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Immune repertoire sequencing

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https://www.readbyqxmd.com/read/28520808/proteomic-analysis-of-biomphalaria-glabrata-plasma-proteins-with-binding-affinity-to-those-expressed-by-early-developing-larval-schistosoma-mansoni
#1
Xiao-Jun Wu, Nathalie Dinguirard, Grzegorz Sabat, Hong-di Lui, Laura Gonzalez, Michael Gehring, Utibe Bickham-Wright, Timothy P Yoshino
Interactions between early developing Schistosoma mansoni larval stages and the hemolymph of its snail intermediate host represent the first molecular encounter with the snail's immune system. To gain a more comprehensive understanding of this early parasite-host interaction, biotinylated sporocyst tegumental membrane (Mem) proteins and larval transformation proteins (LTP) were affixed to streptavidin-agarose beads and used as affinity matrices to enrich for larval-reactive plasma proteins from susceptible (NMRI) and resistant (BS-90) strains of the snail Biomphalaria glabrata...
May 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28520789/antigen-specific-immunoglobulin-variable-region-sequencing-measures-humoral-immune-response-to-vaccination-in-the-equine-neonate
#2
Rebecca L Tallmadge, Steven C Miller, Stephen A Parry, Maria Julia B Felippe
The value of prophylactic neonatal vaccination is challenged by the interference of passively transferred maternal antibodies and immune competence at birth. Taken our previous studies on equine B cell ontogeny, we hypothesized that the equine neonate generates a diverse immunoglobulin repertoire in response to vaccination, independently of circulating maternal antibodies. In this study, equine neonates were vaccinated with 3 doses of keyhole limpet hemocyanin (KLH) or equine influenza vaccine, and humoral immune responses were assessed using antigen-specific serum antibodies and B cell Ig variable region sequencing...
2017: PloS One
https://www.readbyqxmd.com/read/28517930/middle-down-193-nm-ultraviolet-photodissociation-for-unambiguous-antibody-identification-and-its-implications-for-immunoproteomic-analysis
#3
Victoria C Cotham, Andrew Pitchford Horton, Jiwon Lee, George Georgiou, Jennifer S Brodbelt
Mass spectrometry (MS) has emerged as a powerful tool within the growing field of immunoproteomics, which aims to understand antibody-mediated immunity at the molecular-level based on the direct determination of serological antibody repertoire. To date, these methods have relied on the use of high-resolution bottom-up proteomic strategies that require effective sampling and characterization of low abundance peptides derived from the antigen-binding domains of polyclonal antibody mixtures. Herein, we describe a method that uses restricted Lys-C enzymatic digestion to increase the average mass of proteolytic IgG peptides (≥4...
May 18, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28515723/different-somatic-hypermutation-levels-among-antibody-subclasses-disclosed-by-a-new-next-generation-sequencing-based-antibody-repertoire-analysis
#4
Kazutaka Kitaura, Hiroshi Yamashita, Hitomi Ayabe, Tadasu Shini, Takaji Matsutani, Ryuji Suzuki
A diverse antibody repertoire is primarily generated by the rearrangement of V, D, and J genes and subsequent somatic hypermutation (SHM). Class-switch recombination (CSR) produces various isotypes and subclasses with different functional properties. Although antibody isotypes and subclasses are considered to be produced by both direct and sequential CSR, it is still not fully understood how SHMs accumulate during the process in which antibody subclasses are generated. Here, we developed a new next-generation sequencing (NGS)-based antibody repertoire analysis capable of identifying all antibody isotype and subclass genes and used it to examine the peripheral blood mononuclear cells of 12 healthy individuals...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28514665/systems-analysis-reveals-high-genetic-and-antigen-driven-predetermination-of-antibody-repertoires-throughout-b-cell-development
#5
Victor Greiff, Ulrike Menzel, Enkelejda Miho, Cédric Weber, René Riedel, Skylar Cook, Atijeh Valai, Telma Lopes, Andreas Radbruch, Thomas H Winkler, Sai T Reddy
Antibody repertoire diversity and plasticity is crucial for broad protective immunity. Repertoires change in size and diversity across multiple B cell developmental stages and in response to antigen exposure. However, we still lack fundamental quantitative understanding of the extent to which repertoire diversity is predetermined. Therefore, we implemented a systems immunology framework for quantifying repertoire predetermination on three distinct levels: (1) B cell development (pre-B cell, naive B cell, plasma cell), (2) antigen exposure (three structurally different proteins), and (3) four antibody repertoire components (V-gene usage, clonal expansion, clonal diversity, repertoire size) extracted from antibody repertoire sequencing data (400 million reads)...
May 16, 2017: Cell Reports
https://www.readbyqxmd.com/read/28510537/converging-evolution-leads-to-near-maximal-junction-diversity-through-parallel-mechanisms-in-b-and-t-cell-receptors
#6
Jennifer Israel Cohen, Jeroen Heijst, Jacob Glanville, Yoram Louzoun
T and B cell receptor (TCR and BCR) complementarity determining region 3 (CDR3) genetic diversity is produced through multiple diversification and selection stages. Potential holes in the CDR3 repertoire were argued to be linked to immunodeficiencies and diseases. In contrast with BCRs, TCRs have practically no Dβ germline genetic diversity, and the question whether they can produce a diverse CDR3 repertoire emerges. In order to address the genetic diversity of the adaptive immune system, appropriate quantitative measures for diversity and large scale sequencing are required...
May 16, 2017: Physical Biology
https://www.readbyqxmd.com/read/28507788/adaptive-t-cell-responses-induced-by-oncolytic-herpes-simplex-virus-granulocyte-macrophage-colony-stimulating-factor-therapy-expanded-by-dendritic-cell-and-cytokine-induced-killer-cell-adoptive-therapy
#7
Jun Ren, William R Gwin, Xinna Zhou, Xiaoli Wang, Hongyan Huang, Ni Jiang, Lei Zhou, Pankaj Agarwal, Amy Hobeika, Erika Crosby, Zachary C Hartman, Michael A Morse, Kevin H Eng, H Kim Lyerly
Purpose: Although local oncolytic viral therapy (OVT) may enhance tumor lysis, antigen release, and adaptive immune responses, systemic antitumor responses post-therapy are limited. Adoptive immunotherapy with autologous dendritic cells (DC) and cytokine-induced killer cells (DC-CIK) synergizes with systemic therapies. We hypothesized that OVT with Herpes Simplex Virus-granulocyte macrophage-colony-stimulating factor (HSV-GM-CSF) would induce adaptive T cell responses that could be expanded systemically with sequential DC-CIK therapy...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/28502716/neuropeptides-predicted-from-the-transcriptome-analysis-of-the-gray-garden-slug-deroceras-reticulatum
#8
Seung-Joon Ahn, Ruth Martin, Sujaya Rao, Man-Yeon Choi
The gray garden slug, Deroceras reticulatum (Gastropoda: Pulmonata), is one of the most common terrestrial molluscs. Research for this slug has focused mainly on its ecology, biology, and management due to the severe damage it causes on a wide range of vegetables and field crops. However, little is known about hormonal signaling and neuropeptide sequences. This study, therefore, aimed to establish the transcriptome of D. reticulatum and to identify a comprehensive repertoire of neuropeptides in this slug. Illumina high-throughput sequencing of the whole body transcriptome of D...
May 11, 2017: Peptides
https://www.readbyqxmd.com/read/28500641/t-and-b-cell-clonal-expansion-in-ras-associated-lymphoproliferative-disease-rald-as-revealed-by-next-generation-sequencing
#9
Sarina Levy-Mendelovich, Atar Lev, Erez Rechavi, Ortal Barel, Hana Golan, Bela Bielorai, Yoram Neumann, Amos J Simon, Raz Somech
Ras associated lymphoproliferative disease (RALD) is an autoimmune lymphoproliferative syndrome (ALPS)-like disease caused by mutations in KRAS or NRAS. The immunological phenotype and pathogenesis of RALD have yet to be extensively studied. Here we report a thorough immunological investigation of a RALD patient with a somatic KRAS mutation. Patient lymphocytes were analyzed for phenotype, immunoglobulin levels and T cell proliferation capacity. T and B cell receptor excision circles (TREC and KREC, respectively), markers of naïve T and B cell production, were serially measured over three years...
May 12, 2017: Clinical and Experimental Immunology
https://www.readbyqxmd.com/read/28494274/personalized-t-cell-mediated-cancer-immunotherapy-progress-and-challenges
#10
REVIEW
Michael T Bethune, Alok V Joglekar
Immunotherapies are yielding effective treatments for several previously untreatable cancers. Until recently, vaccines and adoptive cell therapies have been designed to target public tumor antigens common to multiple patients rather than private antigens specific to a single patient. Due to the difficulty of identifying public antigens that are expressed exclusively on tumor cells, these studies have yielded both clinical successes and serious immune-related adverse events. Multiple avenues of research now underscore the centrality of tumor-specific mutated private antigens to endogenous anti-tumor immunity...
May 8, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28461509/evidence-of-strain-structure-in-plasmodium-falciparum-var-gene-repertoires-in-children-from-gabon-west-africa
#11
Karen P Day, Yael Artzy-Randrup, Kathryn E Tiedje, Virginie Rougeron, Donald S Chen, Thomas S Rask, Mary M Rorick, Florence Migot-Nabias, Philippe Deloron, Adrian J F Luty, Mercedes Pascual
Existing theory on competition for hosts between pathogen strains has proposed that immune selection can lead to the maintenance of strain structure consisting of discrete, weakly overlapping antigenic repertoires. This prediction of strain theory has conceptual overlap with fundamental ideas in ecology on niche partitioning and limiting similarity between coexisting species in an ecosystem, which oppose the hypothesis of neutral coexistence. For Plasmodium falciparum, strain theory has been specifically proposed in relation to the major surface antigen of the blood stage, known as PfEMP1 and encoded by the multicopy multigene family known as the var genes...
May 1, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28450864/specificity-privacy-and-degeneracy-in-the-cd4-t-cell-receptor-repertoire-following-immunization
#12
Yuxin Sun, Katharine Best, Mattia Cinelli, James M Heather, Shlomit Reich-Zeliger, Eric Shifrut, Nir Friedman, John Shawe-Taylor, Benny Chain
T cells recognize antigen using a large and diverse set of antigen-specific receptors created by a complex process of imprecise somatic cell gene rearrangements. In response to antigen-/receptor-binding-specific T cells then divide to form memory and effector populations. We apply high-throughput sequencing to investigate the global changes in T cell receptor sequences following immunization with ovalbumin (OVA) and adjuvant, to understand how adaptive immunity achieves specificity. Each immunized mouse contained a predominantly private but related set of expanded CDR3β sequences...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28446674/broadening-cd4-and-cd8-t-cell-responses-against-hepatitis-c-virus-by-vaccination-with-ns3-overlapping-peptide-panels-in-cross-priming-liposomes
#13
Jonathan Filskov, Marianne Mikkelsen, Paul R Hansen, Jan P Christensen, Allan R Thomsen, Peter Andersen, Jens Bukh, Else Marie Agger
Despite the introduction of effective drugs to treat patients with chronic hepatitis C virus (HCV) infection, a vaccine would be the only means to substantially reduce the worldwide disease burden. An incomplete understanding of how HCV interacts with its human host and evades immune surveillance has hampered vaccine development. It is generally accepted that in infected individuals, a narrow repertoire of exhausted T cells is a hallmark of persistent infection, whereas broad vigorous CD4(+) and CD8(+) T cell responses are associated with control of acute hepatitis C...
April 26, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28446171/oral-immune-priming-with-bacillus-thuringiensis-induces-a-shift-in-the-gene-expression-of-tribolium-castaneum-larvae
#14
Jenny M Greenwood, Barbara Milutinović, Robert Peuß, Sarah Behrens, Daniela Esser, Philip Rosenstiel, Hinrich Schulenburg, Joachim Kurtz
BACKGROUND: The phenomenon of immune priming, i.e. enhanced protection following a secondary exposure to a pathogen, has now been demonstrated in a wide range of invertebrate species. Despite accumulating phenotypic evidence, knowledge of its mechanistic underpinnings is currently very limited. Here we used the system of the red flour beetle, Tribolium castaneum and the insect pathogen Bacillus thuringiensis (Bt) to further our molecular understanding of the oral immune priming phenomenon...
April 26, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28443097/large-diversity-of-functional-nanobodies-from-a-camelid-immune-library-revealed-by-an-alternative-analysis-of-next-generation-sequencing-data
#15
Pieter Deschaght, Ana Paula Vintém, Marc Logghe, Miguel Conde, David Felix, Rob Mensink, Juliana Gonçalves, Jorn Audiens, Yanik Bruynooghe, Rita Figueiredo, Diana Ramos, Robbe Tanghe, Daniela Teixeira, Liesbeth Van de Ven, Catelijne Stortelers, Bruno Dombrecht
Next-generation sequencing (NGS) has been applied successfully to the field of therapeutic antibody discovery, often outperforming conventional screening campaigns which tend to identify only the more abundant selective antibody sequences. We used NGS to mine the functional nanobody repertoire from a phage-displayed camelid immune library directed to the recepteur d'origine nantais (RON) receptor kinase. Challenges to this application of NGS include accurate removal of read errors, correct identification of related sequences, and establishing meaningful inclusion criteria for sequences-of-interest...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28442504/characterization-of-the-tumor-t-cell-receptor-repertoire-and-immune-microenvironment-in-patients-with-locoregionally-advanced-squamous-cell-carcinoma-of-the-head-and-neck
#16
Vassiliki Saloura, Aiman Fatima, Makda Zewde, Kazuma Kiyotani, Ryan J Brisson, Jae-Hyun Park, Yuji Ikeda, Theodore Vougiouklakis, Riyue Bao, Tanguy Y Seiwert, Nicole A Cipriani, Mark W Lingen, Everett E Vokes, Yusuke Nakamura
Squamous cell carcinoma of the head and neck (SCCHN) is a lethal cancer with a suboptimal 5-year overall survival of approximately 50% with surgery and/or definitive chemoradiotherapy. Novel treatments are thus urgently awaited. Immunotherapy with checkpoint blockade has emerged as a promising option for patients with recurrent/metastatic SCCHN, however it has not been investigated in the curative-intent setting yet. The purpose of this study was to investigate the T-cell receptor repertoire and the tumor microenvironment in tumor tissues of SCCHN patients with locoregionally advanced disease...
April 25, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28442219/virulence-potential-of-staphylococcus-aureus-isolates-from-buruli-ulcer-patients
#17
Nana Ama Amissah, Monika A Chlebowicz, Anthony Ablordey, Caitlin S Tetteh, Isaac Prah, Tjip S van der Werf, Alex W Friedrich, Jan Maarten van Dijl, Ymkje Stienstra, John W Rossen
Buruli ulcer (BU) is a necrotizing infection of the skin and subcutaneous tissue caused by Mycobacterium ulcerans. BU wounds may also be colonized with other microorganisms including Staphylococcus aureus. This study aimed to characterize the virulence factors of S. aureus isolated from BU patients. Previously sequenced genomes of 21 S. aureus isolates from BU patients were screened for the presence of virulence genes. The results show that all S. aureus isolates harbored on their core genomes genes for known virulence factors like α-hemolysin, and the α- and β-phenol soluble modulins...
April 19, 2017: International Journal of Medical Microbiology: IJMM
https://www.readbyqxmd.com/read/28423320/sequence-and-structural-analyses-reveal-distinct-and-highly-diverse-human-cd8-tcr-repertoires-to-immunodominant-viral-antigens
#18
Guobing Chen, Xinbo Yang, Annette Ko, Xiaoping Sun, Mingming Gao, Yongqing Zhang, Alvin Shi, Roy A Mariuzza, Nan-Ping Weng
A diverse T cell receptor (TCR) repertoire is essential for controlling viral infections. However, information about TCR repertoires to defined viral antigens is limited. We performed a comprehensive analysis of CD8(+) TCR repertoires for two dominant viral epitopes: pp65495-503 (NLV) of cytomegalovirus and M158-66 (GIL) of influenza A virus. The highly individualized repertoires (87-5,533 α or β clonotypes per subject) comprised thousands of unique TCRα and TCRβ sequences and dozens of distinct complementary determining region (CDR)3α and CDR3β motifs...
April 18, 2017: Cell Reports
https://www.readbyqxmd.com/read/28422742/multi-omics-study-revealing-the-complexity-and-spatial-heterogeneity-of-tumor-infiltrating-lymphocytes-in-primary-liver-carcinoma
#19
Lijun Shi, Yang Zhang, Lin Feng, Liming Wang, Weiqi Rong, Fan Wu, Jianxiong Wu, Kaitai Zhang, Shujun Cheng
Intratumoral heterogeneity has been revealed in primary liver carcinoma (PLC). However, spatial heterogeneity of tumor-infiltrating lymphocytes (TILs), which reflects one dimension of a tumor's spatial heterogeneity, and the relationship between TIL diversity, local immune response and mutation burden remain unexplored in PLC. Therefore, we performed immune repertoire sequencing, gene expression profiling analysis and whole-exome sequencing in parallel on five regions of each tumor and on matched adjacent normal tissues and peripheral blood from five PLC patients...
March 31, 2017: Oncotarget
https://www.readbyqxmd.com/read/28416602/antigen-receptor-galaxy-a-user-friendly-web-based-tool-for-analysis-and-visualization-of-t-and-b-cell-receptor-repertoire-data
#20
Hanna IJspeert, Pauline A van Schouwenburg, David van Zessen, Ingrid Pico-Knijnenburg, Andrew P Stubbs, Mirjam van der Burg
Antigen Receptor Galaxy (ARGalaxy) is a Web-based tool for analyses and visualization of TCR and BCR sequencing data of 13 species. ARGalaxy consists of four parts: the demultiplex tool, the international ImMunoGeneTics information system (IMGT) concatenate tool, the immune repertoire pipeline, and the somatic hypermutation (SHM) and class switch recombination (CSR) pipeline. Together they allow the analysis of all different aspects of the immune repertoire. All pipelines can be run independently or combined, depending on the available data and the question of interest...
May 15, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
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