Genomics of Adaptive Immunity M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry RAS Moscow Russia
| | - Mikhail Pogorelyy
- Department of Genomics of Adaptive Immunity M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry RAS Moscow Russia
- Institute of Translational Medicine Pirogov Russian National Research Medical University Moscow Russia
| | - Ilgar Mamedov
- Department of Genomics of Adaptive Immunity M M Shemyakin and Yu A Ovchinnikov Institute of Bioorganic Chemistry RAS Moscow Russia
- Institute of Translational Medicine Pirogov Russian National Research Medical University Moscow Russia
- Laboratory of Molecular Biology Rogachev Federal Scientific and Clinical Centre of Pediatric Hematology Oncology and Immunology Moscow Russia
| |
Collapse
|
35
|
Afzal S, Gil-Farina I, Gabriel R, Ahmad S, von Kalle C, Schmidt M, Fronza R. Systematic comparative study of computational methods for T-cell receptor sequencing data analysis. Brief Bioinform 2019; 20:222-234. [PMID: 29028876 DOI: 10.1093/bib/bbx111] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 08/10/2017] [Indexed: 12/20/2022] Open
Abstract
High-throughput sequencing technologies have exposed the possibilities for the in-depth evaluation of T-cell receptor (TCR) repertoires. These studies are highly relevant to gain insights into human adaptive immunity and to decipher the composition and diversity of antigen receptors in physiological and disease conditions. The major objective of TCR sequencing data analysis is the identification of V, D and J gene segments, complementarity-determining region 3 (CDR3) sequence extraction and clonality analysis. With the advancement in sequencing technologies, new TCR analysis approaches and programs have been developed. However, there is still a deficit of systematic comparative studies to assist in the selection of an optimal analysis approach. Here, we present a detailed comparison of 10 state-of-the-art TCR analysis tools on samples with different complexities by taking into account many aspects such as clonotype detection [unique V(D)J combination], CDR3 identification or accuracy in error correction. We used our in silico and experimental data sets with known clonalities enabling the identification of potential tool biases. We also established a new strategy, named clonal plane, which allows quantifying and comparing the clonality of multiple samples. Our results provide new insights into the effect of method selection on analysis results, and it will assist users in the selection of an appropriate analysis method.
Collapse
Affiliation(s)
- Saira Afzal
- National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg Germany
| | - Irene Gil-Farina
- National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg Germany
| | - Richard Gabriel
- National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg Germany
| | - Shahzad Ahmad
- National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg Germany
| | - Christof von Kalle
- National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg Germany
| | - Manfred Schmidt
- National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg Germany
| | - Raffaele Fronza
- National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg Germany
| |
Collapse
|
36
|
Bioinformatic methods for cancer neoantigen prediction. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2019; 164:25-60. [PMID: 31383407 DOI: 10.1016/bs.pmbts.2019.06.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Tumor cells accumulate aberrations not present in normal cells, leading to presentation of neoantigens on MHC molecules on their surface. These non-self neoantigens distinguish tumor cells from normal cells to the immune system and are thus targets for cancer immunotherapy. The rapid development of molecular profiling platforms, such as next-generation sequencing, has enabled the generation of large datasets characterizing tumor cells. The simultaneous development of algorithms has enabled rapid and accurate processing of these data. Bioinformatic software tools encoding the algorithms can be strung together in a workflow to identify neoantigens. Here, with a focus on high-throughput sequencing, we review state-of-the art bioinformatic tools along with the steps and challenges involved in neoantigen identification and recognition.
Collapse
|
37
|
Killer-like receptors and GPR56 progressive expression defines cytokine production of human CD4 + memory T cells. Nat Commun 2019; 10:2263. [PMID: 31118448 PMCID: PMC6531457 DOI: 10.1038/s41467-019-10018-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 04/10/2019] [Indexed: 12/15/2022] Open
Abstract
All memory T cells mount an accelerated response on antigen reencounter, but significant functional heterogeneity is present within the respective memory T-cell subsets as defined by CCR7 and CD45RA expression, thereby warranting further stratification. Here we show that several surface markers, including KLRB1, KLRG1, GPR56, and KLRF1, help define low, high, or exhausted cytokine producers within human peripheral and intrahepatic CD4+ memory T-cell populations. Highest simultaneous production of TNF and IFN-γ is observed in KLRB1+KLRG1+GPR56+ CD4 T cells. By contrast, KLRF1 expression is associated with T-cell exhaustion and reduced TNF/IFN-γ production. Lastly, TCRβ repertoire analysis and in vitro differentiation support a regulated, progressive expression for these markers during CD4+ memory T-cell differentiation. Our results thus help refine the classification of human memory T cells to provide insights on inflammatory disease progression and immunotherapy development. Despite the current human CD4 memory T cell stratification by CD45RA/CCR7, functional heterogeneities still exist within the respective subsets. Here the authors show that several surface markers, including KLRB1, KLRG1, GPR56 and KLRF1, help to further refine the subsetting of human CD4 memory T cells and provide insights for their differentiation.
Collapse
|
38
|
López-Santibáñez-Jácome L, Avendaño-Vázquez SE, Flores-Jasso CF. The Pipeline Repertoire for Ig-Seq Analysis. Front Immunol 2019; 10:899. [PMID: 31114573 PMCID: PMC6503734 DOI: 10.3389/fimmu.2019.00899] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 04/08/2019] [Indexed: 11/22/2022] Open
Abstract
With the advent of high-throughput sequencing of immunoglobulin genes (Ig-Seq), the understanding of antibody repertoires and their dynamics among individuals and populations has become an exciting area of research. There is an increasing number of computational tools that aid in every step of the immune repertoire characterization. However, since not all tools function identically, every pipeline has its unique rationale and capabilities, creating a rich blend of useful features that may appear intimidating for newcomer laboratories with the desire to plunge into immune repertoire analysis to expand and improve their research; hence, all pipeline strengths and differences may not seem evident. In this review we provide a practical and organized list of the current set of computational tools, focusing on their most attractive features and differences in order to carry out the characterization of antibody repertoires so that the reader better decides a strategic approach for the experimental design, and computational pathways for the analyses of immune repertoires.
Collapse
Affiliation(s)
- Laura López-Santibáñez-Jácome
- Consorcio de Metabolismo de RNA, Instituto Nacional de Medicina Genómica, Mexico City, Mexico.,Maestría en Ciencia de Datos, Instituto Tecnológico Autónomo de México, Mexico City, Mexico
| | | | | |
Collapse
|
39
|
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] [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
|
40
|
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] [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
|
41
|
Heyer EE, Deveson IW, Wooi D, Selinger CI, Lyons RJ, Hayes VM, O'Toole SA, Ballinger ML, Gill D, Thomas DM, Mercer TR, Blackburn J. Diagnosis of fusion genes using targeted RNA sequencing. Nat Commun 2019; 10:1388. [PMID: 30918253 PMCID: PMC6437215 DOI: 10.1038/s41467-019-09374-9] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 02/22/2019] [Indexed: 01/05/2023] Open
Abstract
Fusion genes are a major cause of cancer. Their rapid and accurate diagnosis can inform clinical action, but current molecular diagnostic assays are restricted in resolution and throughput. Here, we show that targeted RNA sequencing (RNAseq) can overcome these limitations. First, we establish that fusion gene detection with targeted RNAseq is both sensitive and quantitative by optimising laboratory and bioinformatic variables using spike-in standards and cell lines. Next, we analyse a clinical patient cohort and improve the overall fusion gene diagnostic rate from 63% with conventional approaches to 76% with targeted RNAseq while demonstrating high concordance for patient samples with previous diagnoses. Finally, we show that targeted RNAseq offers additional advantages by simultaneously measuring gene expression levels and profiling the immune-receptor repertoire. We anticipate that targeted RNAseq will improve clinical fusion gene detection, and its increasing use will provide a deeper understanding of fusion gene biology. Rapid and accurate detection of fusion genes is important in cancer diagnostics. Here, the authors demonstrate that targeted RNA sequencing provides fast, sensitive and quantitative gene fusion detection and overcomes the limitations of approaches currently in clinical use.
Collapse
Affiliation(s)
- Erin E Heyer
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia
| | - Ira W Deveson
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia.,St. Vincent's Clinical School, UNSW Australia, Sydney, 2031, NSW, Australia
| | - Danson Wooi
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia.,St. Vincent's Clinical School, UNSW Australia, Sydney, 2031, NSW, Australia
| | - Christina I Selinger
- Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Sydney, 2050, NSW, Australia
| | - Ruth J Lyons
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia
| | - Vanessa M Hayes
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia.,St. Vincent's Clinical School, UNSW Australia, Sydney, 2031, NSW, Australia.,Faculty of Health Sciences, University of Limpopo, Turfloop Campus, Mankweng, 0727, South Africa.,School of Health Systems and Public Health, University of Pretoria, Pretoria, 0002, South Africa.,Central Clinical School, University of Sydney, Sydney, 2006, NSW, Australia
| | - Sandra A O'Toole
- St. Vincent's Clinical School, UNSW Australia, Sydney, 2031, NSW, Australia.,Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Sydney, 2050, NSW, Australia.,Central Clinical School, University of Sydney, Sydney, 2006, NSW, Australia.,The Kinghorn Cancer Centre and Cancer Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia.,Australian Clinical Labs, Sydney, 2010, NSW, Australia
| | - Mandy L Ballinger
- The Kinghorn Cancer Centre and Cancer Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia
| | - Devinder Gill
- Department of Haematology, Princess Alexandra Hospital, Brisbane, 4102, QLD, Australia
| | - David M Thomas
- The Kinghorn Cancer Centre and Cancer Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia
| | - Tim R Mercer
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia. .,St. Vincent's Clinical School, UNSW Australia, Sydney, 2031, NSW, Australia. .,Altius Institute for Biomedical Sciences, Seattle, 98121, WA, USA.
| | - James Blackburn
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, 2010, NSW, Australia. .,St. Vincent's Clinical School, UNSW Australia, Sydney, 2031, NSW, Australia.
| |
Collapse
|
42
|
Bacher P, Hohnstein T, Beerbaum E, Röcker M, Blango MG, Kaufmann S, Röhmel J, Eschenhagen P, Grehn C, Seidel K, Rickerts V, Lozza L, Stervbo U, Nienen M, Babel N, Milleck J, Assenmacher M, Cornely OA, Ziegler M, Wisplinghoff H, Heine G, Worm M, Siegmund B, Maul J, Creutz P, Tabeling C, Ruwwe-Glösenkamp C, Sander LE, Knosalla C, Brunke S, Hube B, Kniemeyer O, Brakhage AA, Schwarz C, Scheffold A. Human Anti-fungal Th17 Immunity and Pathology Rely on Cross-Reactivity against Candida albicans. Cell 2019; 176:1340-1355.e15. [PMID: 30799037 DOI: 10.1016/j.cell.2019.01.041] [Citation(s) in RCA: 272] [Impact Index Per Article: 54.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 11/06/2018] [Accepted: 01/24/2019] [Indexed: 12/19/2022]
Abstract
Th17 cells provide protection at barrier tissues but may also contribute to immune pathology. The relevance and induction mechanisms of pathologic Th17 responses in humans are poorly understood. Here, we identify the mucocutaneous pathobiont Candida albicans as the major direct inducer of human anti-fungal Th17 cells. Th17 cells directed against other fungi are induced by cross-reactivity to C. albicans. Intestinal inflammation expands total C. albicans and cross-reactive Th17 cells. Strikingly, Th17 cells cross-reactive to the airborne fungus Aspergillus fumigatus are selectively activated and expanded in patients with airway inflammation, especially during acute allergic bronchopulmonary aspergillosis. This indicates a direct link between protective intestinal Th17 responses against C. albicans and lung inflammation caused by airborne fungi. We identify heterologous immunity to a single, ubiquitous member of the microbiota as a central mechanism for systemic induction of human anti-fungal Th17 responses and as a potential risk factor for pulmonary inflammatory diseases.
Collapse
Affiliation(s)
- Petra Bacher
- Institute of Immunology, Christian-Albrechts Universität zu Kiel and Universitätsklinik Schleswig-Holstein, Kiel, Germany; Institute of Clinical Molecular Biology, Christian-Albrechts Universität zu Kiel, Kiel, Germany
| | - Thordis Hohnstein
- Department of Cellular Immunology, Clinic for Rheumatology and Clinical Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Eva Beerbaum
- Department of Cellular Immunology, Clinic for Rheumatology and Clinical Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Marie Röcker
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute (HKI), Jena, Germany
| | - Matthew G Blango
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute (HKI), Jena, Germany
| | - Svenja Kaufmann
- Department of Pediatric Pulmonology, Immunology and Intensive Care Medicine, Cystic Fibrosis Centre Berlin, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Jobst Röhmel
- Department of Pediatric Pulmonology, Immunology and Intensive Care Medicine, Cystic Fibrosis Centre Berlin, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Patience Eschenhagen
- Department of Pediatric Pulmonology, Immunology and Intensive Care Medicine, Cystic Fibrosis Centre Berlin, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Claudia Grehn
- Department of Pediatric Pulmonology, Immunology and Intensive Care Medicine, Cystic Fibrosis Centre Berlin, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | | | | | - Laura Lozza
- Department of Immunology, Max Planck Institute for Infection Biology, Berlin, Germany
| | - 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
- Institute for Medical Immunology, 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
| | | | | | - Oliver A Cornely
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Department I of Internal Medicine, Clinical Trials Centre Cologne (ZKS Köln), German Centre for Infection Research (DZIF) partner site Bonn-Cologne, Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Maren Ziegler
- Labor Dr. Wisplinghoff, Institute for Virology and Microbiology, Witten/Herdecke University, Witten, Germany; Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany
| | - Hilmar Wisplinghoff
- Labor Dr. Wisplinghoff, Institute for Virology and Microbiology, Witten/Herdecke University, Witten, Germany; Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, Germany
| | - Guido Heine
- Department of Dermatology and Allergy, Division of Allergy and Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Margitta Worm
- Department of Dermatology and Allergy, Division of Allergy and Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Britta Siegmund
- Department of Gastroenterology, Rheumatology and Infectious Diseases, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Jochen Maul
- Department of Gastroenterology, Rheumatology and Infectious Diseases, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Gastroenterologie am Bayerischen Platz, Berlin, Germany
| | - Petra Creutz
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Christoph Tabeling
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Division of Pulmonary Inflammation, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Christoph Ruwwe-Glösenkamp
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Leif E Sander
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; German Center for Lung Research (DZL), Berlin, Germany
| | - Christoph Knosalla
- Department of Cardiothoracic and Vascular Surgery, German Heart Center Berlin, Germany; DZHK (German Centre for Cardiovascular Research), partner site Berlin, Berlin, Germany
| | - Sascha Brunke
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute (HKI), Jena, Germany
| | - Bernhard Hube
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute (HKI), Jena, Germany; Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Olaf Kniemeyer
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute (HKI), Jena, Germany
| | - Axel A Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology-Hans Knoell Institute (HKI), Jena, Germany; Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Carsten Schwarz
- Department of Pediatric Pulmonology, Immunology and Intensive Care Medicine, Cystic Fibrosis Centre Berlin, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Alexander Scheffold
- Institute of Immunology, Christian-Albrechts Universität zu Kiel and Universitätsklinik Schleswig-Holstein, Kiel, Germany.
| |
Collapse
|
43
|
Kovaltsuk A, Krawczyk K, Kelm S, Snowden J, Deane CM. Filtering Next-Generation Sequencing of the Ig Gene Repertoire Data Using Antibody Structural Information. THE JOURNAL OF IMMUNOLOGY 2018; 201:3694-3704. [PMID: 30397033 DOI: 10.4049/jimmunol.1800669] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 10/02/2018] [Indexed: 01/29/2023]
Abstract
Next-generation sequencing of the Ig gene repertoire (Ig-seq) produces large volumes of information at the nucleotide sequence level. Such data have improved our understanding of immune systems across numerous species and have already been successfully applied in vaccine development and drug discovery. However, the high-throughput nature of Ig-seq means that it is afflicted by high error rates. This has led to the development of error-correction approaches. Computational error-correction methods use sequence information alone, primarily designating sequences as likely to be correct if they are observed frequently. In this work, we describe an orthogonal method for filtering Ig-seq data, which considers the structural viability of each sequence. A typical natural Ab structure requires the presence of a disulfide bridge within each of its variable chains to maintain the fold. Our Ab Sequence Selector (ABOSS) uses the presence/absence of this bridge as a way of both identifying structurally viable sequences and estimating the sequencing error rate. On simulated Ig-seq datasets, ABOSS is able to identify more than 99% of structurally viable sequences. Applying our method to six independent Ig-seq datasets (one mouse and five human), we show that our error calculations are in line with previous experimental and computational error estimates. We also show how ABOSS is able to identify structurally impossible sequences missed by other error-correction methods.
Collapse
Affiliation(s)
- Aleksandr Kovaltsuk
- Department of Statistics, University of Oxford, Oxford OX1 3LB, United Kingdom; and
| | - Konrad Krawczyk
- Department of Statistics, University of Oxford, Oxford OX1 3LB, United Kingdom; and
| | | | | | - Charlotte M Deane
- Department of Statistics, University of Oxford, Oxford OX1 3LB, United Kingdom; and
| |
Collapse
|
44
|
Simon S, Wu Z, Cruard J, Vignard V, Fortun A, Khammari A, Dreno B, Lang F, Rulli SJ, Labarriere N. TCR Analyses of Two Vast and Shared Melanoma Antigen-Specific T Cell Repertoires: Common and Specific Features. Front Immunol 2018; 9:1962. [PMID: 30214446 PMCID: PMC6125394 DOI: 10.3389/fimmu.2018.01962] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 08/09/2018] [Indexed: 12/11/2022] Open
Abstract
Among Immunotherapeutic approaches for cancer treatment, the adoptive transfer of antigen specific T cells is still a relevant approach, that could have higher efficacy when further combined with immune check-point blockade. A high number of adoptive transfer trials have been performed in metastatic melanoma, due to its high immunogenic potential, either with polyclonal TIL or antigen-specific polyclonal populations. In this setting, the extensive characterization of T cell functions and receptor diversity of infused polyclonal T cells is required, notably for monitoring purposes. We developed a clinical grade procedure for the selection and amplification of polyclonal CD8 T cells, specific for two shared and widely expressed melanoma antigens: Melan-A and MELOE-1. This procedure is currently used in a clinical trial for HLA-A2 metastatic melanoma patients. In this study, we characterized the T-cell diversity (T-cell repertoire) of such T cell populations using a new RNAseq strategy. We first assessed the added-value of TCR receptor sequencing, in terms of sensitivity and specificity, by direct comparison with cytometry analysis of the T cell populations labeled with anti-Vß-specific antibodies. Results from these analyzes also confirmed specific features already reported for Melan-A and MELOE-1 specific T cell repertoires in terms of V-alpha recurrence usage, on a very high number of T cell clonotypes. Furthermore, these analyses also revealed undescribed features, such as the recurrence of a specific motif in the CDR3α region for MELOE-1 specific T cell repertoire. Finally, the analysis of a large number of T cell clonotypes originating from various patients revealed the existence of public CDR3α and ß clonotypes for Melan-A and MELOE-1 specific T cells. In conclusion, this method of high throughput TCR sequencing is a reliable and powerful approach to deeply characterize polyclonal T cell repertoires, and to reveal specific features of a given TCR repertoire, that would be useful for immune follow-up of cancer patients treated by immunotherapeutic approaches.
Collapse
Affiliation(s)
- Sylvain Simon
- CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology," Nantes, France
| | - Zhong Wu
- Qiagen Sciences, Frederick, MD, United States
| | - J Cruard
- CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology," Nantes, France
| | - Virginie Vignard
- CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology," Nantes, France.,Centre Hospitalier Universitaire Nantes, Nantes, France
| | - Agnes Fortun
- CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology," Nantes, France
| | - Amir Khammari
- CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology," Nantes, France.,Department of Dermato-Cancerology of Nantes Hospital, Nantes, France
| | - Brigitte Dreno
- CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology," Nantes, France.,Department of Dermato-Cancerology of Nantes Hospital, Nantes, France
| | - Francois Lang
- CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology," Nantes, France
| | | | - Nathalie Labarriere
- CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France.,LabEx IGO "Immunotherapy, Graft, Oncology," Nantes, France.,Centre Hospitalier Universitaire Nantes, Nantes, France
| |
Collapse
|
45
|
Heather JM, Ismail M, Oakes T, Chain B. High-throughput sequencing of the T-cell receptor repertoire: pitfalls and opportunities. Brief Bioinform 2018; 19:554-565. [PMID: 28077404 PMCID: PMC6054146 DOI: 10.1093/bib/bbw138] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 11/21/2016] [Indexed: 02/06/2023] Open
Abstract
T-cell specificity is determined by the T-cell receptor, a heterodimeric protein coded for by an extremely diverse set of genes produced by imprecise somatic gene recombination. Massively parallel high-throughput sequencing allows millions of different T-cell receptor genes to be characterized from a single sample of blood or tissue. However, the extraordinary heterogeneity of the immune repertoire poses significant challenges for subsequent analysis of the data. We outline the major steps in processing of repertoire data, considering low-level processing of raw sequence files and high-level algorithms, which seek to extract biological or pathological information. The latest generation of bioinformatics tools allows millions of DNA sequences to be accurately and rapidly assigned to their respective variable V and J gene segments, and to reconstruct an almost error-free representation of the non-templated additions and deletions that occur. High-level processing can measure the diversity of the repertoire in different samples, quantify V and J usage and identify private and public T-cell receptors. Finally, we discuss the major challenge of linking T-cell receptor sequence to function, and specifically to antigen recognition. Sophisticated machine learning algorithms are being developed that can combine the paradoxical degeneracy and cross-reactivity of individual T-cell receptors with the specificity of the overall T-cell immune response. Computational analysis will provide the key to unlock the potential of the T-cell receptor repertoire to give insight into the fundamental biology of the adaptive immune system and to provide powerful biomarkers of disease.
Collapse
Affiliation(s)
| | | | | | - Benny Chain
- Division of Infection and Immunity, University College of London, Bloomsbury, UK
| |
Collapse
|
46
|
Maramis C, Gkoufas A, Vardi A, Stalika E, Stamatopoulos K, Hatzidimitriou A, Maglaveras N, Chouvarda I. IRProfiler - a software toolbox for high throughput immune receptor profiling. BMC Bioinformatics 2018; 19:144. [PMID: 29669518 PMCID: PMC5907363 DOI: 10.1186/s12859-018-2144-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 04/03/2018] [Indexed: 12/26/2022] Open
Abstract
Background The study of the huge diversity of immune receptors, often referred to as immune repertoire profiling, is a prerequisite for diagnosis, prognostication and monitoring of hematological disorders. In the era of high-throughput sequencing (HTS), the abundance of immunogenetic data has revealed unprecedented opportunities for the thorough profiling of T-cell receptors (TR) and B-cell receptors (BcR). However, the volume of the data to be analyzed mandates for efficient and ease-to-use immune repertoire profiling software applications. Results This work introduces Immune Repertoire Profiler (IRProfiler), a novel software pipeline that delivers a number of core receptor repertoire quantification and comparison functionalities on high-throughput TR and BcR sequencing data. Adopting 5 alternative clonotype definitions, IRProfiler implements a series of algorithms for 1) data filtering, 2) calculation of clonotype diversity and expression, 3) calculation of gene usage for the V and J subgroups, 4) detection of shared and exclusive clonotypes among multiple repertoires, and 5) comparison of gene usage for V and J subgroups among multiple repertoires. IRProfiler has been implemented as a toolbox of the Galaxy bioinformatics platform, comprising 6 tools. Theoretical and experimental evaluation has shown that the tools of IRProfiler are able to scale well with respect to the size of input dataset(s). IRProfiler has been utilized by a number of recently published studies concerning hematological disorders. Conclusion IRProfiler is made freely available via 3 distribution channels, including the Galaxy Tool Shed. Despite being a new entry in a crowded ecosystem of immune repertoire profiling software, IRProfiler founds its added value on its support for alternative clonotype definitions in conjunction with a combination of properties stemming from its user-centric design, namely ease-of-use, ease-of-access, exploitability of the output data, and analysis flexibility.
Collapse
Affiliation(s)
- Christos Maramis
- Lab of Computing, Medical Informatics & Biomedical-Imaging Technologies, Department of Medicine, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece. .,Institute of Applied Biosiences, Centre for Research & Technology Hellas, 57001, Thermi, Greece.
| | - Athanasios Gkoufas
- Lab of Computing, Medical Informatics & Biomedical-Imaging Technologies, Department of Medicine, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece.,Institute of Applied Biosiences, Centre for Research & Technology Hellas, 57001, Thermi, Greece
| | - Anna Vardi
- Institute of Applied Biosiences, Centre for Research & Technology Hellas, 57001, Thermi, Greece
| | - Evangelia Stalika
- Institute of Applied Biosiences, Centre for Research & Technology Hellas, 57001, Thermi, Greece
| | - Kostas Stamatopoulos
- Institute of Applied Biosiences, Centre for Research & Technology Hellas, 57001, Thermi, Greece
| | | | - Nicos Maglaveras
- Lab of Computing, Medical Informatics & Biomedical-Imaging Technologies, Department of Medicine, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece.,Institute of Applied Biosiences, Centre for Research & Technology Hellas, 57001, Thermi, Greece
| | - Ioanna Chouvarda
- Lab of Computing, Medical Informatics & Biomedical-Imaging Technologies, Department of Medicine, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece.,Institute of Applied Biosiences, Centre for Research & Technology Hellas, 57001, Thermi, Greece
| |
Collapse
|
47
|
Baseline IL-2 and the AIH score can predict the response to standard therapy in paediatric autoimmune hepatitis. Sci Rep 2018; 8:419. [PMID: 29323192 PMCID: PMC5764983 DOI: 10.1038/s41598-017-18818-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 12/18/2017] [Indexed: 12/23/2022] Open
Abstract
Although autoimmune hepatitis (AIH) can be treated with corticosteroid-based first-line therapy, incomplete remission is associated with progressive liver fibrosis. So far accepted predictors of the subsequent treatment response of AIH patients are lacking. Therefore, we analysed baseline parameters, including iron homeostasis and cytokine levels, in 60 children with paediatric AIH (pAIH). In contrast to adults, elevated serum markers indicating iron overload were not commonly found in children. Therefore, ferritin was not predictive of the treatment response in pAIH. Although baseline immunoglobulins were lower in pAIH children with subsequent complete biochemical remission (BR) upon standard first-line therapy, only lower AIH scores (≤16 points) could predict BR upon standard therapy in our training and validation cohorts. Additionally, higher baseline IL-2 and MCP-1/CCL2 levels were associated with BR in a sub-cohort. A combined score of IL-2 level and a simplified AIH score predicted treatment response more precisely than both parameter alone in this sub-cohort. In conclusion, the baseline AIH score could be validated as a predictor of treatment response in pAIH. Additionally, low baseline IL-2 may help identify children who need salvage therapy. This could be important because the use of low-dose IL-2 therapies is being tested in various autoimmune diseases.
Collapse
|
48
|
Christley S, Levin MK, Toby IT, Fonner JM, Monson NL, Rounds WH, Rubelt F, Scarborough W, Scheuermann RH, Cowell LG. VDJPipe: a pipelined tool for pre-processing immune repertoire sequencing data. BMC Bioinformatics 2017; 18:448. [PMID: 29020925 PMCID: PMC5637252 DOI: 10.1186/s12859-017-1853-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 10/02/2017] [Indexed: 12/20/2022] Open
Abstract
Background Pre-processing of high-throughput sequencing data for immune repertoire profiling is essential to insure high quality input for downstream analysis. VDJPipe is a flexible, high-performance tool that can perform multiple pre-processing tasks with just a single pass over the data files. Results Processing tasks provided by VDJPipe include base composition statistics calculation, read quality statistics calculation, quality filtering, homopolymer filtering, length and nucleotide filtering, paired-read merging, barcode demultiplexing, 5′ and 3′ PCR primer matching, and duplicate reads collapsing. VDJPipe utilizes a pipeline approach whereby multiple processing steps are performed in a sequential workflow, with the output of each step passed as input to the next step automatically. The workflow is flexible enough to handle the complex barcoding schemes used in many immunosequencing experiments. Because VDJPipe is designed for computational efficiency, we evaluated this by comparing execution times with those of pRESTO, a widely-used pre-processing tool for immune repertoire sequencing data. We found that VDJPipe requires <10% of the run time required by pRESTO. Conclusions VDJPipe is a high-performance tool that is optimized for pre-processing large immune repertoire sequencing data sets.
Collapse
Affiliation(s)
- Scott Christley
- Department of Clinical Sciences, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | | | - Inimary T Toby
- Department of Clinical Sciences, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - John M Fonner
- Texas Advanced Computing Center, Austin, TX, 78758-4497, USA
| | - Nancy L Monson
- Department of Neurology and Neurotherapeutics, UT Southwestern Medical Center, Dallas, TX, 75390, USA.,Department of Immunology, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - William H Rounds
- Department of Clinical Sciences, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Florian Rubelt
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | | | - Richard H Scheuermann
- J. Craig Venter Institute, La Jolla, CA, 92037, USA.,Department of Pathology, University of California, San Diego, CA, 92093, USA.,La Jolla Institute for Allergy & Immunology, La Jolla, CA, 92037, USA
| | - Lindsay G Cowell
- Department of Clinical Sciences, UT Southwestern Medical Center, Dallas, TX, 75390, USA.
| |
Collapse
|
49
|
Abstract
PURPOSE OF REVIEW The genetic susceptibility and dominant protection for type 1 diabetes (T1D) associated with human leukocyte antigen (HLA) haplotypes, along with minor risk variants, have long been thought to shape the T cell receptor (TCR) repertoire and eventual phenotype of autoreactive T cells that mediate β-cell destruction. While autoantibodies provide robust markers of disease progression, early studies tracking autoreactive T cells largely failed to achieve clinical utility. RECENT FINDINGS Advances in acquisition of pancreata and islets from T1D organ donors have facilitated studies of T cells isolated from the target tissues. Immunosequencing of TCR α/β-chain complementarity determining regions, along with transcriptional profiling, offers the potential to transform biomarker discovery. Herein, we review recent studies characterizing the autoreactive TCR signature in T1D, emerging technologies, and the challenges and opportunities associated with tracking TCR molecular profiles during the natural history of T1D.
Collapse
Affiliation(s)
- Laura M Jacobsen
- Department of Pediatrics, College of Medicine, University of Florida Diabetes Institute, Gainesville, FL, USA
| | - Amanda Posgai
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida Diabetes Institute, Gainesville, FL, USA
| | - Howard R Seay
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida Diabetes Institute, Gainesville, FL, USA
| | - Michael J Haller
- Department of Pediatrics, College of Medicine, University of Florida Diabetes Institute, Gainesville, FL, USA
| | - Todd M Brusko
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida Diabetes Institute, Gainesville, FL, USA.
| |
Collapse
|
50
|
Shlemov A, Bankevich S, Bzikadze A, Turchaninova MA, Safonova Y, Pevzner PA. Reconstructing Antibody Repertoires from Error-Prone Immunosequencing Reads. THE JOURNAL OF IMMUNOLOGY 2017; 199:3369-3380. [PMID: 28978691 DOI: 10.4049/jimmunol.1700485] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 08/24/2017] [Indexed: 12/16/2022]
Abstract
Transforming error-prone immunosequencing datasets into Ab repertoires is a fundamental problem in immunogenomics, and a prerequisite for studies of immune responses. Although various repertoire reconstruction algorithms were released in the last 3 y, it remains unclear how to benchmark them and how to assess the accuracy of the reconstructed repertoires. We describe an accurate IgReC algorithm for constructing Ab repertoires from high-throughput immunosequencing datasets and a new framework for assessing the quality of reconstructed repertoires. Surprisingly, Ab repertoires constructed by IgReC from barcoded immunosequencing datasets in the blind mode (without using information about unique molecular identifiers) improved upon the repertoires constructed by the state-of-the-art tools that use barcoding. This finding suggests that IgReC may alleviate the need to generate repertoires using the barcoding technology (the workhorse of current immunogenomics efforts) because our computational approach to error correction of immunosequencing data is nearly as powerful as the experimental approach based on barcoding.
Collapse
Affiliation(s)
- Alexander Shlemov
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg University, St. Petersburg, Russia 199034
| | - Sergey Bankevich
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg University, St. Petersburg, Russia 199034
| | - Andrey Bzikadze
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg University, St. Petersburg, Russia 199034
| | - Maria A Turchaninova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia 117997
| | - Yana Safonova
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg University, St. Petersburg, Russia 199034; .,Information Theory and Applications Center, University of California, San Diego, La Jolla, CA 92093; and
| | - Pavel A Pevzner
- Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg University, St. Petersburg, Russia 199034.,Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093
| |
Collapse
|