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Immune repertoire sequencing

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https://www.readbyqxmd.com/read/28934479/targeted-reconstruction-of-t-cell-receptor-sequence-from-single-cell-rna-seq-links-cdr3-length-to-t-cell-differentiation-state
#1
Shaked Afik, Kathleen B Yates, Kevin Bi, Samuel Darko, Jernej Godec, Ulrike Gerdemann, Leo Swadling, Daniel C Douek, Paul Klenerman, Eleanor J Barnes, Arlene H Sharpe, W Nicholas Haining, Nir Yosef
The T cell compartment must contain diversity in both T cell receptor (TCR) repertoire and cell state to provide effective immunity against pathogens. However, it remains unclear how differences in the TCR contribute to heterogeneity in T cell state. Single cell RNA-sequencing (scRNA-seq) can allow simultaneous measurement of TCR sequence and global transcriptional profile from single cells. However, current methods for TCR inference from scRNA-seq are limited in their sensitivity and require long sequencing reads, thus increasing the cost and decreasing the number of cells that can be feasibly analyzed...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28928742/a-streamlined-approach-to-antibody-novel-germline-allele-prediction-and-validation
#2
Ben S Wendel, Chenfeng He, Peter D Crompton, Susan K Pierce, Ning Jiang
Advancements in high-throughput sequencing and molecular identifier-based error correction have opened the door to antibody repertoire sequencing with single mutation precision, increasing both the breadth and depth of immune response characterization. However, improvements in sequencing technology cannot resolve one key aspect of antibody repertoire sequencing accuracy: the possibility of undocumented novel germline alleles. Somatic hypermutation (SHM) calling requires a reference germline sequence, and the antibody variable region gene alleles collected by the IMGT database, although large in number, are not comprehensive...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28927942/microfluidic-single-cell-technology-in-immunology-and-antibody-screening
#3
REVIEW
Yu Fen Samantha Seah, Hongxing Hu, Christoph A Merten
Single-cell technology has a major impact on the field of immunology. It enables the kinetics and logic of immune signaling and immune cell migration to be elucidated, facilitates antibody screening and allows massively parallelized analysis of B- and T-cell repertoires. Impressive progress has been made over the last decade, strongly boosted by microfluidic approaches. In this review, we summarize the most powerful microfluidic systems based on continuous-flow, nanowells, valves and droplets and we analyze their benefits for phenotypic characterization, drug discovery and next generation sequencing experiments...
September 16, 2017: Molecular Aspects of Medicine
https://www.readbyqxmd.com/read/28924003/learning-the-high-dimensional-immunogenomic-features-that-predict-public-and-private-antibody-repertoires
#4
Victor Greiff, Cédric R Weber, Johannes Palme, Ulrich Bodenhofer, Enkelejda Miho, Ulrike Menzel, Sai T Reddy
Recent studies have revealed that immune repertoires contain a substantial fraction of public clones, which may be defined as Ab or TCR clonal sequences shared across individuals. It has remained unclear whether public clones possess predictable sequence features that differentiate them from private clones, which are believed to be generated largely stochastically. This knowledge gap represents a lack of insight into the shaping of immune repertoire diversity. Leveraging a machine learning approach capable of capturing the high-dimensional compositional information of each clonal sequence (defined by CDR3), we detected predictive public clone and private clone-specific immunogenomic differences concentrated in CDR3's N1-D-N2 region, which allowed the prediction of public and private status with 80% accuracy in humans and mice...
September 18, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28912592/accurate-immune-repertoire-sequencing-reveals-malaria-infection-driven-antibody-lineage-diversification-in-young-children
#5
Ben S Wendel, Chenfeng He, Mingjuan Qu, Di Wu, Stefany M Hernandez, Ke-Yue Ma, Eugene W Liu, Jun Xiao, Peter D Crompton, Susan K Pierce, Pengyu Ren, Keke Chen, Ning Jiang
Accurately measuring antibody repertoire sequence composition in a small amount of blood is challenging yet important for understanding repertoire responses to infection and vaccination. We develop molecular identifier clustering-based immune repertoire sequencing (MIDCIRS) and use it to study age-related antibody repertoire development and diversification before and during acute malaria in infants (< 12 months old) and toddlers (12-47 months old) with 4-8 ml of blood. Here, we show this accurate and high-coverage repertoire-sequencing method can use as few as 1000 naive B cells...
September 14, 2017: Nature Communications
https://www.readbyqxmd.com/read/28910279/longitudinal-multiparameter-single-cell-analysis-of-macaques-immunized-with-pneumococcal-protein-conjugated-or-unconjugated-polysaccharide-vaccines-reveals-distinct-antigen-specific-memory-b-cell-repertoires
#6
Bin Jia, Lisa K McNeil, Christopher D Dupont, Konstantinos Tsioris, Rachel M Barry, Ingrid L Scully, Adebola O Ogunniyi, Christopher Gonzalez, Michael W Pride, Todd M Gierahn, Paul A Liberator, Kathrin U Jansen, J Christopher Love
BACKGROUND: The efficacy of protein-conjugated pneumococcal polysaccharide vaccines has been well characterized for children. The level of protection conferred by unconjugated polysaccharide vaccines remains less clear, particularly for elderly individuals who have had prior antigenic experience through immunization with unconjugated polysaccharide vaccines or natural exposure to Streptococcus pneumoniae. METHODS: We compared the magnitude, diversity and genetic biases of antigen-specific memory B cells in two groups of adult cynomolgus macaques that were immunized with a 7-valent conjugated vaccine and boosted after five years with either a 13-valent pneumococcal polysaccharide conjugate vaccine (13vPnC) or a 23-valent unconjugated pneumococcal polysaccharide vaccine (23vPS) using microengraving (a single-cell analysis method) and single-cell RT-PCR...
2017: PloS One
https://www.readbyqxmd.com/read/28892827/role-of-microbiota-in-strengthening-ocular-mucosal-barrier-function-through-secretory-iga
#7
Abirami Kugadas, Quentin Wright, Jennifer Geddes-McAlister, Mihaela Gadjeva
Purpose: The purpose of this study was to evaluate mechanisms controlling secretory IgA (SIgA) production, thereby ensuring maintenance of ocular surface health. Methods: To determine whether the presence of specific gut commensal species regulates SIgA levels and IgA transcripts in the eye-associated lymphoid tissues (EALT), specific-pathogen-free (SPF) Swiss Webster (SW) mice were treated with antibiotic cocktails, germ-free (GF) SW mice were reconstituted with diverse commensal gut microbiota, or monocolonized with gut-specific commensals...
September 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28882107/statistical-classifiers-for-diagnosing-disease-from-immune-repertoires-a-case-study-using-multiple-sclerosis
#8
Jared Ostmeyer, Scott Christley, William H Rounds, Inimary Toby, Benjamin M Greenberg, Nancy L Monson, Lindsay G Cowell
BACKGROUND: Deep sequencing of lymphocyte receptor repertoires has made it possible to comprehensively profile the clonal composition of lymphocyte populations. This opens the door for novel approaches to diagnose and prognosticate diseases with a driving immune component by identifying repertoire sequence patterns associated with clinical phenotypes. Indeed, recent studies support the feasibility of this, demonstrating an association between repertoire-level summary statistics (e.g., diversity) and patient outcomes for several diseases...
September 7, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28878861/genome-sequence-of-the-sulfur-oxidizing-bathymodiolus-thermophilus-gill-endosymbiont
#9
Ruby Ponnudurai, Lizbeth Sayavedra, Manuel Kleiner, Stefan E Heiden, Andrea Thürmer, Horst Felbeck, Rabea Schlüter, Stefan M Sievert, Rolf Daniel, Thomas Schweder, Stephanie Markert
Bathymodiolus thermophilus, a mytilid mussel inhabiting the deep-sea hydrothermal vents of the East Pacific Rise, lives in symbiosis with chemosynthetic Gammaproteobacteria within its gills. The intracellular symbiont population synthesizes nutrients for the bivalve host using the reduced sulfur compounds emanating from the vents as energy source. As the symbiont is uncultured, comprehensive and detailed insights into its metabolism and its interactions with the host can only be obtained from culture-independent approaches such as genomics and proteomics...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28877428/what-has-gwas-done-for-hla-and-disease-associations
#10
REVIEW
A E Kennedy, U Ozbek, M T Dorak
The major histocompatibility complex (MHC) is located in chromosome 6p21 and contains crucial regulators of immune response, including human leucocyte antigen (HLA) genes, alongside other genes with nonimmunological roles. More recently, a repertoire of noncoding RNA genes, including expressed pseudogenes, has also been identified. The MHC is the most gene dense and most polymorphic part of the human genome. The region exhibits haplotype-specific linkage disequilibrium patterns, contains the strongest cis- and trans-eQTLs/meQTLs in the genome and is known as a hot spot for disease associations...
October 2017: International Journal of Immunogenetics
https://www.readbyqxmd.com/read/28866292/the-road-to-a-more-effective-influenza-vaccine-up-to-date-studies-and-future-prospects
#11
REVIEW
Kaori Sano, Akira Ainai, Tadaki Suzuki, Hideki Hasegawa
Influenza virus causes an acute respiratory infection in humans. Frequent point mutations in the influenza genome and occasional exchange of genetic segments between virus strains help the virus evade the pre-existing immunity, resulting in epidemics and pandemics. Although vaccination is the most effective intervention, mismatches between circulating viruses and vaccine strains reduce vaccine efficacy. Furthermore, current injectable vaccines induce IgG antibodies in serum (which limit progression of influenza symptoms) but not secretory IgA antibodies in the respiratory mucosa (which prevent virus infection efficiently)...
September 25, 2017: Vaccine
https://www.readbyqxmd.com/read/28855898/quantitative-analysis-of-repertoire-scale-immunoglobulin-properties-in-vaccine-induced-b-cell-responses
#12
Ilja V Khavrutskii, Sidhartha Chaudhury, Sabrina M Stronsky, Donald W Lee, Jacqueline G Benko, Anders Wallqvist, Sina Bavari, Christopher L Cooper
Recent advances in the next-generation sequencing of B-cell receptors (BCRs) enable the characterization of humoral responses at a repertoire-wide scale and provide the capability for identifying unique features of immune repertoires in response to disease, vaccination, or infection. Immunosequencing now readily generates 10(3)-10(5) sequences per sample; however, statistical analysis of these repertoires is challenging because of the high genetic diversity of BCRs and the elaborate clonal relationships among them...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28846506/rare-high-affinity-mouse-anti-pd-1-antibodies-that-function-in-checkpoint-blockade-discovered-using-microfluidics-and-molecular-genomics
#13
Adam S Adler, Rena A Mizrahi, Matthew J Spindler, Matthew S Adams, Michael A Asensio, Robert C Edgar, Jackson Leong, Renee Leong, David S Johnson
Conventionally, mouse hybridomas or well-plate screening are used to identify therapeutic monoclonal antibody candidates. In this study, we present an alternative to hybridoma-based discovery that combines microfluidics, yeast single-chain variable fragment (scFv) display, and deep sequencing to rapidly interrogate and screen mouse antibody repertoires. We used our approach on six wild-type mice to identify 269 molecules that bind to programmed cell death protein 1 (PD-1), which were present at an average of 1 in 2,000 in the pre-sort scFv libraries...
August 28, 2017: MAbs
https://www.readbyqxmd.com/read/28835491/hiv-1-cross-reactive-primary-virus-neutralizing-antibody-response-elicited-by-immunization-in-non-human-primate
#14
Yimeng Wang, Sijy O'Dell, Hannah L Turner, Chi-I Chiang, Lin Lei, Javier Guenaga, Richard Wilson, Paola Martinez-Murillo, Nicole Doria-Rose, Andrew B Ward, John R Mascola, Richard T Wyatt, Gunilla B Karlsson Hedestam, Yuxing Li
Elicitation of broadly neutralizing antibody (bNAb) responses is a major goal for the development of an HIV-1 vaccine. Current HIV-1 envelope glycoprotein (Env) vaccine candidates predominantly elicit tier 1 and/or autologous tier 2 virus neutralizing antibody (NAb) responses, as well as weak and/or sporadic cross-reactive tier 2 virus NAb responses with unknown specificity. To delineate the specificity of vaccine-elicited cross-reactive tier 2 virus NAb responses, we performed single memory B cell sorting from the peripheral blood of a rhesus macaque immunized with YU2gp140-F trimers in adjuvant, using JR-FL SOSIP...
August 23, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28825667/viral-infection-identifies-micropeptides-differentially-regulated-in-smorf-containing-lncrnas
#15
Brandon S Razooky, Benedikt Obermayer, Joshua Biggs O'May, Alexander Tarakhovsky
Viral infection leads to a robust cellular response whereby the infected cell produces hundreds of molecular regulators to combat infection. Currently, non-canonical components, e.g., long noncoding RNAs (lncRNAs) have been added to the repertoire of immune regulators involved in the antiviral program. Interestingly, studies utilizing next-generation sequencing technologies show that a subset of the >10,000 lncRNAs in the mammalian genome contain small open reading frames (smORFs) associated with active translation, i...
August 21, 2017: Genes
https://www.readbyqxmd.com/read/28818634/mining-na%C3%A3-ve-rabbit-antibody-repertoires-by-phage-display-for-monoclonal-antibodies-of-therapeutic-utility
#16
Haiyong Peng, Thomas Nerreter, Jing Chang, Junpeng Qi, Xiuling Li, Pabalu Karunadharma, Gustavo J Martinez, Mohammad Fallahi, Jo Soden, Jim Freeth, Roger R Beerli, Ulf Grawunder, Michael Hudecek, Christoph Rader
Owing to their high affinities and specificities, rabbit monoclonal antibodies (mAbs) have demonstrated value and potential primarily as basic research and diagnostic reagents, but, in some cases, also as therapeutics. To accelerate access to rabbit mAbs bypassing immunization, we generated a large naïve rabbit antibody repertoire represented by a phage display library encompassing >10 billion independent antibodies in chimeric rabbit/human Fab format and validated it by next-generation sequencing. Panels of rabbit mAbs selected from this library against two emerging cancer targets, ROR1 and ROR2, revealed high diversity, affinity, and specificity...
September 15, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28813462/a-comprehensive-profiling-of-t-and-b-lymphocyte-receptor-repertoires-from-a-chinese-origin-rhesus-macaque-by-high-throughput-sequencing
#17
Longfei Fu, Xinyang Li, Wei Zhang, Changxi Wang, Jinghua Wu, Huanming Yang, Jian Wang, Xiao Liu
Due to the close genetic background, high similarity of physiology, and susceptibility to infectious and metabolic diseases with humans, rhesus macaques have been widely used as an important animal model in biomedical research, especially in the study of vaccine development and human immune-related diseases. In recent years, high-throughput sequencing based immune repertoire sequencing (IR-SEQ) has become a powerful tool to study the dynamic adaptive immune responses. Several previous studies had analyzed the responses of B cells to HIV-1 trimer vaccine or T cell repertoire of rhesus macaques using this technique, however, there are little studies that had performed a comprehensive analysis of immune repertoire of rhesus macaques, including T and B lymphocytes...
2017: PloS One
https://www.readbyqxmd.com/read/28811963/characterization-of-the-cryoablation-induced-immune-response-in-kidney-cancer-patients
#18
Taigo Kato, Tomoyuki Iwasaki, Motohide Uemura, Akira Nagahara, Hiroki Higashihara, Keigo Osuga, Yuji Ikeda, Kazuma Kiyotani, Jae-Hyun Park, Norio Nonomura, Yusuke Nakamura
Cryoablation is one of treatment modalities for kidney cancer and is expected to induce strong local immune responses as well as systemic T-cell-mediated immune reactions that may lead to the regression of distant metastatic lesions. Thus, the characterization of T cell repertoire and immune environment in tumors before and after treatment should contribute to the better understanding of the cryoablation-induced anticancer immune responses. In this study, we collected tumor tissues from 22 kidney cancer patients, before cryoablation and at 3 mo after cryoablation...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/28803690/new-insights-into-non-conventional-epitopes-as-t-cell-targets-the-missing-link-for-breaking-immune-tolerance-in-autoimmune-disease
#19
REVIEW
James Harbige, Martin Eichmann, Mark Peakman
The mechanism by which immune tolerance is breached in autoimmune disease is poorly understood. One possibility is that post-translational modification of self-antigens leads to peripheral recognition of neo-epitopes against which central and peripheral tolerance is inadequate. Accumulating evidence points to multiple mechanisms through which non-germline encoded sequences can give rise to these non-conventional epitopes which in turn engage the immune system as T cell targets. In particular, where these modifications alter the rules of epitope engagement with MHC molecules, such non-conventional epitopes offer a persuasive explanation for associations between specific HLA alleles and autoimmune diseases...
August 10, 2017: Journal of Autoimmunity
https://www.readbyqxmd.com/read/28798410/a-novel-signature-for-stratifying-the-molecular-heterogeneity-of-the-tissue-infiltrating-t-cell-receptor-repertoire-reflects-gastric-cancer-prognosis
#20
Manchao Kuang, Jieyao Cheng, Chengli Zhang, Lin Feng, Xue Xu, Yajing Zhang, Ming Zu, Jianfang Cui, Hang Yu, Kaitai Zhang, Aiming Yang, Shujun Cheng
Many basic properties of the T-cell receptor (TCR) repertoire require clarification, and the changes occurring in the TCR repertoire during carcinogenesis, especially during precancerous stages, remain unclear. This study used deep sequencing analyses to examine 41 gastric tissue samples at different pathological stages, including low-grade intraepithelial neoplasia, high-grade intraepithelial neoplasia, early gastric cancer and matched adjacent tissues, to define the characteristics of the infiltrating TCRβ repertoire during gastric carcinogenesis...
August 10, 2017: Scientific Reports
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