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Immune repertoire sequencing

Holger Winkels, Erik Ehinger, Melanie Vassallo, Konrad Buscher, Huy Dinh, Kouji Kobiyama, Anouk Hamers, Clément Cochain, Ehsan Vafadarnejad, Antoine-Emmanuel Saliba, Alma Zernecke, Akula Pramod, Amlan Ghosh, Nathaly Anto Michel, Natalie Hoppe, Ingo Hilgendorf, Andreas Zirlik, Catherine Hedrick, Klaus Ley, Dennis Wolf
<u>Rationale:</u> Atherosclerosis is a chronic inflammatory disease that is driven by the interplay of pro- and anti-inflammatory leukocytes in the aorta. Yet, the phenotypic and transcriptional diversity of aortic leukocytes is only poorly understood. <u>Objective:</u> We characterized leukocytes from healthy and atherosclerotic mouse aortas in-depth by single cell RNA-sequencing (scRNAseq) and mass cytometry (CyTOF) to define an atlas of the immune cell landscape in atherosclerosis...
March 15, 2018: Circulation Research
Taigo Kato, Tatsuo Matsuda, Yuji Ikeda, Jae-Hyun Park, Matthias Leisegang, Sachiko Yoshimura, Tetsuro Hikichi, Makiko Harada, Makda Zewde, Sho Sato, Kosei Hasegawa, Kazuma Kiyotani, Yusuke Nakamura
Neoantigens are the main targets of tumor-specific T cells reactivated by immune checkpoint-blocking antibodies or when using tumor-infiltrating T cells for adoptive therapy. While cancers often accumulate hundreds of mutations and harbor several immunogenic neoantigens, the repertoire of mutation-specific T cells in patients might be restricted. To bypass suboptimal conditions, which impede the reactivation of existing T cells or the priming of neoantigen-specific T cells in a patient, we employ T cells of healthy donors with an overlapping HLA repertoire to target cancer neoantigens...
February 16, 2018: Oncotarget
Mikhail V Pogorelyy, Anastasia A Minervina, Dmitriy M Chudakov, Ilgar Z Mamedov, Yuri B Lebedev, Thierry Mora, Aleksandra M Walczak
Diverse repertoires of hypervariable immunoglobulin receptors (TCR and BCR) recognize antigens in the adaptive immune system. The development of immunoglobulin receptor repertoire sequencing methods makes it possible to perform repertoire-wide disease association studies of antigen receptor sequences. We developed a statistical framework for associating receptors to disease from only a small cohort of patients, with no need for a control cohort. Our method successfully identifies previously validated Cytomegalovirus and type 1 diabetes responsive TCR β sequences...
March 13, 2018: ELife
Kostas Patas, Anne Willing, Cüneyt Demiralay, Jan Broder Engler, Andreea Lupu, Caren Ramien, Tobias Schäfer, Christian Gach, Laura Stumm, Kenneth Chan, Marissa Vignali, Petra C Arck, Manuel A Friese, Ole Pless, Klaus Wiedemann, Agorastos Agorastos, Stefan M Gold
While a link between inflammation and the development of neuropsychiatric disorders, including major depressive disorder (MDD) is supported by a growing body of evidence, little is known about the contribution of aberrant adaptive immunity in this context. Here, we conducted in-depth characterization of T cell phenotype and T cell receptor (TCR) repertoire in MDD. For this cross-sectional case-control study, we recruited antidepressant-free patients with MDD without any somatic or psychiatric comorbidities ( n  = 20), who were individually matched for sex, age, body mass index, and smoking status to a non-depressed control subject ( n  = 20)...
2018: Frontiers in Immunology
Enkelejda Miho, Alexander Yermanos, Cédric R Weber, Christoph T Berger, Sai T Reddy, Victor Greiff
The adaptive immune system recognizes antigens via an immense array of antigen-binding antibodies and T-cell receptors, the immune repertoire. The interrogation of immune repertoires is of high relevance for understanding the adaptive immune response in disease and infection (e.g., autoimmunity, cancer, HIV). Adaptive immune receptor repertoire sequencing (AIRR-seq) has driven the quantitative and molecular-level profiling of immune repertoires, thereby revealing the high-dimensional complexity of the immune receptor sequence landscape...
2018: Frontiers in Immunology
Chaofei Cheng, Bei Wang, Lei Gao, Jianmin Liu, Xinchun Chen, He Huang, Zhendong Zhao
Tuberculosis (TB) is a severe global threat to human health. The immune protection initiated by γδ T cells play an important role in mycobacterial infection. Vaccines for Mycobacterium tuberculosis (Mtb) based on γδ T cells provide a novel approach for TB control. In our previous studies, we found a preponderant complementarity-determining region 3 (CDR3) sequence of the γδ T cell receptor (TCR) in TB patients, and successfully identified a tuberculosis antigen that can effectively activate γδ T cells with a reverse genetic strategy...
March 2, 2018: Scientific Reports
Linnea Thörnqvist, Mats Ohlin
Inference of antibody gene repertoires using transcriptome data has emerged as an alternative approach to the complex process of sequencing of adaptive immune receptor germline gene loci. The diversity introduced during rearrangement of immunoglobulin heavy chain variable (IGHV), diversity, and joining genes has however been identified as potentially affecting inference specificity. In this study, we have addressed this issue by analysing the nucleotide composition of unmutated human immunoglobulin heavy chains-encoding transcripts, focusing on the 3ö most bases of 47 IGHV germline genes...
February 27, 2018: Molecular Immunology
João Luís Reis-Cunha, Hugo O Valdivia, Daniella Castanheira Bartholomeu
Trypanosomatids are a group of kinetoplastid parasites including some of great public health importance, causing debilitating and life-long lasting diseases that affect more than 24 million people worldwide. Among the trypanosomatids, Trypanosoma cruzi, Trypanosoma brucei and species from the Leishmania genus are the most well studied parasites, due to their high prevalence in human infections. These parasites have an extreme genomic and phenotypic variability, with a massive expansion in the copy number of species-specific multigene families enrolled in host-parasite interactions that mediate cellular invasion and immune evasion processes...
February 2018: Current Genomics
Xiao Liu, Jinghua Wu
The diversity of T and B cells in terms of their receptor sequences is huge in the vertebrate's immune system and provides broad protection against the vast diversity of pathogens. Immune repertoire is defined as the sum of T cell receptors and B cell receptors (also named immunoglobulin) that makes the organism's adaptive immune system. Before the emergence of high-throughput sequencing, the studies on immune repertoire were limited by the underdeveloped methodologies, since it was impossible to capture the whole picture by the low-throughput tools...
February 27, 2018: Cell Biology and Toxicology
Ekaterina A Komech, Mikhail V Pogorelyy, Evgeniy S Egorov, Olga V Britanova, Denis V Rebrikov, Anna G Bochkova, Evgeniya I Shmidt, Nadejda A Shostak, Mikhail Shugay, Sergey Lukyanov, Ilgar Z Mamedov, Yuriy B Lebedev, Dmitriy M Chudakov, Ivan V Zvyagin
Objective: The risk of AS is associated with genomic variants related to antigen presentation and specific cytokine signalling pathways, suggesting the involvement of cellular immunity in disease initiation/progression. The aim of the present study was to explore the repertoire of TCR sequences in healthy donors and AS patients to uncover AS-linked TCR variants. Methods: Using quantitative molecular-barcoded 5'-RACE, we performed deep TCR β repertoire profiling of peripheral blood (PB) and SF samples for 25 AS patients and 108 healthy donors...
February 22, 2018: Rheumatology
Claire Ward, Trisha A Rettig, Savannah Hlavacek, Bailey A Bye, Michael J Pecaut, Stephen K Chapes
Spaceflight has been shown to suppress the adaptive immune response, altering the distribution and function of lymphocyte populations. B lymphocytes express highly specific and highly diversified receptors, known as immunoglobulins (Ig), that directly bind and neutralize pathogens. Ig diversity is achieved through the enzymatic splicing of gene segments within the genomic DNA of each B cell in a host. The collection of Ig specificities within a host, or Ig repertoire, has been increasingly characterized in both basic research and clinical settings using high-throughput sequencing technology (HTS)...
February 2018: Life Sciences in Space Research
Gesine Behrens, Reinhard Winzen, Nina Rehage, Anneke Dörrie, Monika Barsch, Anne Hoffmann, Jörg Hackermüller, Christopher Tiedje, Vigo Heissmeyer, Helmut Holtmann
The expression of proteins during inflammatory and immune reactions is coordinated by post-transcriptional mechanisms. A particularly strong suppression of protein expression is exerted by a conserved translational silencing element (TSE) identified in the 3' UTR of NFKBIZ mRNA, which is among the targets of the RNA-binding proteins Roquin-1/2 and MCPIP1/Regnase-1. We present evidence that in the context of the TSE MCPIP1, so far known for its endonuclease activity toward mRNAs specified by distinct stem-loop (SL) structures, also suppresses translation...
February 19, 2018: Nucleic Acids Research
Ke-Yue Ma, Chenfeng He, Ben S Wendel, Chad M Williams, Jun Xiao, Hui Yang, Ning Jiang
Unique molecular identifiers (MIDs) have been demonstrated to effectively improve immune repertoire sequencing (IR-seq) accuracy, especially to identify somatic hypermutations in antibody repertoire sequencing. However, evaluating the sensitivity to detect rare T cells and the degree of clonal expansion in IR-seq has been difficult due to the lack of knowledge of T cell receptor (TCR) RNA molecule copy number and a generalized approach to estimate T cell clone size from TCR RNA molecule quantification. This limited the application of TCR repertoire sequencing (TCR-seq) in clinical settings, such as detecting minimal residual disease in lymphoid malignancies after treatment, evaluating effectiveness of vaccination and assessing degree of infection...
2018: Frontiers in Immunology
Binbin Hong, Yanling Wu, Wei Li, Xun Wang, Yumei Wen, Shibo Jiang, Dimiter S Dimitrov, Tianlei Ying
Although high-throughput sequencing and associated bioinformatics technologies have enabled the in-depth, sequence-based characterization of human immune repertoires, only a few studies on a relatively small number of sequences explored the characteristics of antibody repertoires in neonates, with contradictory conclusions. To gain a more comprehensive understanding of the human IgM antibody repertoire, we performed Illumina sequencing and IMGT/HighV-QUEST analysis of IgM heavy chain repertoire of the B lymphocytes from the cord blood (CB) of neonates, as well as the repertoire from peripheral blood of healthy human adults (HH)...
2018: Frontiers in Immunology
Arjun K Mishra, Roy A Mariuzza
Affinity maturation is the process whereby the immune system generates antibodies of higher affinities during a response to antigen. It is unique in being the only evolutionary mechanism known to operate on a molecule in an organism's own body. Deciphering the structural mechanisms through which somatic mutations in antibody genes increase affinity is critical to understanding the evolution of immune repertoires. Next-generation sequencing (NGS) has allowed the reconstruction of antibody clonal lineages in response to viral pathogens, such as HIV-1, which was not possible in earlier studies of affinity maturation...
2018: Frontiers in Immunology
Malte Mohme, Simon Schliffke, Cecile L Maire, Alessandra Rünger, Laura Glau, Klaus C Mende, Jakob Matschke, Christina Gehbauer, Nuray Akyüz, Svenja Zapf, Mareike Holz, Miriam Schaper, Tobias Martens, Nils O Schmidt, Sven Peine, Manfred Westphal, Mascha Binder, Eva Tolosa, Katrin Lamszus
PURPOSE: Immunotherapeutic treatment strategies for glioblastoma (GBM) are under investigation in clinical trials. However, our understanding of the immune phenotype of GBM-infiltrating T-cells (TILs) and changes during disease progression is limited. Deeper insight is urgently needed to therapeutically overcome tumor-induced immune exhaustion. EXPERIMENTAL DESIGN: We used flow-cytometry and cytokine assays to profile TILs and blood lymphocytes (PBL) from GBM patients, comparing newly diagnosed or recurrent GBM to long-term survivors (LTS) and healthy donors...
February 14, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
Fleur S van de Bovenkamp, Ninotska I L Derksen, Pleuni Ooijevaar-de Heer, Karin A van Schie, Simone Kruithof, Magdalena A Berkowska, C Ellen van der Schoot, Hanna IJspeert, Mirjam van der Burg, Ann Gils, Lise Hafkenscheid, René E M Toes, Yoann Rombouts, Rosina Plomp, Manfred Wuhrer, S Marieke van Ham, Gestur Vidarsson, Theo Rispens
A hallmark of B-cell immunity is the generation of a diverse repertoire of antibodies from a limited set of germline V(D)J genes. This repertoire is usually defined in terms of amino acid composition. However, variable domains may also acquire N -linked glycans, a process conditional on the introduction of consensus amino acid motifs ( N -glycosylation sites) during somatic hypermutation. High levels of variable domain glycans have been associated with autoantibodies in rheumatoid arthritis, as well as certain follicular lymphomas...
February 5, 2018: Proceedings of the National Academy of Sciences of the United States of America
Quentin Marcou, Thierry Mora, Aleksandra M Walczak
High-throughput immune repertoire sequencing is promising to lead to new statistical diagnostic tools for medicine and biology. Successful implementations of these methods require a correct characterization, analysis, and interpretation of these data sets. We present IGoR (Inference and Generation Of Repertoires)-a comprehensive tool that takes B or T cell receptor sequence reads and quantitatively characterizes the statistics of receptor generation from both cDNA and gDNA. It probabilistically annotates sequences and its modular structure can be used to investigate models of increasing biological complexity for different organisms...
February 8, 2018: Nature Communications
Valentina Giudice, Xingmin Feng, Zenghua Lin, Wei Hu, Fanmao Zhang, Wangmin Qiao, Maria Del Pilar Fernandez Ibanez, Olga Rios, Neal S Young
Oligoclonal expansion of CD8+CD28- lymphocytes has been considered indirect evidence for a pathogenic immune response in acquired aplastic anemia. A subset of CD8+CD28- cells with CD57 expression termed effector memory cells is expanded in several immune mediated diseases and may have a role in immune surveillance. We hypothesized that effector memory CD8+CD28-CD57+ cells may drive aberrant oligoclonal expansion in aplastic anemia. We found CD8+CD57+ cells frequently expanded in the blood of aplastic anemia patients, with oligoclonal characteristics by flow cytometric Vβ usage analysis: skewing in 1 to 5 Vβ families and frequencies of immunodominant clones ranging from 1...
February 1, 2018: Haematologica
Katja Sonntag, Hisayoshi Hashimoto, Matthias Eyrich, Moritz Menzel, Max Schubach, Dennis Döcker, Florian Battke, Carolina Courage, Helmut Lambertz, Rupert Handgretinger, Saskia Biskup, Karin Schilbach
BACKGROUND: Cancer vaccines can effectively establish clinically relevant tumor immunity. Novel sequencing approaches rapidly identify the mutational fingerprint of tumors, thus allowing to generate personalized tumor vaccines within a few weeks from diagnosis. Here, we report the case of a 62-year-old patient receiving a four-peptide-vaccine targeting the two sole mutations of his pancreatic tumor, identified via exome sequencing. METHODS: Vaccination started during chemotherapy in second complete remission and continued monthly thereafter...
February 6, 2018: Journal of Translational Medicine
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