Article
Biochemistry & Molecular Biology
Fabian C. Spoendlin, Brennan Abanades, Matthew I. J. Raybould, Wing Ki Wong, Guy Georges, Charlotte M. Deane
Summary: The function of an antibody is related to its binding epitope. Clonal clustering methods neglect the diversity of antibody sequences, while structural clustering can predict epitopes more accurately. SPACE2 combines machine learning technology and a new clustering protocol to accurately cluster antibodies on binding data with epitope-level resolution.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Article
Medicine, Research & Experimental
Pierre Roques, Andrea Fritzer, Nathalie Dereuddre-Bosquet, Nina Wressnigg, Romana Hochreiter, Laetitia Bossevot, Quentin Pascal, Fabienne Guehenneux, Annegret Bitzer, Irena Corbic Ramljak, Roger Le Grand, Urban Lundberg, Andreas Meinke
Summary: This study evaluates the effectiveness of the CHIKV vaccine VLA1553 and establishes a surrogate of protection. The results show that transfer of vaccinated volunteers' sera to nonhuman primates provides complete protection from CHIKV infection. This is an important step towards reducing the medical burden caused by chikungunya.
Article
Microbiology
Michael Mor, Michal Werbner, Joel Alter, Modi Safra, Elad Chomsky, Jamie C. Lee, Smadar Hada-Neeman, Ksenia Polonsky, Cameron J. Nowell, Alex E. Clark, Anna Roitburd-Berman, Noam Ben-Shalom, Michal Navon, Dor Rafael, Hila Sharim, Evgeny Kiner, Eric R. Griffis, Jonathan M. Gershoni, Oren Kobiler, Sandra Lawrynowicz Leibel, Oren Zimhony, Aaron F. Carlin, Gur Yaari, Moshe Dessau, Meital Gal-Tanamy, David Hagin, Ben A. Croker, Natalia T. Freund
Summary: Severe COVID-19 is associated with unique BCR signatures and multi-clonal neutralizing responses that are relatively frequent in the population. Combination antibody therapy can be effective in preventing and treating COVID-19.
Article
Multidisciplinary Sciences
Natalia Sevillano, Evan M. Green, Jorg Votteler, Dong Young Kim, Xuefeng Ren, Bei Yang, Xi Liu, Andre Luiz Lourenco, James H. Hurley, Shauna Farr-Jones, John D. Gross, Yifan Cheng, Charles S. Craik
Summary: This study identified human, recombinant antibodies from a phage display library that bind to three HIV-host complexes, which were further converted into scFvs for structural and functional studies, providing essential antibody reagents for research and clinical applications. The rapid screening pipeline developed in this study can be applied to other challenging antigens, facilitating the generation of specific, reproducible, and renewable antibody reagents.
Article
Biotechnology & Applied Microbiology
Evgenij Fiskin, Caleb A. Lareau, Leif S. Ludwig, Gokcen Eraslan, Feimei Liu, Aaron M. Ring, Ramnik J. Xavier, Aviv Regev
Summary: The study introduces a novel method called PHAGE-ATAC for simultaneous single-cell measurements of protein levels and chromatin accessibility profiles, using mitochondrial DNA-based clonal tracing. PHAGE-ATAC is utilized for multimodal analysis in primary human immune cells, sample multiplexing, intracellular protein analysis, and detection of SARS-CoV-2 spike protein. Additionally, a synthetic high-complexity phage library is constructed for selection of antigen-specific nanobodies, enabling protein detection, cell characterization, and screening with single-cell genomics.
NATURE BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Elsa Brunet-Ratnasingham, Sai Priya Anand, Pierre Gantner, Alina Dyachenko, Gael Moquin-Beaudry, Nathalie Brassard, Guillaume Beaudoin-Bussieres, Amelie Pagliuzza, Romain Gasser, Mehdi Benlarbi, Floriane Point, Jeremie Prevost, Annemarie Laumaea, Julia Niessl, Manon Nayrac, Geremy Sannier, Catherine Orban, Marc Messier-Peet, Guillaume Butler-Laporte, David R. Morrison, Sirui Zhou, Tomoko Nakanishi, Marianne Boutin, Jade Descoteaux-Dinelle, Gabrielle Gendron-Lepage, Guillaume Goyette, Catherine Bourassa, Halima Medjahed, Laetitia Laurent, Rose-Marie Rebillard, Jonathan Richard, Mathieu Dube, Remi Fromentin, Nathalie Arbour, Alexandre Prat, Catherine Larochelle, Madeleine Durand, J. Brent Richards, Michael Chasse, Martine Tetreault, Nicolas Chomont, Andres Finzi, Daniel E. Kaufmann
Summary: This study conducted immunovirological assessments on plasma from 279 individuals to identify early predictors of mortality in patients infected with SARS-CoV-2. High vRNA, low specific immunoglobulin G and antibody-dependent cellular cytotoxicity, and elevated cytokines and tissue injury markers were strongly associated with mortality. A three-variable model combining vRNA, age, and sex was able to robustly identify patients with fatal outcomes.
Article
Multidisciplinary Sciences
Edurne Rujas, Daniel P. Leaman, Sara Insausti, Pablo Carravilla, Miguel Garcia-Porras, Eneko Largo, Izaskun Morillo, Ruben Sanchez-Eugenia, Lei Zhang, Hong Cui, Ibon Iloro, Felix Elortza, Jean-Philippe Julien, Christian Eggeling, Michael B. Zwick, Jose M. M. Caaveiro, Jose L. Nieva
Summary: The study successfully improved the bnAb 4E10 targeting HIV-1 through chemical modification, preserving neutralization potency and breadth while reducing autoreactivity.
Article
Immunology
Gemma L. Gordon, Henriette L. Capel, Bora Guloglu, Eve Richardson, Ryan L. Stafford, Charlotte M. Deane
Summary: Antibodies and single-domain antibodies (sdAbs) differ in the structures of their binding sites, but sdAbs can target epitopes of equal size to antibodies despite their smaller paratopes. The paratopes of sdAbs contribute more interactions per residue, and conserved framework residues play a crucial role in achieving comparable affinity. The accessibility of sdAb epitopes is only slightly less than that of antibodies, possibly due to differences in the orientation and compaction of CDR-H3 loops.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Aiping Wang, Jinran Du, Hua Feng, Jingming Zhou, Yumei Chen, Yankai Liu, Min Jiang, Rui Jia, Yuanyuan Tian, Gaiping Zhang
Summary: This study successfully cloned the BTV1 VP2 gene and expressed the protein in insect cells, leading to the production of effective vaccines. Three anti-BTV1 VP2 monoclonal antibodies were generated, and a novel B-cell epitope on the VP2 protein was identified, laying a foundation for the development of diagnostic and prophylactic methods for bluetongue disease.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Multidisciplinary Sciences
Yiwei Chen, Kai Xu, Luca Piccoli, Mathilde Foglierini, Joshua Tan, Wenjie Jin, Jason Gorman, Yaroslav Tsybovsky, Baoshan Zhang, Boubacar Traore, Chiara Silacci-Fregni, Claudia Daubenberger, Peter D. Crompton, Roger Geiger, Federica Sallusto, Peter D. Kwong, Antonio Lanzavecchia
Summary: This study demonstrates that Plasmodium falciparum RIFINs can bind to LILRB1 through D3, and inserting receptor domains into the VH-CH1 elbow can generate novel antibodies, as shown by a naturally selected example.
Article
Multidisciplinary Sciences
Meng Yuan, Deli Huang, Chang-Chun D. Lee, Nicholas C. Wu, Abigail M. Jackson, Xueyong Zhu, Hejun Liu, Linghang Peng, Marit J. Van Gils, Rogier W. Sanders, Dennis R. Burton, S. Momsen Reincke, Harald Pruss, Jakob Kreye, David Nemazee, Andrew B. Ward, Ian A. Wilson
Summary: Mutations in the RBS residues of new variant strains of the coronavirus can affect the binding and neutralizing effects of antibodies, but have little impact on antibodies targeting more conserved neutralizing sites.
Article
Biochemical Research Methods
Hyunsu An, Minho Eun, Jawoon Yi, Jihwan Park
Summary: This study developed a scalable immunoinformatics pipeline to identify cross-reactive epitopes between SARS-CoV-2 and human proteins, providing a foundation for the investigation of molecular mimicry in the pathogenesis of autoimmune and chronic inflammatory diseases following COVID-19.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Chemistry, Multidisciplinary
Jixue Sun, Meijiang Liu, Na Yang
Summary: Research has shown that SARS-CoV-2 binds to human ACE2 receptors in a similar way to Pangolin-CoV, and more strongly than Bat-CoV-RaTG13 or SARS-CoV. This suggests that Pangolins may serve as intermediate hosts for SARS-CoV-2. The study provides guidance for the design of future antiviral drugs and vaccines.
Article
Biology
Vibha Kumra Ahnlide, Johannes Kumra Ahnlide, Sebastian Wrighton, Jason P. Beech, Pontus Nordenfelt
Summary: Antibodies play a crucial role in the immune system by targeting harmful pathogens, but identifying specific binding sites can be challenging. The SiteLoc method developed by Kumra Ahnlide et al. uses fluorescent probes to measure nanoscale distances between antibodies and cell surfaces, overcoming previous limitations and offering potential applications in therapeutic development and research.
Article
Cell Biology
Huan Ma, Xinghai Zhang, Weihong Zeng, Junhui Zhou, Xiangyang Chi, Shaohong Chen, Peiyi Zheng, Meihua Wang, Yan Wu, Dan Zhao, Fanwu Gong, Haofeng Lin, Hancong Sun, Changming Yu, Zhengli Shi, Xiaowen Hu, Huajun Zhang, Tengchuan Jin, Sandra Chiu
Summary: This study identifies a nanobody that strongly cross-reacts with the receptor binding domain of both SARS-CoV-1 and wild-type SARS-CoV-2, and demonstrates its potential for neutralizing these viruses. The researchers also engineered a bispecific nanobody dimer that effectively neutralizes major variants, including Omicron. The findings expand the options for combating SARS-CoV-1 and provide potential therapeutic and prophylactic candidates against major SARS-CoV-2 variants.
