Article
Immunology
Brian L. Le, Renan Sper, Sandra C. A. Nielsen, Silvia Pineda, Quoc-Hung Nguyen, Ji-Yeun Lee, Scott D. Boyd, Tippi C. MacKenzie, Marina Sirota
Summary: Preterm labor is the leading cause of neonatal morbidity and mortality worldwide. The study found that preterm infants display immature features and clonal overlap with maternal TCR-beta clones. In preterm pregnancies, there is significantly higher clonal convergence between mother and baby pairs compared to term pregnancies.
JOURNAL OF IMMUNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Ayelet Peres, William D. Lees, Oscar L. Rodriguez, Noah Y. Lee, Pazit Polak, Ronen Hope, Meirav Kedmi, Andrew M. Collins, Mats Ohlin, Steven H. Kleinstein, Corey T. Watson, Gur Yaari
Summary: In adaptive immune receptor repertoire analysis, determining the germline variable (V) allele associated with each T- and B-cell receptor sequence is challenging. In this study, we propose an alternative naming scheme for V alleles and a novel method to infer individual genotypes. We validate the effectiveness of our approach and implement it in a freely available R package (PIgLET).
NUCLEIC ACIDS RESEARCH
(2023)
Article
Immunology
Katherine Bao, Juan Zhang, Alexis Scherl, James Ziai, Azi Hadadianpour, Daqi Xu, Christopher Dela Cruz, John Liu, Yuxin Liang, Lucinda Tam, Cesar A. Corzo, Merone Roose-Girma, Soren Warming, Zora Modrusan, Wyne P. Lee, Kam Hon Hoi, Ali A. Zarrin
Summary: This study utilized a novel inducible AID-knockout mouse model and found that deleting AID in adult mice caused spontaneous germinal center formation. Deep sequencing of the IgH repertoire revealed that antibody diversification begins early in life and evolves over time. The findings suggest that activated B cells form germinal centers at steady state and facilitate continuous diversification of the B cell repertoire.
JOURNAL OF IMMUNOLOGY
(2022)
Article
Pathology
Michiel van den Brand, Jos Rijntjes, Markus Mobs, Julia Steinhilber, Michele Y. van der Klift, Kim C. Heezen, Leonie I. Kroeze, Tomas Reigl, Jakub Porc, Nikos Darzentas, Jeroen A. C. W. Luijks, Blanca Scheijen, Frederic Davi, Hesham ElDaly, Hongxiang Liu, Ioannis Anagnostopoulos, Michael Hummel, Falko Fend, Anton W. Langerak, Patricia J. T. A. Groenen
Summary: NGS-based IG clonality analysis shows high interlaboratory concordance and concordance with conventional analysis, with a higher ability to detect clonal rearrangements. NGS and conventional analysis detect clonality in 96% and 95% of B-cell neoplasms, respectively, with the majority of reactive cases being polyclonal.
JOURNAL OF MOLECULAR DIAGNOSTICS
(2021)
Article
Cell Biology
Jong-Chan Park, Jinsung Noh, Sukjin Jang, Ki Hyun Kim, Hayoung Choi, Dongjoon Lee, Jieun Kim, Junho Chung, Dong Young Lee, Yonghee Lee, Hyunho Lee, Duck Kyun Yoo, Amos Chungwon Lee, Min Soo Byun, Dahyun Yi, Sun-Ho Han, Sunghoon Kwon, Inhee Mook-Jung
Summary: This study suggests that changes in B lymphocytes play a role in the development of Alzheimer's disease. The increase in B lymphocytes is associated with increased amyloid deposition in the brain and hyperactivation of microglia, leading to impaired clearance of beta-amyloid. Furthermore, despite high somatic hypermutation rates, patients with Alzheimer's disease share similar B cell receptor sequences.
Article
Immunology
Christoph Ruschil, Gisela Gabernet, Constanze Louisa Kemmerer, Mohamed Ali Jarboui, Franziska Klose, Sven Poli, Ulf Ziemann, Sven Nahnsen, Markus Christian Kowarik
Summary: This study investigated the effects of cladribine treatment on B cell repertoire in multiple sclerosis patients. The results showed that cladribine therapy decreased memory B cell numbers and increased naive B cell numbers. However, it had minimal impact on the composition and diversity of immunoglobulins. The study also found that a proportion of B cell clones were maintained during treatment.
FRONTIERS IN IMMUNOLOGY
(2023)
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.
Review
Biology
Johannes Truck, Anne Eugster, Pierre Barennes, Christopher M. Tipton, Eline T. Luning Prak, Davide Bagnara, Cinque Soto, Jacob S. Sherkow, Aimee S. Payne, Marie-Paule Lefranc, Andrew Farmer, Magnolia Bostick, Encarnita Mariotti-Ferrandiz
Summary: The use of adaptive immune receptor repertoire sequencing (AIRR-seq) has provided new insights into the immune system but also comes with challenges. The AIRR Community's Biological Resources Working Group conducted a survey to understand the need for standards and controls in generating and annotating AIRR-seq data, and offered recommendations for developing AIRR-seq standards and controls based on the survey results.
Article
Immunology
Amy L. Kenter, Corey T. Watson, Jan-Hendrik Spille
Summary: During development, B and T lymphocytes generate diverse antigen receptors which allow organisms to respond to a wide range of pathogens. Studies suggest that genetic polymorphisms in the immunoglobulin heavy chain locus may influence immune-repertoire formation.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biology
Marie Ghraichy, Valentin von Niederhausern, Aleksandr Kovaltsuk, Jacob D. Galson, Charlotte M. Deane, Johannes Truck
Summary: This study sequenced the IgH repertoire of different B cell subpopulations in the peripheral blood of healthy adults, revealing distinct characteristics at both individual sequence and repertoire levels through advanced bioinformatic analysis and machine learning. Sorted B cell subpopulations shared similar repertoire characteristics with their in silico separated subsets, and certain IgH repertoire characteristics correlated with the position of the constant region on the IgH locus. Overall, the study provides unprecedented insight into mechanisms of B cell repertoire control in peripherally circulating B cell subpopulations.
Article
Cell Biology
Debopam Ghosh, Tho D. Pham, Padma P. Nanaware, Deepanwita Sengupta, Lital N. Adler, Caiyun G. Li, Xiao He, Mary E. O'Mara, Aaron B. Kantor, Khoa D. Nguyen, Yang Yang, Laurence C. Eisenlohr, Peter E. Jensen, Leonore A. Herzenberg, Lawrence J. Stern, Scott D. Boyd, Eliver E. B. Ghosn, Elizabeth D. Mellins
Summary: The absence of H2-M protein affects the survival and immunoglobulin selection of B-1 cells, and also alters the specificity of the B-1 cell clonal repertoire.
Article
Biochemical Research Methods
Nika Abdollahi, Lucile Jeusset, Anne Langlois De Septenville, Hugues Ripoche, Frederic Davi, Juliana Silva Bernardes
Summary: The study proposes a new method based on multi-objective clustering for improved identification of clonal lineages in B cell repertoire analysis. The method outperforms other tools in simulated and experimental repertoire datasets and has the shortest running time. The study is of significant importance for understanding the development and evolution of B cell malignancies.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Immunology
Zuhui Su, Yabin Jin, Yu Zhang, Zhanwen Guan, Huishi Li, Xiangping Chen, Chao Xie, Chuling Zhang, Xiaofen Liu, Peixian Li, Peiyi Ye, Lifang Zhang, Yaozhong Kong, Wei Luo
Summary: Membranous nephropathy (MN) is a common autoimmune glomerular disease that requires renal tissue biopsy for diagnosis, indicating the need for new diagnostic and prognostic monitoring methods. High-throughput sequencing analysis revealed abnormalities in multiple aspects of the immunoglobulin heavy chain in patients, with certain gene transcripts and parameters showing potential for predicting therapeutic effects.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Transplantation
Hiroki Yamaguchi, Shin Goto, Nao Takahashi, Masafumi Tsuchida, Hirofumi Watanabe, Suguru Yamamoto, Yoshikatsu Kaneko, Koichi Higashi, Hiroshi Mori, Yukio Nakamura, Arata Horii, Ken Kurokawa, Ichiei Narita
Summary: The study shows that aberrant mucosal immune responses to tonsillar anaerobic microbiota, primarily consisting of members of the phylum Bacteroidetes, are involved in IgAN pathophysiology.
NEPHROLOGY DIALYSIS TRANSPLANTATION
(2021)
Article
Cell Biology
Carolina Monzo, Lisonia Gkioni, Andreas Beyer, Dario Riccardo Valenzano, Sebastian Gronke, Linda Partridge
Summary: Aging impairs immune function, but dietary restriction (DR) can attenuate this decline. In this study, it was shown that DR preserves B cell receptor (BCR) repertoire diversity and reduces clonal expansions during aging in mice. Remarkably, mice starting DR in mid-life have similar BCR diversity and clonal expansion rates as mice on chronic DR. These findings suggest a potential role of B cell repertoire dynamics in age-related health.
Article
Hematology
John M. Gansner, Mahboubeh Rahmani, A. Helena Jonsson, Brooke M. Fortin, Idayat Brimah, Martha Ellis, Robin Smeland-Wagman, Zhihan J. Li, Jason M. Schenkel, Michael B. Brenner, Revital Yefidoff-Freedman, Steven R. Sloan, Nancy Berliner, Nicolas C. Issa, Lindsey R. Baden, Dan L. Longo, Duane R. Wesemann, Donna Neuberg, Deepak A. Rao, Richard M. Kaufman
Editorial Material
Critical Care Medicine
Julie Ng, Kyle Wright, Maura Alvarez, Gary M. Hunninghake, Duane R. Wesemann
Review
Immunology
Teng Zuo, Avneesh Gautam, Duane R. Wesemann
CURRENT OPINION IN IMMUNOLOGY
(2019)
Editorial Material
Multidisciplinary Sciences
Duane R. Wesemann, Cathryn R. Nagler
Article
Multidisciplinary Sciences
Jingyou Yu, Lisa H. Tostanoski, Lauren Peter, Noe B. Mercado, Katherine McMahan, Shant H. Mahrokhian, Joseph P. Nkolola, Jinyan Liu, Zhenfeng Li, Abishek Chandrashekar, David R. Martinez, Carolin Loos, Caroline Atyeo, Stephanie Fischinger, John S. Burke, Matthew D. Slein, Yuezhou Chen, Adam Zuiani, Felipe J. N. Lelis, Meghan Travers, Shaghayegh Habibi, Laurent Pessaint, Alex Van Ry, Kelvin Blade, Renita Brown, Anthony Cook, Brad Finneyfrock, Alan Dodson, Elyse Teow, Jason Velasco, Roland Zahn, Frank Wegmann, Esther A. Bondzie, Gabriel Dagotto, Makda S. Gebre, Xuan He, Catherine Jacob-Dolan, Marinela Kirilova, Nicole Kordana, Zijin Lin, Lori F. Maxfield, Felix Nampanya, Ramya Nityanandam, John D. Ventura, Huahua Wan, Yongfei Cai, Bing Chen, Aaron G. Schmidt, Duane R. Wesemann, Ralph S. Baric, Galit Alter, Hanne Andersen, Mark G. Lewis, Dan H. Barouch
Article
Biochemical Research Methods
Vicky Roy, Stephanie Fischinger, Caroline Atyeo, Matthew Slein, Carolin Loos, Alejandro Balazs, Corinne Luedemann, Michael Gerino Astudillo, Diane Yang, Duane R. Wesemann, Richelle Charles, A. John Lafrate, Jared Feldman, Blake Hauser, Tim Caradonna, Tyler E. Miller, Mandakolathur R. Murali, Lindsey Baden, Eric Nilles, Edward Ryan, Douglas Lauffenburger, Wilfredo Garcia Beltran, Galit Alter
JOURNAL OF IMMUNOLOGICAL METHODS
(2020)
Article
Multidisciplinary Sciences
Ellen Shrock, Eric Fujimura, Tomasz Kula, Richard T. Timms, I-Hsiu Lee, Yumei Leng, Matthew L. Robinson, Brandon M. Sie, Mamie Z. Li, Yuezhou Chen, Jennifer Logue, Adam Zuiani, Denise McCulloch, Felipe J. N. Lelis, Stephanie Henson, Daniel R. Monaco, Meghan Travers, Shaghayegh Habibi, William A. Clarke, Patrizio Caturegli, Oliver Laeyendecker, Alicja Piechocka-Trocha, Jonathan Z. Li, Ashok Khatri, Helen Y. Chu, Alexandra-Chloe Villani, Kyle Kays, Marcia B. Goldberg, Nir Hacohen, Michael R. Filbin, Xu G. Yu, Bruce D. Walker, Duane R. Wesemann, H. Benjamin Larman, James A. Lederer, Stephen J. Elledge
Article
Immunology
J. A. Johnson, J. C. Pearson, D. W. Kubiak, B. Dionne, S. E. Little, D. R. Wesemann
OPEN FORUM INFECTIOUS DISEASES
(2020)
Article
Biochemistry & Molecular Biology
Yuezhou Chen, Adam Zuiani, Stephanie Fischinger, Jyotsna Mullur, Caroline Atyeo, Meghan Travers, Felipe J. N. Lelis, Krista M. Pullen, Hannah Martin, Pei Tong, Avneesh Gautam, Shaghayegh Habibi, Jillian Bensko, Deborah Gakpo, Jared Feldman, Blake M. Hauser, Timothy M. Caradonna, Yongfei Cai, John S. Burke, Junrui Lin, James A. Lederer, Evan Christopher Lam, Christy L. Lavine, Michael S. Seaman, Bing Chen, Aaron G. Schmidt, Alejandro Benjamin Balazs, Douglas A. Lauffenburger, Galit Alter, Duane R. Wesemann
Article
Medicine, Research & Experimental
Caroline Atyeo, Matthew D. Slein, Stephanie Fischinger, John Burke, Alexandra Schafer, Sarah R. Leist, Natalia A. Kuzmina, Chad Mire, Anna Honko, Rebecca Johnson, Nadia Storm, Matthew Bernett, Pei Tong, Teng Zuo, Junrui Lin, Adam Zuiani, Caitlyn Linde, Todd Suscovich, Duane R. Wesemann, Anthony Griffiths, John R. Desjarlais, Boris D. Juelg, Jaap Goudsmit, Alexander Bukreyev, Ralph Baric, Galit Alter
Summary: The study highlights the critical need for strategic Fc engineering to treat SARS-CoV-2 infection. Experiment results show that functionally enhanced Fc variants can exacerbate pathological effects in mouse and hamster models, leading to weight loss and increased viral replication.
Article
Multidisciplinary Sciences
Yongfei Cai, Jun Zhang, Tianshu Xiao, Christy L. Lavine, Shaun Rawson, Hanqin Peng, Haisun Zhu, Krishna Anand, Pei Tong, Avneesh Gautam, Shen Lu, Sarah M. Sterling, Richard M. Walsh, Sophia Rits-Volloch, Jianming Lu, Duane R. Wesemann, Wei Yang, Michael S. Seaman, Bing Chen
Summary: The study found that the B.1.1.7 variant has increased receptor binding affinity, while the B.1.351 variant has developed resistance to some neutralizing antibodies by reshaping antigenic surfaces on the spike protein.
Editorial Material
Biochemistry & Molecular Biology
Duane R. Wesemann
Summary: Three studies in this issue of Cell confirm that SARS-CoV-2 Omicron effectively evades key immune defense-neutralizing antibodies. However, one or two doses of vaccine fail to induce anti-Omicron neutralizing antibodies, whereas a homologous third-dose booster restores neutralization function to some extent, highlighting the adaptability of immune memory to extend antibody reach across SARS-CoV-2 variants.
Article
Immunology
Ryan W. Nelson, Yuezhou Chen, Olivia L. Venezia, Richard M. Majerus, Daniel S. Shin, Mary N. Carrington, Xu G. Yu, Duane R. Wesemann, James J. Moon, Andrew D. Luster
Summary: CD4(+) T cells play a crucial role in COVID-19 immunity. We found that individuals with milder disease course and sustained antibody responses had a higher proportion of cT(FH) cells and TH1 cells among SARS-CoV-2-specific cells. Effective early disease control predicts favorable long-term adaptive immunity.
SCIENCE IMMUNOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Peter M. Bruno, Richard T. Timms, Nouran S. Abdelfattah, Yumei Leng, Felipe J. N. Lelis, Duane R. Wesemann, Xu G. Yu, Stephen J. Elledge
Summary: Identification of CD8(+) T cell epitopes is crucial for immunotherapy development. The EpiScan method, using surface MHC class I levels as a readout for ligand discovery, can screen large-scale MHC class I peptides and predict binding affinities. The EpiScan Predictor performs comparably to other algorithms and overcomes the underrepresentation of cysteine-containing peptides. This targeted immunopeptidomics approach will accelerate individual-specific immunotherapy.
NATURE BIOTECHNOLOGY
(2023)
Editorial Material
Allergy
Chrysanthi Skevaki, Duane R. Wesemann
JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
(2023)