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Immune repertoire sequencing

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https://www.readbyqxmd.com/read/29159447/transcriptome-sequencing-of-the-long-nosed-bandicoot-perameles-nasuta-reveals-conservation-and-innovation-of-immune-genes-in-the-marsupial-order-peramelemorphia
#1
Katrina M Morris, Haylee J Weaver, Denis O'Meally, Marion Desclozeaux, Amber Gillett, Adam Polkinghorne
Bandicoots are omnivorous marsupials of the order Peramelemorphia. Conservation concerns and their unique biological characteristics suggest peramelomorphs are worthy research subjects, but knowledge of their genetics and immunology has lagged behind that of other high-profile marsupials. Here, we characterise the transcriptome of the long-nose bandicoot (Perameles nasuta), the first high-throughput data set from any peramelomorph. We investigate the immune gene repertoire of the bandicoot, with a focus on key immune gene families, and compare to previously characterised marsupial and mammalian species...
November 20, 2017: Immunogenetics
https://www.readbyqxmd.com/read/29144493/adaptive-immune-receptor-repertoire-community-recommendations-for-sharing-immune-repertoire-sequencing-data
#2
Florian Rubelt, Christian E Busse, Syed Ahmad Chan Bukhari, Jean-Philippe Bürckert, Encarnita Mariotti-Ferrandiz, Lindsay G Cowell, Corey T Watson, Nishanth Marthandan, William J Faison, Uri Hershberg, Uri Laserson, Brian D Corrie, Mark M Davis, Bjoern Peters, Marie-Paule Lefranc, Jamie K Scott, Felix Breden, Eline T Luning Prak, Steven H Kleinstein
No abstract text is available yet for this article.
November 16, 2017: Nature Immunology
https://www.readbyqxmd.com/read/29140551/b-cell-receptor-repertoire-sequencing-in-patients-with-primary-immunodeficiency-a-review
#3
REVIEW
Marie Ghraichy, Jacob D Galson, Dominic F Kelly, Johannes Trück
The advent of next-generation sequencing now allows a detailed assessment of the adaptive immune system in health and disease. In particular, high-throughput B-cell receptor (BCR) repertoire sequencing provides detailed information about the functionality and abnormalities of the B-cell system. However, it is mostly unknown how the BCR repertoire is altered in the context of primary immunodeficiencies (PID) and whether findings are consistent across phenotypes and genotypes. We have performed an extensive literature search of the published work on BCR repertoire sequencing in PID patients, including several forms of predominantly antibody disorders and combined immunodeficiencies...
November 15, 2017: Immunology
https://www.readbyqxmd.com/read/29138980/cd28-neg-t-lymphocytes-of-a-melanoma-patient-harbor-tumor-immunity-and-a-high-frequency-of-germline-encoded-and-public-tcrs
#4
Hisayoshi Hashimoto, Marco Sterk, Karin Schilbach
Increased numbers of CD8(+)CD28(neg.) T cells have been detected in the peripheral blood of patients with several types of malignancies. However, the role of these cells in anticancer immunity are not yet clear and CD8(+)CD28(neg.) T cells are a controversially discussed subpopulation reported both as immunosuppressive and cytotoxic. In this study, we examined the T cell receptor (TCR) repertoire and complementarity-determining region 3 sequences of CD28(neg.) T cells in a melanoma patient with recurrent disease who achieved long-term disease-free status...
November 14, 2017: Immunologic Research
https://www.readbyqxmd.com/read/29138313/t-cell-receptor-sequencing-of-early-stage-breast-cancer-tumors-identifies-altered-clonal-structure-of-the-t-cell-repertoire
#5
John F Beausang, Amanda J Wheeler, Natalie H Chan, Violet R Hanft, Frederick M Dirbas, Stefanie S Jeffrey, Stephen R Quake
Tumor-infiltrating T cells play an important role in many cancers, and can improve prognosis and yield therapeutic targets. We characterized T cells infiltrating both breast cancer tumors and the surrounding normal breast tissue to identify T cells specific to each, as well as their abundance in peripheral blood. Using immune profiling of the T cell beta-chain repertoire in 16 patients with early-stage breast cancer, we show that the clonal structure of the tumor is significantly different from adjacent breast tissue, with the tumor containing ∼2...
November 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29133401/multiple-legionella-pneumophila-effector-virulence-phenotypes-revealed-through-high-throughput-analysis-of-targeted-mutant-libraries
#6
Stephanie R Shames, Luying Liu, James C Havey, Whitman B Schofield, Andrew L Goodman, Craig R Roy
Legionella pneumophila is the causative agent of a severe pneumonia called Legionnaires' disease. A single strain of L. pneumophila encodes a repertoire of over 300 different effector proteins that are delivered into host cells by the Dot/Icm type IV secretion system during infection. The large number of L. pneumophila effectors has been a limiting factor in assessing the importance of individual effectors for virulence. Here, a transposon insertion sequencing technology called INSeq was used to analyze replication of a pool of effector mutants in parallel both in a mouse model of infection and in cultured host cells...
November 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29123959/immunological-efficacy-of-glypican-3-peptide-vaccine-in-patients-with-advanced-hepatocellular-carcinoma
#7
Nobuhiro Tsuchiya, Toshiaki Yoshikawa, Norihiro Fujinami, Keigo Saito, Shoichi Mizuno, Yu Sawada, Itaru Endo, Tetsuya Nakatsura
We have previously conducted a phase I trial to test the efficacy of a glypican-3 (GPC3) peptide vaccine in patients with advanced hepatocellular carcinoma (HCC); however, its immunological mechanism of action remains unclear. Here, we report a pilot study conducted to evaluate the immunological mechanisms of action of this GPC3 peptide vaccine (UMIN-CTR number 000005093). Eleven patients with advanced HCC were vaccinated with the GPC3 peptide in this trial. The primary end point was GPC3 peptide-specific immune response induced by the GPC3 peptide vaccination...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/29123260/combining-dna-damaging-therapeutics-with-immunotherapy-more-haste-less-speed
#8
REVIEW
Jessica S Brown, Raghav Sundar, Juanita Lopez
The idea that chemotherapy can be used in combination with immunotherapy may seem somewhat counterproductive, as it can theoretically eliminate the immune cells needed for antitumour immunity. However, much preclinical work has now demonstrated that in addition to direct cytotoxic effects on cancer cells, a proportion of DNA damaging agents may actually promote immunogenic cell death, alter the inflammatory milieu of the tumour microenvironment and/or stimulate neoantigen production, thereby activating an antitumour immune response...
November 9, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/29116515/antibody-isolation-from-a-human-synthetic-combinatorial-and-other-libraries-of-single-chain-antibodies
#9
Almog Bitton, Limor Nahary, Itai Benhar
Antibody libraries came into existence 25 years ago when the accumulating sequence data of immunoglobulin genes and the advent of the PCR technology made it possible to clone antibody gene repertoires. Phage display (most common) and additional display and screening technologies were applied to pan out desired binding specificities from antibody libraries. "Synthetic" or "semisynthetic" libraries are from naive-non-immunized source and considered to be a source for many different targets, including self-antigens...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29106696/the-mechanisms-shaping-the-repertoire-of-cd4-foxp3-treg-cells
#10
REVIEW
Piotr Kraj, Leszek Ignatowicz
Regulatory T (Treg ) cells expressing Foxp3 transcription factor control homeostasis of the immune system, antigenic responses to commensal and pathogenic microbiota, and immune responses to self and tumor antigens. Treg cells differentiate in the thymus, (tTreg ) along with conventional CD4(+) T cells, in processes of positive and negative selection. Another class of Treg cells is generated in peripheral tissues (pTreg ) by inducing Foxp3 expression in conventional CD4(+) T cells in response to antigenic stimulation...
November 6, 2017: Immunology
https://www.readbyqxmd.com/read/29105221/analysis-of-recombinational-switching-at-the-antigenic-variation-locus-of-the-lyme-spirochete-using-a-novel-pacbio-sequencing-pipeline
#11
Theodore B Verhey, Mildred Castellanos, George Chaconas
The Lyme disease spirochete evades the host immune system by combinatorial variation of VlsE, a surface antigen. Antigenic variation occurs via segmental gene conversion from contiguous silent cassettes into the vlsE locus. Because of the high degree of similarity between switch variants and the size of vlsE, short-read NGS technologies have been unsuitable for sequencing vlsE populations. Here we use PacBio sequencing technology coupled with the first fully-automated software pipeline (VAST) to accurately process NGS data by minimizing error frequency, eliminating heteroduplex errors and accurately aligning switch variants...
November 4, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/29097753/secretoneurin-a-regulates-neurogenic-and-inflammatory-transcriptional-networks-in-goldfish-carassius-auratus-radial-glia
#12
Dillon F Da Fonte, Christopher J Martyniuk, Lei Xing, Adrian Pelin, Nicolas Corradi, Wei Hu, Vance L Trudeau
Radial glial cells (RGCs) are the most abundant macroglia in the teleost brain and have established roles in neurogenesis and neurosteroidogenesis; however, their transcriptome remains uncharacterized, which limits functional understanding of this important cell type. Using cultured goldfish RGCs, RNA sequencing and de novo transcriptome assembly were performed, generating the first reference transcriptome for fish RGCs with 17,620 unique genes identified. These data revealed that RGCs express a diverse repertoire of receptors and signaling molecules, suggesting that RGCs may respond to and synthesize an array of hormones, peptides, cytokines, and growth factors...
November 2, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29089018/rapid-turnover-of-effectors-in-grass-powdery-mildew-blumeria-graminis
#13
Fabrizio Menardo, Coraline R Praz, Thomas Wicker, Beat Keller
BACKGROUND: Grass powdery mildew (Blumeria graminis, Ascomycota) is a major pathogen of cereal crops and has become a model organism for obligate biotrophic fungal pathogens of plants. The sequenced genomes of two formae speciales (ff.spp.), B.g. hordei and B.g. tritici (pathogens of barley and wheat), were found to be enriched in candidate effector genes (CEGs). Similar to other filamentous pathogens, CEGs in B. graminis are under positive selection. Additionally, effectors are more likely to have presence-absence polymorphisms than other genes among different strains...
October 31, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29077880/repetitive-sequences-in-malaria-parasite-proteins
#14
Heledd M Davies, Stephanie D Nofal, Emilia J McLaughlin, Andrew R Osborne
Five species of parasite cause malaria in humans with the most severe disease caused by Plasmodium falciparum. Many of the proteins encoded in the P. falciparum genome are unusually enriched in repetitive low-complexity sequences containing a limited repertoire of amino acids. These repetitive sequences expand and contract dynamically and are among the most rapidly changing sequences in the genome. The simplest repetitive sequences consist of single amino acid repeats such as poly-asparagine tracts that are found in approximately 25% of P...
November 1, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/29065388/targeted-sequencing-of-clade-specific-markers-from-skin-microbiomes-for-forensic-human-identification
#15
Sarah E Schmedes, August E Woerner, Nicole M M Novroski, Frank R Wendt, Jonathan L King, Kathryn M Stephens, Bruce Budowle
The human skin microbiome is comprised of diverse communities of bacterial, eukaryotic, and viral taxa and contributes millions of additional genes to the repertoire of human genes, affecting human metabolism and immune response. Numerous genetic and environmental factors influence the microbiome composition and as such contribute to individual-specific microbial signatures which may be exploited for forensic applications. Previous studies have demonstrated the potential to associate skin microbial profiles collected from touched items to their individual owner, mainly using unsupervised methods from samples collected over short time intervals...
October 18, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29063126/the-antibody-loci-of-the-domestic-goat-capra-hircus
#16
John C Schwartz, Rebecca L Philp, Derek M Bickhart, Timothy P L Smith, John A Hammond
The domestic goat (Capra hircus) is an important ruminant species both as a source of antibody-based reagents for research and biomedical applications and as an economically important animal for agriculture, particularly for developing nations that maintain most of the global goat population. Characterization of the loci encoding the goat immune repertoire would be highly beneficial for both vaccine and immune reagent development. However, in goat and other species whose reference genomes were generated using short-read sequencing technologies, the immune loci are poorly assembled as a result of their repetitive nature...
October 23, 2017: Immunogenetics
https://www.readbyqxmd.com/read/29046389/the-antibody-repertoire-of-colorectal-cancer
#17
Seong Won Cha, Stefano Bonissone, Seungjin Na, Pavel A Pevzner, Vineet Bafna
Immunotherapy is becoming increasingly important in the fight against cancers, utilizing and manipulating the body's immune response to treat tumors. Understanding the immune repertoire - the collection of immunological proteins - of treated and untreated cells is possible at the genomic, but technically difficult at the protein level. Standard protein databases do not include the highly divergent sequences of somatic rearranged immunoglobulin genes, and may lead to missed identifications in a mass spectrometry search...
October 18, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29040265/analysis-of-peripheral-b-cells-and-autoantibodies-against-the-anti-nicotinic-acetylcholine-receptor-derived-from-patients-with-myasthenia-gravis-using-single-cell-manipulation-tools
#18
Tomohiro Makino, Ryuichi Nakamura, Maki Terakawa, Satoshi Muneoka, Kazuhiro Nagahira, Yuriko Nagane, Jyoji Yamate, Masakatsu Motomura, Kimiaki Utsugisawa
The majority of patients with myasthenia gravis (MG), an organ-specific autoimmune disease, harbor autoantibodies that attack the nicotinic acetylcholine receptor (nAChR-Abs) at the neuromuscular junction of skeletal muscles, resulting in muscle weakness. Single cell manipulation technologies coupled with genetic engineering are very powerful tools to examine T cell and B cell repertoires and the dynamics of adaptive immunity. These tools have been utilized to develop mAbs in parallel with hybridomas, phage display technologies and B-cell immortalization...
2017: PloS One
https://www.readbyqxmd.com/read/29038795/immune-engineering-from-systems-immunology-to-engineering-immunity
#19
Ning Jiang
The smallpox vaccine represents the earliest attempt in engineering immunity. The recent success of chimeric antigen receptor T cells (CAR-T cells) in cancer once again demonstrates the clinical potential of immune engineering. Inspired by this success, diverse approaches have been used to boost various aspects of immunity: engineering dendritic cells (DCs), natural killer (NK) cells, T cells, antibodies, cytokines, small peptides, and others. With recent development of various high-throughput technologies (of which engineers, especially biomedical engineers/bioengineers contributed significantly), such as immune repertoire sequencing, and analytical methods, a systems level of understanding immunity (or the lack of it) beyond model animals has provided critical insights into the human immune system...
March 2017: Curr Opin Biomed Eng
https://www.readbyqxmd.com/read/29038659/in-silico-prediction-analysis-of-idiotope-driven-t-b-cell-collaboration-in-multiple-sclerosis
#20
Rune A Høglund, Andreas Lossius, Jorunn N Johansen, Jane Homan, Jūratė Šaltytė Benth, Harlan Robins, Bjarne Bogen, Robert D Bremel, Trygve Holmøy
Memory B cells acting as antigen-presenting cells are believed to be important in multiple sclerosis (MS), but the antigen they present remains unknown. We hypothesized that B cells may activate CD4(+) T cells in the central nervous system of MS patients by presenting idiotopes from their own immunoglobulin variable regions on human leukocyte antigen (HLA) class II molecules. Here, we use bioinformatics prediction analysis of B cell immunoglobulin variable regions from 11 MS patients and 6 controls with other inflammatory neurological disorders (OINDs), to assess whether the prerequisites for such idiotope-driven T-B cell collaboration are present...
2017: Frontiers in Immunology
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