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Immune repertoire sequencing

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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
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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...
April 17, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28412367/deciphering-antigen-responding-antibody-repertoires-by-using-next-generation-sequencing-and-confirming-them-through-antibody-gene-synthesis
#7
Naoko Kono, Lin Sun, Hiroyuki Toh, Takeyuki Shimizu, Hanbing Xue, Osamu Numata, Manabu Ato, Kazuo Ohnishi, Shigeyuki Itamura
Vast diversity and high specificity of antigen recognition by antibodies are hallmarks of the acquired immune system. Although the molecular mechanisms that yield the extremely large antibody repertoires are precisely understood, comprehensive description of the global antibody repertoire generated in individual bodies has been hindered by the lack of powerful measures. To obtain holistic understanding of the antibody-repertoire space, we used next-generation sequencing (NGS) to analyze the deep profiles of naive and antigen-responding repertoires of the IgM, IgG1, and IgG2c classes formed in individual mice...
April 12, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28400082/immune-dysregulation-in-immunodeficiency-disorders-the-role-of-t-cell-receptor-sequencing
#8
REVIEW
Gabriel K Wong, James M Heather, Sara Barmettler, Mark Cobbold
Immune dysregulation is a prominent feature of primary immunodeficiency disorders, which commonly manifested as autoimmunity, cytopenias and inflammatory bowel disease. In partial T-cell immunodeficiency disorders, it has been proposed that the imbalance between effector and regulatory T-cells drives the breakdown of peripheral tolerance. While there is no robust test for immune dysregulation, the T-cell receptor repertoire is used as a surrogate marker, and has been shown to be perturbed in a number of immunodeficiency disorders featuring immune dysregulation including Omenn's Syndrome, Wiskott-Aldrich Syndrome, and common variable immunodeficiency...
April 8, 2017: Journal of Autoimmunity
https://www.readbyqxmd.com/read/28388445/parallel-antibody-germline-gene-and-haplotype-analyses-support-the-validity-of-immunoglobulin-germline-gene-inference-and-discovery
#9
Ufuk Kirik, Lennart Greiff, Fredrik Levander, Mats Ohlin
Analysis of antibody repertoire development and specific antibody responses important for e.g. autoimmune conditions, allergy, and protection against disease is supported by high throughput sequencing and associated bioinformatics pipelines that describe the diversity of the encoded antibody variable domains. Proper assignment of sequences to germline genes are important for many such processes, for instance in the analysis of somatic hypermutation. Germline gene inference from antibody-encoding transcriptomes, by using tools such as TIgGER or IgDiscover, has a potential to enhance the quality of such analyses...
April 4, 2017: Molecular Immunology
https://www.readbyqxmd.com/read/28376793/comparative-genomic-identification-and-validation-of-%C3%AE-defensin-genes-in-the-ovis-aries-genome
#10
T J Hall, C McQuillan, E K Finlay, C O'Farrelly, S Fair, K G Meade
BACKGROUND: β-defensins are small, cationic, antimicrobial peptides found in species across the plant and animal kingdoms. In addition to microbiocidal activity, roles in immunity as well as reproduction have more recently been documented. β-defensin genes in Ovis aries (domestic sheep) have been poorly annotated, having been identified only by automatic gene prediction algorithms. The objective of this study was to use a comparative genomics approach to identify and characterise the β-defensin gene repertoire in sheep using the bovine genome as the primary reference...
April 4, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28358435/clinical-significance-of-t-cell-clonality-and-expression-levels-of-immune-related-genes-in-endometrial-cancer
#11
Yuji Ikeda, Kazuma Kiyotani, Poh Yin Yew, Sho Sato, Yuichi Imai, Rui Yamaguchi, Satoru Miyano, Keiichi Fujiwara, Kosei Hasegawa, Yusuke Nakamura
Immune microenvironment characterized by T cell clonality as well as expression signatures of immune-related genes in endometrial cancer tissues may play significant roles in clinical outcome of patients. We aimed to investigate the clinical significance of immune-related gene expression and TCR repertoire in endometrial cancer. Using total RNAs extracted from 32 endometrioid endometrial cancer cases, we performed quantitative real-time PCR to measure mRNA expression levels of immune-related genes including TRB, CD8, GZMA, HLA-A, CD11c and PD-L1...
March 29, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28351419/new-var-reconstruction-algorithm-exposes-high-var-sequence-diversity-in-a-single-geographic-location-in-mali
#12
Antoine Dara, Elliott F Drábek, Mark A Travassos, Kara A Moser, Arthur L Delcher, Qi Su, Timothy Hostelley, Drissa Coulibaly, Modibo Daou, Ahmadou Dembele, Issa Diarra, Abdoulaye K Kone, Bourema Kouriba, Matthew B Laurens, Amadou Niangaly, Karim Traore, Youssouf Tolo, Claire M Fraser, Mahamadou A Thera, Abdoulaye A Djimde, Ogobara K Doumbo, Christopher V Plowe, Joana C Silva
BACKGROUND: Encoded by the var gene family, highly variable Plasmodium falciparum erythrocyte membrane protein-1 (PfEMP1) proteins mediate tissue-specific cytoadherence of infected erythrocytes, resulting in immune evasion and severe malaria disease. Sequencing and assembling the 40-60 var gene complement for individual infections has been notoriously difficult, impeding molecular epidemiological studies and the assessment of particular var elements as subunit vaccine candidates. METHODS: We developed and validated a novel algorithm, Exon-Targeted Hybrid Assembly (ETHA), to perform targeted assembly of var gene sequences, based on a combination of Pacific Biosciences and Illumina data...
March 28, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28348050/differential-ifn-%C3%AE-and-tnf-%C3%AE-driven-cytokine-response-distinguishes-acute-infection-of-a-metatherian-host-with-toxoplasma-gondii-and-neospora-caninum
#13
Shannon L Donahoe, David N Phalen, Bronwyn M McAllan, Denis O'Meally, Milton M McAllister, John Ellis, Jan Šlapeta
Toxoplasma gondii and Neospora caninum (both Apicomplexa) are closely related cyst-forming coccidian parasites that differ significantly in their host range and ability to cause disease. Unlike eutherian mammals, Australian marsupials (metatherian mammals) have long been thought to be highly susceptible to toxoplasmosis and neosporosis because of their historical isolation from the parasites. In this study, the carnivorous fat-tailed dunnart (Sminthopsis crassicaudata) was used as a disease model to investigate the immune response and susceptibility to infection of an Australian marsupial to T...
March 27, 2017: Infection and Immunity
https://www.readbyqxmd.com/read/28343731/endoplasmic-reticulum-aminopeptidase-2-a-common-immunological-link-to-adverse-pregnancy-outcomes-and-cancer-clearance
#14
Eun D Lee
Endoplasmic Reticulum Aminopeptidase 2 (ERAP2) trims HLA class I-binding peptides, determining the peptide repertoire presented for immune recognition. Variation in the ERAP2 amino acid sequence could affect the ability of some fetuses and tumors to achieve immune evasion. For example, homozygosity for an ERAP2 variant that has increased trimming efficiency for hydrophobic molecules has never been detected in mothers and fetuses. Thus, it is possible that this single nucleotide polymorphism (SNP) in the ERAP2 gene has been selected against in order to prevent alteration of the immune privileged uterine environment, and to allow tumors to escape immune recognition...
March 18, 2017: Placenta
https://www.readbyqxmd.com/read/28341999/immunological-memory-to-hyperphosphorylated-tau-in-asymptomatic-individuals
#15
Gabriel Pascual, Jehangir S Wadia, Xueyong Zhu, Elissa Keogh, Başak Kükrer, Jeroen van Ameijde, Hanna Inganäs, Berdien Siregar, Gerrard Perdok, Otto Diefenbach, Tariq Nahar, Imke Sprengers, Martin H Koldijk, Els C Brinkman-van der Linden, Laura A Peferoen, Heng Zhang, Wenli Yu, Xinyi Li, Michelle Wagner, Veronica Moreno, Julie Kim, Martha Costa, Kiana West, Zara Fulton, Lucy Chammas, Nancy Luckashenak, Lauren Fletcher, Trevin Holland, Carrie Arnold, R Anthony Williamson, Jeroen J Hoozemans, Adrian Apetri, Frederique Bard, Ian A Wilson, Wouter Koudstaal, Jaap Goudsmit
Several reports have described the presence of antibodies against Alzheimer's disease-associated hyperphosphorylated forms of tau in serum of healthy individuals. To characterize the specificities that can be found, we interrogated peripheral IgG(+) memory B cells from asymptomatic blood donors for reactivity to a panel of phosphorylated tau peptides using a single-cell screening assay. Antibody sequences were recovered, cloned, and expressed as full-length IgGs. In total, 52 somatically mutated tau-binding antibodies were identified, corresponding to 35 unique clonal families...
May 2017: Acta Neuropathologica
https://www.readbyqxmd.com/read/28341036/advanced-methodologies-in-high-throughput-sequencing-of-immune-repertoires
#16
REVIEW
Simon Friedensohn, Tarik A Khan, Sai T Reddy
In recent years, major efforts have been made to develop sophisticated experimental and bioinformatic workflows for sequencing adaptive immune repertoires. The immunological insight gained has been applied to fields as varied as lymphocyte biology, immunodiagnostics, vaccines, cancer immunotherapy, and antibody engineering. In this review, we provide a detailed overview of these advanced methodologies, focusing specifically on strategies to reduce sequencing errors and bias and to achieve high-throughput pairing of variable regions (e...
March 2017: Trends in Biotechnology
https://www.readbyqxmd.com/read/28332079/gorilla-mhc-class-i-gene-and-sequence-variation-in-a-comparative-context
#17
Jörg B Hans, Richard A Bergl, Linda Vigilant
Comparisons of MHC gene content and diversity among closely related species can provide insights into the evolutionary mechanisms shaping immune system variation. After chimpanzees and bonobos, gorillas are humans' closest living relatives; but in contrast, relatively little is known about the structure and variation of gorilla MHC class I genes (Gogo). Here, we combined long-range amplifications and long-read sequencing technology to analyze full-length MHC class I genes in 35 gorillas. We obtained 50 full-length genomic sequences corresponding to 15 Gogo-A alleles, 4 Gogo-Oko alleles, 21 Gogo-B alleles, and 10 Gogo-C alleles including 19 novel coding region sequences...
March 22, 2017: Immunogenetics
https://www.readbyqxmd.com/read/28323873/a-three-monoclonal-antibody-combination-potently-neutralizes-multiple-botulinum-neurotoxin-serotype-f-subtypes
#18
Yongfeng Fan, Consuelo Garcia-Rodriguez, Jianlong Lou, Weihua Wen, Fraser Conrad, Wenwu Zhai, Theresa J Smith, Leonard A Smith, James D Marks
Human botulism is primarily caused by botulinum neurotoxin (BoNT) serotypes A, B and E, with around 1% caused by serotype F (BoNT/F). BoNT/F comprises at least seven different subtypes with the amino acid sequence difference between subtypes as high as 36%. The sequence differences present a significant challenge for generating monoclonal antibodies (mAbs) that can bind, detect and neutralize all BoNT/F subtypes. We used repertoire cloning of immune mouse antibody variable (V) regions and yeast display to generate a panel of 33 lead single chain Fv (scFv) mAbs that bound one or more BoNT/F subtypes with a median equilibrium dissociation constant (KD) of 4...
2017: PloS One
https://www.readbyqxmd.com/read/28321219/computational-model-reveals-limited-correlation-between-germinal-center-b-cell-subclone-abundancy-and-affinity-implications-for-repertoire-sequencing
#19
Polina Reshetova, Barbera D C van Schaik, Paul L Klarenbeek, Marieke E Doorenspleet, Rebecca E E Esveldt, Paul-Peter Tak, Jeroen E J Guikema, Niek de Vries, Antoine H C van Kampen
Immunoglobulin repertoire sequencing has successfully been applied to identify expanded antigen-activated B-cell clones that play a role in the pathogenesis of immune disorders. One challenge is the selection of the Ag-specific B cells from the measured repertoire for downstream analyses. A general feature of an immune response is the expansion of specific clones resulting in a set of subclones with common ancestry varying in abundance and in the number of acquired somatic mutations. The expanded subclones are expected to have BCR affinities for the Ag higher than the affinities of the naive B cells in the background population...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28318808/t-cell-receptor-assessment-in-autoimmune-disease-requires-access-to-the-most-adjacent-immunologically-active-organ
#20
Bergithe E Oftedal, Brita Ardesjö Lundgren, David Hamm, Poh-Yi Gan, Stephen R Holdsworth, Christopher N Hahn, Andreas W Schreiber, Hamish S Scott
Next generation sequencing of T and B cell receptors is emerging as a valuable and effective method to diagnose and monitor hematopoietic malignancies. So far, this approach has not been fully explored in regard to autoimmune diseases. T cells develop in the thymus where they undergo positive and negative selection, and the autoimmune regulator (Aire) is central in the establishment of immunological tolerance. Loss of Aire leads to severe multiorgan autoimmune disease with infiltration of autoreactive T cells in affected organs...
March 15, 2017: Journal of Autoimmunity
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