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Immune repertoire sequencing

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https://www.readbyqxmd.com/read/29328543/the-sarda-sheep-host-fecal-proteome
#1
Antonio Palomba, Alessandro Tanca, Maria Filippa Addis, Daniela Pagnozzi, Sergio Uzzau
We recently reported the first characterization of the sheep fecal microbiota, obtained by using a multi-meta-omic approach. Here, the mass spectra generated by single-run LC/high-resolution MS in the context of that study were reanalyzed using a host-specific database, in order to gain insights for the first time into the host fecal proteome of healthy Sarda sheep. On the whole, 5349 non-redundant tryptic peptide sequences were identified, belonging to 1046 different proteins. The "core" fecal proteome (common to all animals) comprised 431 proteins, mainly related to biological processes as immune response and proteolysis...
January 12, 2018: Proteomics
https://www.readbyqxmd.com/read/29325279/-characteristics-of-igh-cdr3-repertoire-of-peripheral-b-cells-in-a-patient-with-primary-biliary-cholangitis-a-preliminary-study-using-high-throughput-sequencing
#2
D T Zhao, C L Guo, H P Yan, H Y Liao, Y M Liu, H P Zhang, L S An, C Y Huang, Y Han, Y Zhao
Objective: To analyze the characteristics of immunoglobulin heavy chain complementarity-determining region (IgH-CDR3) repertoire of peripheral B cells in a patient with primary biliary cholangitis (PBC) and to investigate the diversity of the immune system. Methods: Arm-PCR was used to amplify the IgH-CDR3 region of circulating B cells isolated from a PBC patient, and high-throughput sequencing was used to analyze the amplified product. The characteristics of immune repertoire were analyzed by bioinformatics...
November 20, 2017: Zhonghua Gan Zang Bing za Zhi, Zhonghua Ganzangbing Zazhi, Chinese Journal of Hepatology
https://www.readbyqxmd.com/read/29320582/thyroid-transcriptome-analysis-reveals-different-adaptive-responses-to-cold-environmental-conditions-between-two-chicken-breeds
#3
Shanshan Xie, Xukai Yang, Dehe Wang, Feng Zhu, Ning Yang, Zhuocheng Hou, Zhonghua Ning
Selection for cold tolerance in chickens is important for improving production performance and animal welfare. The identification of chicken breeds with higher cold tolerance and production performance will help to target candidates for the selection. The thyroid gland plays important roles in thermal adaptation, and its function is influenced by breed differences and transcriptional plasticity, both of which remain largely unknown in the chicken thyroid transcriptome. In this study, we subjected Bashang Long-tail (BS) and Rhode Island Red (RIR) chickens to either cold or warm environments for 21 weeks and investigated egg production performance, body weight changes, serum thyroid hormone concentrations, and thyroid gland transcriptome profiles...
2018: PloS One
https://www.readbyqxmd.com/read/29315680/solexa-sequencing-and-custom-microrna-chip-reveal-repertoire-of-micrornas-in-mammary-gland-of-bovine-suffering-from-natural-infectious-mastitis
#4
Zhihua Ju, Qiang Jiang, Gang Liu, Xiuge Wang, Guojing Luo, Yan Zhang, Jibin Zhang, Jifeng Zhong, Jinming Huang
Identification of microRNAs (miRNAs), target genes and regulatory networks associated with innate immune and inflammatory responses and tissue damage is essential to elucidate the molecular and genetic mechanisms for resistance to mastitis. In this study, a combination of Solexa sequencing and custom miRNA chip approaches was used to profile the expression of miRNAs in bovine mammary gland at the late stage of natural infection with Staphylococcus aureus, a widespread mastitis pathogen. We found 383 loci corresponding to 277 known and 49 putative novel miRNAs, two potential mitrons and 266 differentially expressed miRNAs in the healthy and mastitic cows' mammary glands...
January 8, 2018: Animal Genetics
https://www.readbyqxmd.com/read/29289741/immune-monitoring-of-transplant-patients-in-transient-mixed-chimerism-tolerance-trials
#5
REVIEW
Megan Sykes
This review focuses on mechanistic studies performed in recipients of non-myeloablative bone marrow transplant regimens developed at Massachusetts General Hospital in HLA-identical and HLA-mismatched haploidentical combinations, initially as a platform for treatment of hematologic malignancies with immunotherapy in the form of donor leukocyte infusions, and later in combination with donor kidney transplantation for the induction of allograft tolerance. These studies point to a prominent early role for regulatory T cells in tolerance induction, followed by partial and gradual deletion of donor-reactive T cells...
December 28, 2017: Human Immunology
https://www.readbyqxmd.com/read/29288089/exploring-the-molecular-complexity-of-triatoma-dimidiata-sialome
#6
Paula Beatriz Santiago, Carla Nunes de Araújo, Sébastien Charneau, Izabela Marques Dourado Bastos, Teresa Cristina F Assumpção, Rayner Myr Lauterjung Queiroz, Yanna Reis Praça, Thuany de Moura Cordeiro, Carlos Henrique Saraiva Garcia, Ionizete Garcia da Silva, Tainá Raiol, Flávia Nader Motta, João Victor de Araújo Oliveira, Marcelo Valle de Sousa, José Marcos C Ribeiro, Jaime Martins de Santana
Triatoma dimidiata, a Chagas disease vector widely distributed along Central America, has great capability for domestic adaptation as the majority of specimens caught inside human dwellings or in peridomestic areas fed human blood. Exploring the salivary compounds that overcome host haemostatic and immune responses is of great scientific interest. Here, we provide a deeper insight into its salivary gland molecules. We used high-throughput RNA sequencing to examine in depth the T. dimidiata salivary gland transcriptome...
December 26, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29276518/how-b-cell-receptor-repertoire-sequencing-can-be-enriched-with-structural-antibody-data
#7
REVIEW
Aleksandr Kovaltsuk, Konrad Krawczyk, Jacob D Galson, Dominic F Kelly, Charlotte M Deane, Johannes Trück
Next-generation sequencing of immunoglobulin gene repertoires (Ig-seq) allows the investigation of large-scale antibody dynamics at a sequence level. However, structural information, a crucial descriptor of antibody binding capability, is not collected in Ig-seq protocols. Developing systematic relationships between the antibody sequence information gathered from Ig-seq and low-throughput techniques such as X-ray crystallography could radically improve our understanding of antibodies. The mapping of Ig-seq datasets to known antibody structures can indicate structurally, and perhaps functionally, uncharted areas...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/29260260/on-being-the-right-size-antibody-repertoire-formation-in-the-mouse-and-human
#8
REVIEW
Andrew M Collins, Katherine J L Jackson
The immune systems of all mammals include populations of B cells producing antibodies with incredibly diverse specificities. Repertoire diversity has been described as the "miracle of immunology," and it was long thought to be the result of essentially stochastic processes. Recently, however, analysis of high throughput gene sequencing data has shown that hard-wired biases in these processes result in antibody repertoires that are broadly predictable. The repertoires of mice and humans are both predictable, but they are strikingly different...
December 19, 2017: Immunogenetics
https://www.readbyqxmd.com/read/29259996/phenotypic-and-functional-complexity-of-brain-infiltrating-t-cells-in-rasmussen-encephalitis
#9
Faiez Al Nimer, Ivan Jelcic, Christian Kempf, Tom Pieper, Herbert Budka, Mireia Sospedra, Roland Martin
Objective: To characterize the brain-infiltrating immune cell repertoire in Rasmussen encephalitis (RE) with special focus on the subsets, clonality, and their cytokine profile. Methods: The immune cell infiltrate of freshly isolated brain tissue from RE was phenotypically and functionally characterized using immunohistology, flow cytometry, and T-cell receptor (TCR) deep sequencing. Identification of clonally expanded T-cell clones (TCCs) was achieved by combining flow cytometry sorting of CD4+ and CD8+ T cells and high-throughput TCR Vβ-chain sequencing...
January 2018: Neurology® Neuroimmunology & Neuroinflammation
https://www.readbyqxmd.com/read/29249323/characterization-and-comparative-analysis-of-immunoglobulin-lambda-chain-diversity-in-a-neonatal-porcine-model
#10
Nannan Guo, Menghan Su, Zicong Xie, Kankan Wang, Hongming Yuan, Mengjing Li, Jianing Li, Minghao Liu, Jing Bai, Jing Liu, Hongsheng Ouyang, Daxin Pang, Huping Jiao
To elucidate how antigen exposure and selection shape the porcine antibody repertoires, we investigated the immunoglobulin lambda light chain (IGL) gene repertoires of the binary cross-bred (Yorkshire×Landrace) pig at different developmental stages, pre-suckle neonate (0days), wean piglet (35days) and growing pig (75days) under normal farming conditions. Immunoglobulin lambda light transcript (IGLV-J-C) clones of the peripheral blood mononuclear cells (PBMCs) from these different developmental stages were assessed for IGL combination, junction and sequence diversity...
January 2018: Veterinary Immunology and Immunopathology
https://www.readbyqxmd.com/read/29247824/high-throughput-sequencing-of-the-immune-repertoire-in-oncology-applications-for-clinical-diagnosis-monitoring-and-immunotherapies
#11
Baixin Ye, Daniel Smerin, Qingping Gao, Chunsheng Kang, Xiaoxing Xiong
The diagnostic, monitoring and therapeutic options for cancers currently remain limited. These limitations represent a large threat to human health. Adaptive immunity, which is dependent on diverse repertoires of B cell receptors (BCRs) and T cell receptors (TCRs), plays a critical role in the anti-tumor immune response. Modulation and surveillance of adaptive immunity has become a powerful weapon to combat cancers. Recently, the high-throughput sequencing of immune repertoire (HTS-IR) technology, which provides a robust tool for deep sequencing repertoires of BCRs or TCRs, has been applied in the development of tumor biomarkers and immunotherapeutics for cancers...
December 13, 2017: Cancer Letters
https://www.readbyqxmd.com/read/29245903/deep-sequencing-of-the-t-cell-receptor-%C3%AE-repertoire-reveals-signature-patterns-and-clonal-drift-in-atherosclerotic-plaques-and-patients
#12
Zongwei Lin, Shao Qian, Yan Gong, Jianwei Ren, Lixia Zhao, Dongxiao Wang, Xiaowei Wang, Yun Zhang, Zhe Wang, Qunye Zhang
The T cell receptor (TCR) β repertoire directly reflects the status of T cell function. Meanwhile, the immune/inflammatory responses regulated by T cells are the critical determinants of atherosclerosis development. However, due to technical limitations, the composition and molecular characteristics of the TCR repertoire in atherosclerotic patients have not been fully elucidated. In the present study, we use powerful immune repertoire sequencing technology to study this issue. Results show that the utilization of V and/or J genes and the diversity of TCRβ repertoire in atherosclerotic plaques are significantly reduced compared to those in the peripheral blood of normal subjects and atherosclerotic patients...
November 21, 2017: Oncotarget
https://www.readbyqxmd.com/read/29224093/sex-effects-at-the-ramparts-nutrient-and-microbe-mediated-regulation-of-the-immune-metabolic-interface
#13
Nyrie Israelian, Jayne S Danska
The relationships between dietary compounds, derivative metabolites, and host metabolism and immunity are controlled by diverse molecular mechanisms. Essential contributions to these dynamics come from the community of microbes (the microbiome) inhabiting the human digestive tract. The composition and function of the microbiome are shaped by available nutrients, and reciprocally, these organisms produce an as yet poorly defined repertoire of molecules that communicate with the epithelial barrier and the mucosal immune system...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29222257/is-molecular-remission-the-goal-of-multiple-myeloma-therapy
#14
REVIEW
Faith E Davies
The increased number of effective therapies and the wider use of combinations that give deeper remissions have resulted in a reassessment of the goals of myeloma therapy. With the advent of new therapeutic strategies and diagnostic tools, achievement of minimal residual disease (MRD)-negative status has become increasingly important, with some even considering it as the primary endpoint for therapy. The level of MRD that is aimed for is a continuous, rather than an absolute variable, with studies in both transplant-eligible and -noneligible patients showing that the level of MRD achieved is predictive of progression-free survival and overall survival, with an improvement in survival of approximately 1 year for each log-depletion in MRD level...
December 8, 2017: Hematology—the Education Program of the American Society of Hematology
https://www.readbyqxmd.com/read/29211135/longitudinal-evaluation-of-humoral-immune-response-and-merozoite-surface-antigen-diversity-in-calves-naturally-infected-with-babesia-bovis-in-s%C3%A3-o-paulo-brazil
#15
Carlos António Matos, Luiz Ricardo Gonçalves, Dasiel Obregón Alvarez, Carla Roberta Freschi, Jenevaldo Barbosa da Silva, Silvana Pompeia Val-Moraes, Natalia Serra Mendes, Marcos Rogério André, Rosangela Zacarias Machado
Babesiosis is an economically important infectious disease affecting cattle worldwide. In order to longitudinally evaluate the humoral immune response against Babesia bovis and the merozoite surface antigen diversity of B. bovis among naturally infected calves in Taiaçu, Brazil, serum and DNA samples from 15 calves were obtained quarterly, from their birth to 12 months of age. Anti-B. bovis IgG antibodies were detected by means of the indirect fluorescent antibody test (IFAT) and enzyme-linked immunosorbent assay (ELISA)...
October 2017: Revista Brasileira de Parasitologia Veterinária, Brazilian Journal of Veterinary Parasitology
https://www.readbyqxmd.com/read/29209563/comparative-immunologic-characterization-of-autoimmune-giant-cell-myocarditis-with-ipilimumab
#16
Alexandre Reuben, Mariana Petaccia de Macedo, Jennifer McQuade, Aron Joon, Zhiyong Ren, Tiffany Calderone, Brandy Conner, Khalida Wani, Zachary A Cooper, Hussein Tawbi, Michael T Tetzlaff, Robert F Padera, Jean-Bernard Durand, Alexander J Lazar, Jennifer A Wargo, Michael A Davies
Autoimmune myocarditis is a rare but often fatal toxicity of checkpoint inhibitor immunotherapy. To improve the understanding of this complication, we performed immune profiling on post-mortem tissue from a patient with metastatic melanoma who had steroid-responsive hepatitis, steroid-refractory myocarditis, and shrinking lung metastases after ipilimumab treatment. Histological analysis of heart tissue demonstrated findings consistent with giant cell myocarditis (GCM). The immune infiltrate in the heart was largely comprised of CD4+ T cells, whereas the liver had very few T cells, and CD8+ T cells were predominant in the responding lung metastases...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/29194033/immunoproteomic-analysis-of-the-protein-repertoire-of-unsporulated-eimeria-tenella-oocysts
#17
Zhenchao Zhang, Shuai Wang, Charles Li, Liheng Liu
The apicomplexan protozoans Eimeria spp. cause coccidioses, the most common intestinal diseases in chickens. Coccidiosis is associated with significant animal welfare issues and has a high economic impact on the poultry industry. Lack of a full understanding of immunogenic molecules and their precise functions involved in the Eimeria life cycles may limit development of effective vaccines and drug therapies. In this study, immunoproteomic approaches were used to define the antigenic protein repertoire from the total proteins of unsporulated Eimeria tenella oocysts...
2017: Parasite: Journal de la Société Française de Parasitologie
https://www.readbyqxmd.com/read/29192240/characterization-of-the-b-cell-receptor-repertoires-in-peanut-allergic-subjects-undergoing-oral-immunotherapy
#18
Kazuma Kiyotani, Tu H Mai, Rui Yamaguchi, Poh Yin Yew, Mike Kulis, Kelly Orgel, Seiya Imoto, Satoru Miyano, A Wesley Burks, Yusuke Nakamura
B-cell receptors (BCRs) play a critical role in adaptive immunity as they generate highly diverse immunoglobulin repertoires to recognize a wide variety of antigens. To better understand immune responses, it is critically important to establish a quantitative and rapid method to analyze BCR repertoire comprehensively. Here, we developed "Bcrip", a novel approach to characterize BCR repertoire by sequencing millions of BCR cDNA using next-generation sequencer. Using this method and quantitative real-time PCR, we analyzed expression levels and repertoires of BCRs in a total of 17 peanut allergic subjects' peripheral blood samples before and after receiving oral immunotherapy (OIT) or placebo...
November 30, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/29191832/molecular-characterization-of-human-anti-hinge-antibodies-derived-from-single-cell-cloning-of-normal-human-b-cells
#19
Tao Huang, Mary Mathieu, Sophia Lee, Xinhua Wang, Yee Seir Kee, Jack J Bevers, Claudio Ciferri, Alberto Estavez, Manda Wong, Nancy Y Chiang, Gerald Nakamura, Randall J Brezski
Anti-hinge antibodies (AHAs) are an autoantibody subclass that, following proteolytic cleavage, recognize cryptic epitopes exposed in the hinge regions of immunoglobulins (Igs) and do not bind to the intact Ig counterpart. AHAs have been postulated to exacerbate chronic inflammatory disorders such as inflammatory bowel disease and rheumatoid arthritis. On the other hand, AHAs may protect against invasive microbial pathogens and cancer. However, despite more than 50 years of study, the origin and specific B cell compartments that express AHAs remain elusive...
November 30, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29187849/quantification-of-inter-sample-differences-in-t-cell-receptor-repertoires-using-sequence-based-information
#20
Ryo Yokota, Yuki Kaminaga, Tetsuya J Kobayashi
Inter-sample comparisons of T-cell receptor (TCR) repertoires are crucial for gaining a better understanding of the immunological states determined by different collections of T cells from different donor sites, cell types, and genetic and pathological backgrounds. For quantitative comparison, most previous studies utilized conventional methods in ecology, which focus on TCR sequences that overlap between pairwise samples. Some recent studies attempted another approach that is categorized into Poisson abundance models using the abundance distribution of observed TCR sequences...
2017: Frontiers in Immunology
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