Article
Immunology
Jessica H. Lee, Rui Yin, Gilad Ofek, Brian G. Pierce
Summary: This study provides a detailed analysis of antibody-protein antigen complexes targeting linear epitopes. The results reveal that antibody-bound peptides can adopt various conformations and the same peptide sequence can have different conformations when bound by different antibodies. Compared to antibody-protein antigen complexes, antibody-peptide interfaces have lower buried surface areas and fewer hydrogen bonds, but higher calculated binding energy per buried interface area.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Daniel Neumeier, Alexander Yermanos, Andreas Agrafiotis, Lucia Csepregi, Tasnia Chowdhury, Roy A. Ehling, Raphael Kuhn, Tudor-Stefan Cotet, Rapha El Brisset-Di Roberto, Mariangela Di Tacchio, Renan Antonialli, Dale Starkie, Daniel J. Lightwood, Annette Oxenius, Sai T. Reddy
Summary: The capacity of humoral B cell-mediated immunity to effectively respond to and protect against pathogenic infections relies on the presence of diverse polyclonal antibodies in the serum. Recent studies have investigated the balance between deterministic mechanisms and stochasticity of antibody repertoires on a genotypic level. It has been found that clonal expansion drives antigen specificity of the most expanded clones, while the antigen specificity among the rest of the clonal repertoire is stochastic, with implications for effective vaccine assessment.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Keunok Jung, Min-Jeong Son, Se-Young Lee, Jeong-Ah Kim, Deok-Han Ko, Sojung Yoo, Chul-Ho Kim, Yong-Sung Kim
Summary: A new antibody technology has been developed to deliver viral epitopes into tumor cells, aiding immune cells to more effectively attack tumor cells.
Article
Biochemical Research Methods
Raphael Trevizani, Zhen Yan, Jason A. Greenbaum, Alessandro Sette, Morten Nielsen, Bjoern Peters
Summary: An approach to assess the reliability of different metrics for evaluating the performance of MHC class I binding predictors was developed. The study found that using percentile-ranked results improved the stability of the ranks and identified the top-performing tools in the benchmark.
BRIEFINGS IN BIOINFORMATICS
(2022)
Review
Peripheral Vascular Disease
Hironori Nakagami, Hiroki Hayashi, Munehisa Shimamura, Hiromi Rakugi, Ryuichi Morishita
Summary: The rapid advancements in vaccine technology and the impact of COVID-19 have opened up new possibilities for developing vaccines for chronic diseases, such as post-hypertensive cerebrovascular diseases.
HYPERTENSION RESEARCH
(2021)
Article
Immunology
Riccardo Biavasco, Marco De Giovanni
Summary: Humoral immunity is important for defense against pathogens. Broadly neutralizing antibodies provide sterilizing immunity and are the goal of vaccination approaches. However, in the context of influenza and HIV, the induction of broadly protective antibodies has been challenging. This study proposes the theory of immunodominance relativity, which suggests that the relative positioning of B and CD4 epitopes within antigens influences immunodominance. The proposed theory improves the understanding of immunodominance, explains the escape of HIV and influenza from humoral responses, and opens the possibility for the design of universal vaccines.
Article
Virology
Liyan Wang, Fan Yang, Yixin Xiao, Bin Chen, Fumin Liu, Linfang Cheng, Hangping Yao, Nanping Wu, Haibo Wu
Summary: This study obtained three monoclonal antibodies against influenza virus from mice immunized with the HA protein of A/Michigan/45/2015(H1N1), demonstrating strong preventive and therapeutic effects. Two amino acid mutations were discovered, and one of the antibodies still showed protective efficacy after 24 hours of infection.
JOURNAL OF MEDICAL VIROLOGY
(2022)
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
Multidisciplinary Sciences
Alireza Poustforoosh, Sanaz Faramarz, Manica Negahdaripour, Hassan Hashemipour
Summary: B-cell Non-Hodgkin lymphomas are malignancies of lymphocytes, and CD20 is highly expressed on the cell surface of B-cells in NHL. Nanobodies (NBs), with low molecular weights, high specificity, and superior characteristics, can be used as alternatives to monoclonal antibodies (mAbs). In this study, an optimized NB was designed as a CD20 inhibitor with improved binding affinity to CD20. The optimized NB, designated as NB2, showed remarkable binding affinity to CD20 and could be considered as a potential CD20 inhibitor.
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Shunhui Wei, Julian Behn, Charlene Priscilla Poore, See Wee Low, Bernd Nilius, Hao Fan, Ping Liao
Summary: This study designed a mouse monoclonal antibody called M4M to block human TRPM4 channel. Using peptide microarray, a binding epitope EPGF within the A2 peptide was identified. Structural analysis showed that EPGF is located externally to the channel pore and A1 peptide is close to the EPGF binding epitope. Electrophysiological study revealed that M4M can block human TRPM4, but not rodent TRPM4.
SCIENTIFIC REPORTS
(2022)
Article
Immunology
Roc Farriol-Duran, Ruben Lopez-Aladid, Eduard Porta-Pardo, Antoni Torres, Laia Fernandez-Barat
Summary: Brewpitopes is a powerful pipeline that optimizes experimental validation of therapeutic antibodies and candidate vaccines in a high-throughput capacity during public health emergencies.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Microbiology
Alex W. Wessel, Michael P. Doyle, Taylor B. Engdahl, Jessica Rodriguez, James E. Crowe, Michael S. Diamond
Summary: This study isolated human monoclonal antibodies from individuals previously infected with WNV, mapped their epitopes, and evaluated their efficacy in vivo against lethal WNV challenge. The most protective epitopes clustered at three antigenic sites on extracellular NS1 forms. This information may aid in the development of NS1-based countermeasures against flaviviruses.
Article
Biochemistry & Molecular Biology
Rui Chen, Yimin Wen, Enbo Yu, Junpeng Yang, Yixiao Liang, Daili Song, Yiping Wen, Rui Wu, Qin Zhao, Senyan Du, Qigui Yan, Xinfeng Han, Sanjie Cao, Xiaobo Huang
Summary: We identified two monoclonal antibodies that effectively neutralized PDCoV, with one targeting the S280-288 epitope and the other targeting the S506-513 epitope. The S280-288 epitope induced specific neutralizing antibodies and provided partial protection against disease in piglets. This study provides valuable insights for understanding the pathogenic mechanism of PDCoV, vaccine design, and antiviral drug development.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Review
Biochemical Research Methods
Gabriel Cia, Fabrizio Pucci, Marianne Rooman
Summary: Accurate prediction of conformational B-cell epitopes is important for disease diagnostics, drug design, and vaccine development. However, current computational methods show low performance and commonly used consensus strategies provide only marginal improvement. These limitations highlight the need for addressing biases and issues in current methods and exploring new strategies to improve the prediction of conformational B-cell epitopes.
BRIEFINGS IN BIOINFORMATICS
(2023)
Review
Biochemical Research Methods
Gabriel Cia, Fabrizio Pucci, Marianne Rooman
Summary: Accurate prediction of conformational B-cell epitopes is crucial for disease diagnostics, drug design, and vaccine development. However, current computational methods show very low performance, and commonly used consensus strategies are only marginally better than random. Our study highlights the need for caution when using these tools and suggests the use of state-of-the-art evaluation methodologies to improve performance.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Sandeep Kumar Dhanda, Randi Vita, Brendan Ha, Alba Grifoni, Bjoern Peters, Alessandro Sette
Article
Mathematical & Computational Biology
Randi Vita, James A. Overton, Christopher J. Mungall, Alessandro Sette, Bjoern Peters
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2018)
Article
Mathematical & Computational Biology
Randi Vita, James A. Overton, Bjoern Peters
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2018)
Article
Biochemistry & Molecular Biology
Randi Vita, Swapnil Mahajan, James A. Overton, Sandeep Kumar Dhanda, Sheridan Martini, Jason R. Cantrell, Daniel K. Wheeler, Alessandro Sette, Bjoern Peters
NUCLEIC ACIDS RESEARCH
(2019)
Article
Immunology
Swapnil Mahajan, Randi Vita, Deborah Shackelford, Jerome Lane, Veronique Schulten, Laura Zarebski, Martin Closter Jespersen, Paolo Marcatili, Morten Nielsen, Alessandro Sette, Bjoern Peters
FRONTIERS IN IMMUNOLOGY
(2018)
Article
Biochemical Research Methods
James A. Overton, Randi Vita, Patrick Dunn, Julie G. Burel, Syed Ahmad Chan Bukhari, Kei-Hoi Cheung, Steven H. Kleinstein, Alexander D. Diehl, Bjoern Peters
BMC BIOINFORMATICS
(2019)
Article
Immunology
Nima Salimi, Lindy Edwards, Gabriele Foos, Jason A. Greenbaum, Sheridan Martini, Brian Reardon, Deborah Shackelford, Randi Vita, Leora Zalman, Bjoern Peters, Alessandro Sette
Article
Immunology
William D. Chronister, Austin Crinklaw, Swapnil Mahajan, Randi Vita, Zeynep Kosaloglu-Yalcin, Zhen Yan, Jason A. Greenbaum, Leon E. Jessen, Morten Nielsen, Scott Christley, Lindsay G. Cowell, Alessandro Sette, Bjoern Peters
Summary: The study introduces a new tool called TCR Match, which aims to identify epitope specificity of T cell receptors by comparing sequence similarities, providing new insights for the development of strategies for monitoring and treating infectious, allergic, autoimmune diseases, and cancer.
FRONTIERS IN IMMUNOLOGY
(2021)
Review
Microbiology
Alba Grifoni, John Sidney, Randi Vita, Bjoern Peters, Shane Crotty, Daniela Weiskopf, Alessandro Sette
Summary: This review summarizes recent studies on SARS-CoV-2 T cell epitopes, highlighting the significant correlation between epitope number and antigen size. It also presents an analysis of 1,400 different reported SARS-CoV-2 epitopes and identifies discrete immunodominant regions of the virus and more prevalently recognized epitopes.
CELL HOST & MICROBE
(2021)
Article
Immunology
Randi Vita, Apurva Mody, James A. Overton, Soren Buus, Stephen T. Haley, Alessandro Sette, Vamsee Mallajosyula, Mark M. Davis, Dale L. Long, Richard A. Willis, Bjoern Peters, John D. Altman
Summary: This article presents a new data standard, Minimal Information about MHC Multimers, aimed at improving the reproducibility and annotatability of MHC multimer reagent data. The authors provide an online website and validation tool to assist with the adoption of the standard, with the hope of increasing awareness and driving acceptance to ultimately enhance the quality and documentation of multimer data in scientific literature.
JOURNAL OF IMMUNOLOGY
(2022)
Article
Mathematical & Computational Biology
Rebecca Jackson, Nicolas Matentzoglu, James A. Overton, Randi Vita, James P. Balhoff, Pier Luigi Buttigieg, Seth Carbon, Melanie Courtot, Alexander D. Diehl, Damion M. Dooley, William D. Duncan, Nomi L. Harris, Melissa A. Haendel, Suzanna E. Lewis, Darren A. Natale, David Osumi-Sutherland, Alan Ruttenberg, Lynn M. Schriml, Barry Smith, Christian J. Stoeckert, Nicole A. Vasilevsky, Ramona L. Walls, Jie Zheng, Christopher J. Mungall, Bjoern Peters
Summary: Biological ontologies are used to organize and interpret data from experiments, but integrating multiple ontologies can lead to compatibility issues. The OBO Foundry aims to promote the development and sharing of ontologies through a set of principles. Researchers have improved ontology quality and interoperability by encoding principles as operational rules and implementing automated validation checks.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2021)
Article
Biochemical Research Methods
Paul F. Zierep, Randi Vita, Nina Blazeska, Aurelien F. A. Moumbock, Jason A. Greenbaum, Bjoern Peters, Stefan Guenther
Summary: In this study, the authors attempted to predict the epitope activity of non-peptidic compounds and developed a web server for immunogenic investigation. They identified specific molecular substructures that are frequently found in non-peptidic epitopes and may be responsible for immune responses. This knowledge can help explain allergic reactions to chemicals and reduce health risks in industrial production.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Mathematical & Computational Biology
Lindy Edwards, Rebecca Jackson, James A. Overton, Randi Vita, Nina Blazeska, Bjoern Peters, Alessandro Sette
Summary: The Immune Epitope Database (IEDB) provides experimental data on immune epitopes to the scientific community, primarily for immunologists to search for peptidic epitopes via single-letter codes and proteins from specific organisms. However, accessing non-peptidic epitope data remains a challenge due to inconsistencies in naming and searching for carbohydrates, lipids, chemicals, and drugs.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2021)
Article
Mathematical & Computational Biology
Randi Vita, Jie Zheng, Rebecca Jackson, Damion Dooley, James A. Overton, Mark A. Miller, Daniel C. Berrios, Richard H. Scheuermann, Yongqun He, Hande Kucuk McGinty, Mathias Brochhausen, Aisyah Yu Lin, Sagar B. Jain, Marcus C. Chibucos, John Judkins, Michelle G. Giglio, Irene Y. Feng, Gully Burns, Matthew H. Brush, Bjoern Peters, Christian J. Stoeckert
Summary: The Ontology for Biomedical Investigations (OBI) underwent a focused review of assay term annotations to improve and standardize terms, identifying and correcting inconsistencies in W3C Web Ontology Language (OWL) expressions and developing standardized design patterns and maintenance templates. This insightful process provides specific benefits and obstacles for OBI, as well as universal lessons for similar projects.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2021)
Article
Mathematical & Computational Biology
Randi Vita, James A. Overton, Patrick Dunn, Kei-Hoi Cheung, Steven H. Kleinstein, Alessandro Sette, Bjoern Peters
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2020)
