Article
Biochemical Research Methods
Catherine Sutherland, Graeme J. M. Cowan
Summary: Adaptive Immune Receptor Repertoire Sequencing is a rapidly developing field that has improved our understanding of the adaptive immune system. We have developed AIRRSHIP, a Python package that produces synthetic human B cell receptor sequences, which can be used to assess the accuracy of repertoire analysis tools and identify factors contributing to inaccuracies in results.
Letter
Biochemistry & Molecular Biology
Michael J. Pitcher, Jo Spencer
Summary: Human transitional B cells and naive B cells exhibit diversity beyond their B cell receptor repertoire. Individual cells within these subsets display varying phenotypes and transcriptomes, which results in functional biases. We investigated small clones of transitional and naive B cells from different tissue sites and found that cells within the same clone have more similar gene expression than unrelated cells. This suggests that differences between clone members are heritable and that diversity in transitional and naive B cell populations can be sustained.
MOLECULAR IMMUNOLOGY
(2023)
Article
Physics, Multidisciplinary
Hongda Jiang, Shenshen Wang
Summary: The adaptive immune system improves its protection against future pathogens by constantly modifying its lymphocyte repertoire. Recent experiments have shown that B cells physically extract antigens using active forces, and this extraction level determines clonal fitness. These observations challenge the prevailing view that the equilibrium constant of receptor-antigen binding determines selective advantage. A theoretical framework was proposed to explore the impact of tug-of-war antigen extraction on the quality and diversity of an evolved B cell repertoire. The results suggest that active forces play a multifaceted role in immune adaptation, rationalizing key observations on repertoire dynamics.
Article
Computer Science, Artificial Intelligence
Ze Zhang, Woo Yong Chang, Kaiwen Wang, Yuqiu Yang, Xinlei Wang, Chen Yao, Tuoqi Wu, Li Wang, Tao Wang
Summary: This study investigates the relationship between B-cell receptors (BCRs) and B-cell gene expression in COVID-19. The researchers found a stronger coupling between BCRs and B-cell gene expression during COVID-19 infections. They developed the Benisse model, which revealed a gradient of B-cell activation along BCR trajectories.
NATURE MACHINE INTELLIGENCE
(2022)
Article
Immunology
Katharine Yu, Akshay Ravoor, Nuria Malats, Silvia Pineda, Marina Sirota
Summary: This study extracted B cell receptor repertoires from tumor and adjacent non-tumor samples and analyzed their diversity and network features. Differences in diversity and network statistics were observed across tumor types and subtypes, with primary tumors showing increased clonality. Significant associations were found between repertoire features and mutation load, tumor stage, and age, as well as survival in seven tumor types.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Immunology
Akshay J. Patel, Naeem Khan, Alex Richter, Babu Naidu, Mark T. Drayson, Gary W. Middleton
Summary: B cells play a key role in lung cancer pathogenesis and response to immunotherapy. The B cell repertoire differs between tumor and circulation, with a diverse range of plasma cell and memory cell phenotypes in lung cancer. The influence of smoking and tumor type on the B cell repertoire is limited.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Virology
Yukio Nakamura, Meng Ling Moi, Takashi Shiina, Tadasu Shin-I, Ryuji Suzuki
Summary: Recognition of T-cell epitopes is crucial for adaptive immune responses, but existing prediction methods often neglect T-cell receptor-recognized epitope sequences. In this study, we developed a method that identifies T-cell epitopes derived from antigen proteins by analyzing B-cell receptor sequences. Our method successfully identified T-cell epitopes associated with viral infections and demonstrated immunogenicity. Thus, this method is a powerful tool for discovering T-cell epitopes from BCR sequences.
Article
Biotechnology & Applied Microbiology
Pingsen Zhao, Sharula Guo, Zhixiong Zhong, Songtao Yang, Xianzhu Xia
Summary: The study revealed that rabies virus vaccination alters BCR diversity and gene segment usage, inducing B cell clone expansion. Quantitative characterization of human B cell receptor repertoire post rabies virus vaccination can provide new insights into the B cell receptor condition.
HUMAN VACCINES & IMMUNOTHERAPEUTICS
(2021)
Article
Biology
Haocheng Ye, Lin Cheng, Bin Ju, Gang Xu, Yang Liu, Shuye Zhang, Lifei Wang, Zheng Zhang
Summary: A specialized software SCIGA was developed for precise and quick analysis of 10X single-cell immunoglobulin repertoires, which helps researchers to interpret B-cell immunoglobulin repertoires with paired heavy and light chain. SCIGA successfully identified four neutralizing antibodies against SARS-CoV-2 in samples from patients with COVID-19.
Article
Biochemistry & Molecular Biology
Hyunho Lee, Duck Kyun Yoo, Jerome Han, Ki Hyun Kim, Jinsung Noh, Yonghee Lee, Eunjae Lee, Sunghoon Kwon, Junho Chung
Summary: This study compared in silico reconstitution of BCR repertoires from peripheral blood samples of different volumes taken from two volunteers and found that a significant number of functional unique sequences (FUSs) could be detected even in smaller volume samples. This indicates the potential application of BCR repertoire analysis in diagnosis.
Article
Biology
Niels J. M. Verstegen, Sabrina Pollastro, Peter-Paul A. Unger, Casper Marsman, George Elias, Tineke Jorritsma, Marij Streutker, Kevin Bassler, Kristian Haendler, Theo Rispens, Joachim L. Schultze, Anja ten Brinke, Marc Beyer, S. Marieke van Ham
Summary: In this study, the differentiation trajectories of human naive B cells into antibody-secreting cells (ASCs) were investigated using single-cell RNA sequencing. By comparing transcriptomes of B cells at different stages of differentiation from in vitro and ex vivo sources, a novel pre-ASC population was identified in lymphoid tissues. This study also revealed the existence of a germinal-center-like population in vitro, which may undergo an alternative route of differentiation to become memory B cells, mimicking in vivo human germinal center reactions. This work provides a detailed characterization of human B cell differentiation into ASCs or memory B cells under healthy and diseased conditions.
Review
Gastroenterology & Hepatology
Qiao Zhan, Jing-Hang Xu, Yan-Yan Yu, Emily K. N. Lo, Felicianna, Hani El-Nezami, Zheng Zeng
Summary: This review summarizes the methodology and application of immune repertoire sequencing (IRS) in studying the human immune system, focusing on its role in predicting the progression, treatment, and vaccination of Hepatitis B virus (HBV) infection.
WORLD JOURNAL OF GASTROENTEROLOGY
(2021)
Article
Cell Biology
Prasanti Kotagiri, Federica Mescia, William M. Rae, Laura Bergamaschi, Zewen K. Tuong, Lorinda Turner, Kelvin Hunter, Pehuen P. Gerber, Myra Hosmillo, Christoph Hess, Menna R. Clatworthy, Ian G. Goodfellow, Nicholas J. Matheson, Eoin F. McKinney, Mark R. Wills, Ravindra K. Gupta, John R. Bradley, Rachael J. M. Bashford-Rogers, Paul A. Lyons, Kenneth G. C. Smith
Summary: B cell receptor (BCR) repertoire development differs between severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection and vaccination, potentially informing vaccine strategies. After infection, there is an increase in immunoglobulin (Ig)G1/3 and IgA1 BCRs, a decrease in somatic hypermutation (SHM), and expansion of IgM and IgA clones in severe disease. In contrast, vaccination leads to an increase in IgD/M BCRs, unchanged SHM, and prominent expansion of IgG clones.
Article
Immunology
Hongkai Wu, Zhichao Zhou, Shi Xie, Rong Yan, Mingxing Gong, Xingui Tian, Zhanhui Wang
Summary: The study measured the B cell receptor (BCR) repertoire similarity in blood and spleen samples from BALB/c and C57BL/6J mice, finding better convergence in IgM compared to IgA and IgG, and better robustness in IgM somatic mutation networks. It also showed better sharing of CDR3 clonotypes and clonal lineages in spleen samples than in blood samples. Differences in CDR3 evenness, mutated clonotype proportions, and maximal network degrees were detected between animal batches.
Article
Cell Biology
Lingjie Luo, Wenhua Liang, Jianfeng Pang, Gang Xu, Yingying Chen, Xinrong Guo, Xin Wang, Yi Zhao, Yangdian Lai, Yang Liu, Bin Li, Bing Su, Shuye Zhang, Michal Baniyash, Lei Shen, Lei Chen, Yun Ling, Ying Wang, Qiming Liang, Hongzhou Lu, Zheng Zhang, Feng Wang
Summary: The study revealed that the diversity of TCR repertoire in discharged COVID-19 patients increased but returned to baseline level about one week after virus clearance, with the dynamics of T cell repertoire correlated with gene signature changes. Top expanded T cell clones displayed key anti-viral features, confirming the critical role of antigen-specific T cells in fighting against SARS-CoV-2.
Article
Biochemistry & Molecular Biology
Julie M. J. Laffy, Tihomir Dodev, Jamie A. Macpherson, Catherine Townsend, Hui Chun Lu, Deborah Dunn-Walters, Franca Fraternali
PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY
(2017)
Article
Biochemistry & Molecular Biology
Julia Saez de Guinoa, Rebeca Jimeno, Mauro Gaya, David Kipling, Maria Jose Garzon, Deborah Dunn-Walters, Carles Ubeda, Patricia Barral
Article
Allergy
Andrea Bjorkman, Likun Du, Mirjam van der Burg, Valerie Cormier-Daire, Guntram Borck, Juan Pie, Britt-Marie Anderlid, Lennart Hammarstrom, Lena Strom, Jean-Pierre de Villartay, David Kipling, Deborah Dunn Walters, Qiang Pan-Hammarstrom
JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
(2018)
Article
Immunology
Greg Crawford, Mark David Hayes, Rocio Castro Seoane, Sophie Ward, Tim Dalessandri, Chester Lai, Eugene Healy, David Kipling, Charlotte Proby, Colin Moyes, Kile Green, Katie Best, Muzlifah Haniffa, Marina Botto, Deborah Dunn-Walters, Jessica Strid
Article
Biochemistry & Molecular Biology
Christian Margreitter, Hui-Chun Lu, Catherine Townsend, Alexander Stewart, Deborah K. Dunn-Walters, Franca Fraternali
NUCLEIC ACIDS RESEARCH
(2018)
Article
Multidisciplinary Sciences
A. Stewart, R. Hunt, R. Mitchell, V. Muhawenimana, C. A. M. E. Wilson, J. A. Jackson, J. Cable
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2018)
Article
Immunology
Alexander Stewart, Joseph Chi-Fung Ng, Gillian Wallis, Vasiliki Tsioligka, Franca Fraternali, Deborah K. Dunn-Walters
Summary: The separation of B cells into different subsets has provided insights into their diverse functions in immune responses. Advances in single-cell techniques have enabled a deeper understanding of B cell characteristics and functions, though challenges remain. This study offers a reference single-cell dataset for better classification of functional B cell subsets in peripheral blood, highlighting the complexity and diversity of B cell populations.
FRONTIERS IN IMMUNOLOGY
(2021)
Editorial Material
Immunology
Veerle Somers, Deborah K. Dunn-Walters, Mirjam van der Burg, Judith Fraussen
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Cecile F. Frampas, Katie Longman, Matt Spick, Holly-May Lewis, Catia D. S. Costa, Alex Stewart, Deborah Dunn-Walters, Danni Greener, George Evetts, Debra J. Skene, Drupad Trivedi, Andy Pitt, Katherine Hollywood, Perdita Barran, Melanie J. Bailey
Summary: Saliva metabolomics, particularly amino acids, can differentiate between high severity and low severity COVID-19 patients, expanding the understanding of COVID-19 metabolic dysregulation and potentially providing a non-invasive means of sampling patients for timely treatment.
Article
Medicine, General & Internal
Matt Spick, Katherine Longman, Cecile Frampas, Holly Lewis, Catia Costa, Deborah Dunn Walters, Alex Stewart, Michael Wilde, Danni Greener, George Evetts, Drupad Trivedi, Perdita Barran, Andy Pitt, Melanie Bailey
Summary: The study revealed lower lipid levels in COVID-19 positive patients, indicating dyslipidemia. Sebum sampling showed potential for distinguishing between COVID-19 positive and negative patients based on lipidomic analysis.