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Immune repertoire sequencing

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https://www.readbyqxmd.com/read/28230642/strategies-to-obtain-diverse-and-specific-human-monoclonal-antibodies-from-transgenic-animals
#1
Marianne Brüggemann, Michael J Osborn, Biao Ma, Roland Buelow
Techniques to obtain large quantities of antigen-specific monoclonal antibodies, mAbs, were first established in the 1970s when Georges Köhler and César Milstein immortalized antibody-producing mouse B-lymphocytes by fusion with myeloma cells (http://www.whatisbiotechnology.org/exhibitions/milstein). Combined with the expression of human antibodies in transgenic animals, this technique allowed upon immunization the generation of highly specific fully human mAbs for therapeutic applications. Apart from being extremely beneficial, mAbs are a huge success commercially...
February 23, 2017: Transplantation
https://www.readbyqxmd.com/read/28218745/human-%C3%AE-%C3%AE-t-cells-are-quickly-reconstituted-after-stem-cell-transplantation-and-show-adaptive-clonal-expansion-in-response-to-viral-infection
#2
Sarina Ravens, Christian Schultze-Florey, Solaiman Raha, Inga Sandrock, Melanie Drenker, Linda Oberdörfer, Annika Reinhardt, Inga Ravens, Maleen Beck, Robert Geffers, Constantin von Kaisenberg, Michael Heuser, Felicitas Thol, Arnold Ganser, Reinhold Förster, Christian Koenecke, Immo Prinz
To investigate how the human γδ T cell pool is shaped during ontogeny and how it is regenerated after transplantation of hematopoietic stem cells (HSCs), we applied an RNA-based next-generation sequencing approach to monitor the dynamics of the repertoires of γδ T cell antigen receptors (TCRs) before and after transplantation in a prospective cohort study. We found that repertoires of rearranged genes encoding γδ TCRs (TRG and TRD) in the peripheral blood of healthy adults were stable over time. Although a large fraction of human TRG repertoires consisted of public sequences, the TRD repertoires were private...
February 20, 2017: Nature Immunology
https://www.readbyqxmd.com/read/28217133/a-perspective-on-crn-proteins-in-the-genomics-age-evolution-classification-delivery-and-function-revisited
#3
REVIEW
Tiago M M M Amaro, Gaëtan J A Thilliez, Graham B Motion, Edgar Huitema
Plant associated microbes rely on secreted virulence factors (effectors) to modulate host immunity and ensure progressive infection. Amongst the secreted protein repertoires defined and studied in pathogens to date, the CRNs (for CRinkling and Necrosis) have emerged as one of only a few highly conserved protein families, spread across several kingdoms. CRN proteins were first identified in plant pathogenic oomycetes where they were found to be modular factors that are secreted and translocated inside host cells by means of a conserved N-terminal domain...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28213050/reduced-frequency-of-two-activating-kir-genes-in-patients-with-sepsis
#4
Luciana M Oliveira, Pamela Portela, Joice Merzoni, Juliana D Lindenau, Fernando S Dias, Jaqueline Beppler, Pietra Graebin, Clarice S Alho, Gilberto Schwartsmann, Felipe Dal-Pizzol, Luiz Fernando Jobim, Mariana Jobim, Rafael Roesler
Natural killer (NK) cell activity is regulated by activating and inhibitory signals transduced by killer cell immunoglobulin-like receptors (KIR). Diversity in KIR gene repertoire among individuals may affect disease outcome. Sepsis development and severity may be influenced by genetic factors affecting the immune response. Here, we examined sixteen KIR genes and their human leucocyte antigen (HLA) class I ligands in critical patients, aiming to identify patterns that could be associated with sepsis. Male and female patients (ages ranging between 14 and 94years-old) were included...
February 14, 2017: Human Immunology
https://www.readbyqxmd.com/read/28201988/molecular-characterization-of-mhc-class-iib-genes-of-sympatric-neotropical-cichlids
#5
Melinda J Hofmann, Seraina E Bracamonte, Christophe Eizaguirre, Marta Barluenga
BACKGROUND: The Major Histocompatibility Complex (MHC) is a key component of the adaptive immune system of all vertebrates and consists of the most polymorphic genes known to date. Due to this complexity, however, MHC remains to be characterized in many species including any Neotropical cichlid fish. Neotropical crater lake cichlids are ideal models to study evolutionary processes as they display one of the most convincing examples of sympatric and repeated parallel radiation events within and among isolated crater lakes...
February 15, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28196891/insights-into-immune-system-development-and-function-from-mouse-t-cell-repertoires
#6
Zachary Sethna, Yuval Elhanati, Chrissy S Dudgeon, Curtis G Callan, Arnold J Levine, Thierry Mora, Aleksandra M Walczak
The ability of the adaptive immune system to respond to arbitrary pathogens stems from the broad diversity of immune cell surface receptors. This diversity originates in a stochastic DNA editing process (VDJ recombination) that acts on the surface receptor gene each time a new immune cell is created from a stem cell. By analyzing T-cell receptor (TCR) sequence repertoires taken from the blood and thymus of mice of different ages, we quantify the changes in the VDJ recombination process that occur from embryo to young adult...
February 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28193177/anopheline-salivary-protein-genes-and-gene-families-an-evolutionary-overview-after-the-whole-genome-sequence-of-sixteen-anopheles-species
#7
Bruno Arcà, Fabrizio Lombardo, Claudio J Struchiner, José M C Ribeiro
BACKGROUND: Mosquito saliva is a complex cocktail whose pharmacological properties play an essential role in blood feeding by counteracting host physiological response to tissue injury. Moreover, vector borne pathogens are transmitted to vertebrates and exposed to their immune system in the context of mosquito saliva which, in virtue of its immunomodulatory properties, can modify the local environment at the feeding site and eventually affect pathogen transmission. In addition, the host antibody response to salivary proteins may be used to assess human exposure to mosquito vectors...
February 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28187283/applications-of-immunogenomics-to-cancer
#8
REVIEW
X Shirley Liu, Elaine R Mardis
Cancer immunogenomics originally was framed by research supporting the hypothesis that cancer mutations generated novel peptides seen as "non-self" by the immune system. The search for these "neoantigens" has been facilitated by the combination of new sequencing technologies, specialized computational analyses, and HLA binding predictions that evaluate somatic alterations in a cancer genome and interpret their ability to produce an immune-stimulatory peptide. The resulting information can characterize a tumor's neoantigen load, its cadre of infiltrating immune cell types, the T or B cell receptor repertoire, and direct the design of a personalized therapeutic...
February 9, 2017: Cell
https://www.readbyqxmd.com/read/28179494/hierarchical-clustering-can-identify-b-cell-clones-with-high-confidence-in-ig-repertoire-sequencing-data
#9
Namita T Gupta, Kristofor D Adams, Adrian W Briggs, Sonia C Timberlake, Francois Vigneault, Steven H Kleinstein
Adaptive immunity is driven by the expansion, somatic hypermutation, and selection of B cell clones. Each clone is the progeny of a single B cell responding to Ag, with diversified Ig receptors. These receptors can now be profiled on a large scale by next-generation sequencing. Such data provide a window into the microevolutionary dynamics that drive successful immune responses and the dysregulation that occurs with aging or disease. Clonal relationships are not directly measured, but they must be computationally inferred from these sequencing data...
February 8, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28177902/identification-of-patient-specific-and-tumor-shared-t-cell-receptor-sequences-in-renal-cell-carcinoma-patients
#10
Chiara Massa, Harlan Robins, Cindy Desmarais, Dagmar Riemann, Corinna Fahldieck, Paolo Fornara, Barbara Seliger
A major requirement for cancer immunotherapy is the development of biomarkers for prognosis and for monitoring therapy response. In an attempt to evaluate the immune response of renal cell carcinoma (RCC) patients, tumor lesions and / or blood samples from 12 RCC patients underwent deep T cell receptor (TCR) sequencing. Despite the low number of samples, different TCR distribution patterns could be detected. Most of the RCC patients presented "patient-specific" TCR sequences, and those clonotypes were present at higher frequency in tumor lesions suggesting a specific extravasation from the blood...
February 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28167670/salmonella-typhi-lipopolysaccharide-o-antigen-modifications-impact-on-serum-resistance-and-antibody-recognition
#11
Erica Kintz, Christian Heiss, Ian Black, Nicholas Donohue, Naj Brown, Mark R Davies, Parastoo Azadi, Stephen Baker, Paul M Kaye, Marjan van der Woude
Salmonella Typhi is a human restricted Gram-negative bacterial pathogen, responsible for causing an estimated 27 million cases of typhoid fever annually leading to 217,000 deaths, and current vaccines do not offer full protection. The O-antigen side chain of the lipopolysaccharide is an immunodominant antigen, can define host-pathogen interactions, and is under consideration as a vaccine target for some Gram-negative species. The composition of the O-antigen can be modified by activity of glycosyltransferase (gtr) operons acquired by horizontal gene transfer...
February 6, 2017: Infection and Immunity
https://www.readbyqxmd.com/read/28167275/single-amino-acid-fingerprinting-of-the-human-antibody-repertoire-with-high-density-peptide-arrays
#12
Laura K Weber, Andrea Palermo, Jonas Kügler, Olivier Armant, Awale Isse, Simone Rentschler, Thomas Jaenisch, Jürgen Hubbuch, Stefan Dübel, Alexander Nesterov-Mueller, Frank Breitling, Felix F Loeffler
The antibody species that patrol in a patient's blood are an invaluable part of the immune system. While most of them shield us from life-threatening infections, some of them do harm in autoimmune diseases. If we knew exactly all the antigens that elicited all the antibody species within a group of patients, we could learn which ones correlate with immune protection, are irrelevant, or do harm. Here, we demonstrate an approach to this question: First, we use a plethora of phage-displayed peptides to identify many different serum antibody binding peptides...
February 3, 2017: Journal of Immunological Methods
https://www.readbyqxmd.com/read/28159550/characterization-of-the-diversity-of-t-cell-receptor-%C3%AE-%C3%AE-complementary-determinant-region-3-in-human-peripheral-blood-by-immune-repertoire-sequencing
#13
Hui Chen, Mingjin Zou, Da Teng, Jianmin Zhang, Wei He
γδ T cells function as sentinels in early host response to infections and malignancies. Although γδ T cells are regarded as innate immune cells and recognize antigens in a non-MHC restricted manner, they possess a huge diversity of complementary determinant region 3 (CDR3) of T cell receptor (TCR) generated by the rearrangement of germ-line gene V- (D) -J-C fragments. However, the detailed characteristics of the TCRγδ CDR3 repertoire remain unclear. A comprehensive analysis would answer fundamental questions about the diversity of the TCRγδ CDR3 repertoire and elucidate the mechanism underlying γδ T cell recognition of pathogens and tumor antigens...
January 31, 2017: Journal of Immunological Methods
https://www.readbyqxmd.com/read/28137743/genomic-features-of-the-damselfly-calopteryx-splendens-representing-a-sister-clade-to-most-insect-orders
#14
Panagiotis Ioannidis, Felipe A Simao, Robert M Waterhouse, Mosè Manni, Mathieu Seppey, Hugh M Robertson, Bernhard Misof, Oliver Niehuis, Evgeny M Zdobnov
Insects comprise the most diverse and successful animal group with over one million described species that are found in almost every terrestrial and limnic habitat, with many being used as important models in genetics, ecology, and evolutionary research. Genome sequencing projects have greatly expanded the sampling of species from many insect orders, but genomic resources for species of certain insect lineages have remained relatively limited to date. To address this paucity, we sequenced the genome of the banded demoiselle, Calopteryx splendens, a damselfly (Odonata: Zygoptera) belonging to Palaeoptera, the clade containing the first winged insects...
January 30, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28134319/a-comprehensive-analysis-of-the-germline-and-expressed-tcr-repertoire-in-white-peking-duck
#15
Zhi Yang, Yi Sun, Yonghe Ma, Zhenrong Li, Yu Zhao, Liming Ren, Haitang Han, Yunliang Jiang, Yaofeng Zhao
Recently, many immune-related genes have been extensively studied in ducks, but relatively little is known about their TCR genes. Here, we determined the germline and expressed repertoire of TCR genes in White Peking duck. The genomic organization of the duck TCRα/δ, TCRγ and unconventional TCRδ2 loci are highly conserved with their counterparts in mammals or chickens. By contrast, the duck TCRβ locus is organized in an unusual pattern, (Vβ)n-Dβ-(Jβ)2-Cβ1-(Jβ)4-Cβ2, which differs from the tandem-aligned clusters in mammals or the translocon organization in some teleosts...
January 30, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28131552/comparative-analysis-of-the-feline-immunoglobulin-repertoire
#16
Sebastian C J Steiniger, Jacob Glanville, Douglas W Harris, Thomas L Wilson, Gregory C Ippolito, Steven A Dunham
Next-Generation Sequencing combined with bioinformatics is a powerful tool for analyzing the large number of DNA sequences present in the expressed antibody repertoire and these data sets can be used to advance a number of research areas including antibody discovery and engineering. The accurate measurement of the immune repertoire sequence composition, diversity and abundance is important for understanding the repertoire response in infections, vaccinations and cancer immunology and could also be useful for elucidating novel molecular targets...
January 25, 2017: Biologicals: Journal of the International Association of Biological Standardization
https://www.readbyqxmd.com/read/28118945/ro52-autoantibodies-arise-from-self-reactive-progenitors-in-a-mother-of-a-child-with-neonatal-lupus
#17
Joanne H Reed, Miroslaw K Gorny, Liuzhe Li, Timothy Cardozo, Jill P Buyon, Robert M Clancy
The detection of cardiac conduction defects in an 18-24 week old foetus in the absence of structural abnormalities predicts with near certainty the presence of autoantibodies against 60kD and 52kD SSA/Ro in the mother regardless of her health status. Previous studies have emphasized these autoantibodies as key mediators of tissue injury. The aim of this study was to focus on the anti-Ro52 response to determine whether these autoantibodies originate from progenitors that are inherently self-reactive or from B-cells that acquire self-reactivity during an immune response...
January 21, 2017: Journal of Autoimmunity
https://www.readbyqxmd.com/read/28114326/characteristics-peripheral-blood-igg-and-igm-heavy-chain-complementarity-determining-region-3-repertoire-before-and-after-immunization-with-recombinant-hbv-vaccine
#18
Long Ma, Xiaomei Wang, Xiaoying Bi, Jiezuan Yang, Bin Shi, Xiaoyan He, Rui Ma, Qingqing Ma, Xinsheng Yao
Immunization with recombinant HBV vaccine induces specific immune responses in human causing B lymphocytes to produce protective HBsAb, and to form memory B lymphocytes, thereby facilitating HBV immunity in the body. However, B lymphocytes heterogeneity and characteristics are not fully elucidated. In this study, we conducted high-throughput sequencing of BCR heavy chain CDR3 repertoires in 3 healthy volunteers before and after the third immunization with recombinant HBV vaccine. We used Roche 454 Genome Sequencer FLX system to perform a comparative analysis of IgM and IgG H chain CDR3 repertoires...
2017: PloS One
https://www.readbyqxmd.com/read/28109746/diversity-and-evolution-of-tir-domain-containing-proteins-in-bivalves-and-metazoa-new-insights-from-comparative-genomics
#19
Marco Gerdol, Paola Venier, Paolo Edomi, Alberto Pallavicini
The Toll/interleukin-1 receptor (TIR) domain has a fundamental role in the innate defence response of plants, vertebrate and invertebrate animals. Mostly found in the cytosolic side of membrane-bound receptor proteins, it mediates the intracellular signalling upon pathogen recognition via heterotypic interactions. Although a number of TIR-domain-containing (TIR-DC) proteins have been characterized in vertebrates, their evolutionary relationships and functional role in protostomes are still largely unknown. Due to the high abundance and diversity of TIR-DC proteins in bivalve molluscs, we investigated this class of marine invertebrates as a case study...
January 18, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28107438/first-insights-into-the-subterranean-crustacean-bathynellacea-transcriptome-transcriptionally-reduced-opsin-repertoire-and-evidence-of-conserved-homeostasis-regulatory-mechanisms
#20
Bo-Mi Kim, Seunghyun Kang, Do-Hwan Ahn, Jin-Hyoung Kim, Inhye Ahn, Chi-Woo Lee, Joo-Lae Cho, Gi-Sik Min, Hyun Park
Bathynellacea (Crustacea, Syncarida, Parabathynellidae) are subterranean aquatic crustaceans that typically inhabit freshwater interstitial spaces (e.g., groundwater) and are occasionally found in caves and even hot springs. In this study, we sequenced the whole transcriptome of Allobathynella bangokensis using RNA-seq. De novo sequence assembly produced 74,866 contigs including 28,934 BLAST hits. Overall, the gene sequences were most similar to those of the waterflea Daphnia pulex. In the A. bangokensis transcriptome, no opsin or related sequences were identified, and no contig aligned to the crustacean visual opsins and non-visual opsins (i...
2017: PloS One
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