Article
Cell Biology
Kristina M. Geiger, Michael Manoharan, Rachel Coombs, Kathya Arana, Chan-Su Park, Angus Y. Lee, Nilabh Shastri, Ellen A. Robey, Laurent Coscoy
Summary: The endoplasmic reticulum aminopeptidase associated with antigen processing (ERAAP) plays a critical role in shaping the peptide-MHC I repertoire and maintaining immune surveillance. Murine cytomegalovirus (MCMV) modulates ERAAP during infection, leading to Qa-1b-restricted QFL T cell proliferation, which reduces viral load and highlights potential targets for anti-viral therapies.
Article
Medicine, Research & Experimental
Eric T. Son, Pouya Faridi, Moumita Paul-Heng, Mario L. Leong, Kieran English, Sri H. Ramarathinam, Asolina Braun, Nadine L. Dudek, Ian E. Alexander, Leszek Lisowski, Patrick Bertolino, David G. Bowen, Anthony W. Purcell, Nicole A. Mifsud, Alexandra F. Sharland
Summary: This study used a combination of methods to identify the peptide cargo of allogeneic MHC I molecules as a contributing factor to transplant tolerance induction, identifying 17 immunogenic peptides recognized by CD8(+) T cells. The use of as few as 5 different tetramers together was able to identify a high proportion of alloreactive T cells, suggesting the presence of immunodominant allogeneic MHC-peptide complexes.
JOURNAL OF CLINICAL INVESTIGATION
(2021)
Article
Biochemistry & Molecular Biology
Shira Weingarten-Gabbay, Susan Klaeger, Siranush Sarkizova, Leah R. Pearlman, Da-Yuan Chen, Kathleen M. E. Gallagher, Matthew R. Bauer, Hannah B. Taylor, W. Augustine Dunn, Christina Tarr, John Sidney, Suzanna Rachimi, Hasahn L. Conway, Katelin Katsis, Yuntong Wang, Del Leistritz-Edwards, Melissa R. Durkin, Christopher H. Tomkins-Tinch, Yaara Finkel, Aharon Nachshon, Matteo Gentili, Keith D. Rivera, Isabel P. Carulli, Vipheaviny A. Chea, Abishek Chandrashekar, Cansu Cimen Bozkus, Mary Carrington, Nina Bhardwaj, Dan H. Barouch, Alessandro Sette, Marcela Maus, Charles M. Rice, Karl R. Clauser, Derin B. Keskin, Daniel C. Pregibon, Nir Hacohen, Steven A. Carr, Jennifer G. Abelin, Mohsan Saeed, Pardis C. Sabeti
Summary: T cell-mediated immunity plays a crucial role in controlling SARS-CoV-2 infection, with some peptides derived from internal out-of-frame ORFs in spike and nucleocapsid eliciting stronger T cell responses than canonical peptides. Early expressed viral proteins contribute more to HLA-I presentation and immunogenicity, providing insights for vaccine development and immune monitoring.
Review
Immunology
Ksenia V. Zornikova, Saveliy A. Sheetikov, Alexander Yu Rusinov, Rustam N. Iskhakov, Apollinariya V. Bogolyubova
Summary: The T cell response is crucial for controlling and clearing SARS-CoV-2 infection. However, there are still important questions regarding the role of cellular immunity in COVID-19, such as the characteristics of disease-specific T cell repertoires in convalescent patients and vaccinated individuals, and how T cell responses to other pathogens, particularly common cold coronaviruses, affect susceptibility to SARS-CoV-2 infection and disease progression. This review focuses on the shaping of T cell receptor (TCR) repertoires by natural infection and vaccination, cross-reactive T cell responses, and the implications of TCR repertoire diversity and cross-reactivity for the development of vaccines that can provide broad protection against SARS-CoV-2 variants.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Thaiza Aline Pereira-Santos, Anderson Santos da Rocha, Agata Lopes-Ribeiro, Laura Cardoso Correa-Dias, Patricia Melo-Oliveira, Erik Vinicius de Sousa Reis, Flavio Guimaraes da Fonseca, Edel Figueiredo Barbosa-Stancioli, Moriya Tsuji, Jordana Grazziela Alves Coelho-dos-Reis
Summary: This study aimed to identify immunodominant regions of HTLV-1 Tax using peptide microarray analysis. Results showed dose-dependent reactivity of HLA-A*02:01 in all regions, with specific hotspots. In silico analysis revealed IFN-gamma-inducing peptides in the N-terminal portion and IL-4 inducers in the C-terminal portion. This research provides insight for designing immunomodulatory strategies for HTLV-1 chronic diseases.
Review
Immunology
Guangyao Tian, Mingqian Li, Guoyue Lv
Summary: This article reviews the recent advances in TCR sequencing techniques and computational tools, as well as the recent discovery in overall TCR profile and antigen-specific T cells tracking in transplantation. The challenges and potential of using TCR sequencing-based assays to profile alloreactive TCR repertoire as the fingerprint for immune monitoring and prediction of rejection and tolerance are further discussed.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biology
Takehiko Ichikawa, Dong Wang, Keisuke Miyazawa, Kazuki Miyata, Masanobu Oshima, Takeshi Fukuma
Summary: Chemical fixatives have been found to potentially affect the nanoscale structures of cell surfaces by inducing aggregation of membrane proteins. However, research in this area has been limited due to the lack of methods for observing cell surface structures at the nanoscale. In this study, a method using atomic force microscopy and a microporous silicon nitride membrane was developed to observe cell surfaces with high resolution. The results showed that commonly used fixatives increased the size of protrusions on the cell surface, indicating the aggregation of membrane proteins caused by the fixatives.
COMMUNICATIONS BIOLOGY
(2022)
Article
Medicine, Research & Experimental
Wei Zhang, Qian Zhang, Chao Zhu, Zhiyuan Shi, Chen Shao, Yujie Chen, Nan Wang, Yanxia Jiang, Qing Liang, Kejia Wang
Summary: This study revealed diminished T-cell infiltration and increased T-cell receptor immune repertoire diversity in clear cell renal cell cancer (ccRCC). Furthermore, Vimentin expression in ccRCC tissue was positively correlated with the presence of positive T-cell markers. The immune repertoire sequencing results showed increased diversity in the T-cell receptor repertoire in ccRCC.
JOURNAL OF TRANSLATIONAL MEDICINE
(2022)
Review
Biochemistry & Molecular Biology
Tyler J. Bechtel, Tamara Reyes-Robles, Olugbeminiyi O. Fadeyi, Rob C. Oslund
Summary: Multicellular organisms rely on physical cell-cell interactions to regulate physiological processes. Understanding the complexity of these interactions has greatly improved insight into cell-cell engagement biology and led to opportunities for therapeutic development. Emerging approaches that combine chemistry and biology technologies effectively interrogate cell-cell interfaces with molecular-level detail.
NATURE CHEMICAL BIOLOGY
(2021)
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
Dmitrii S. Shcherbinin, Vadim K. Karnaukhov, Ivan V. Zvyagin, Dmitriy M. Chudakov, Mikhail Shugay
Summary: This study aims to extend and analyze the available structures of TCR-peptide-MHC complexes using highly accurate template-based modeling, providing a methodology to predict TCR specificity.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Kerry A. Mullan, Justin B. Zhang, Claerwen M. Jones, Shawn J. R. Goh, Jerico Revote, Patricia T. Illing, Anthony W. Purcell, Nicole L. La Gruta, Chen Li, Nicole A. Mifsud
Summary: This article introduces a web tool called "TCR_Explore" that helps users analyze T cell receptor data from both Sanger sequencing and next generation sequencing platforms. The tool includes automated quality control steps for Sanger sequencing and allows for the generation of publication-ready figures for different sequencing platforms. Users can interact with the web application at https://tcr-explore.erc.monash.edu.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Chemistry, Multidisciplinary
Xavier Guillory, Inesa Hadrovic, Pim J. de Vink, Andrea Sowislok, Luc Brunsveld, Thomas Schrader, Christian Ottmann
Summary: The rational design of protein-protein interaction (PPI) inhibitors presents a challenge, but a novel approach combining a general supramolecular protein binder with a specific peptidic ligand has resulted in a strong PPI inhibitor with significantly increased protein affinity. X-ray crystal structure elucidation and Molecular Dynamics (MD) simulations have provided unique molecular insights into the binding mode of this inhibitor, opening up new avenues for studying PPIs with novel chemical tools.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Review
Immunology
Annaliese Clauze, Yoshimi Enose-Akahata, Steven Jacobson
Summary: This article reviews the research on T cell receptor repertoires and HTLV-1-specific clonotypes in HTLV-1-associated diseases ATL and HAM/TSP and discusses the implications of TCR clonal expansions on the progression and treatment of HTLV-1-associated diseases.
FRONTIERS IN IMMUNOLOGY
(2022)
Editorial Material
Oncology
Winnie Yao, Ansuman T. Satpathy
Summary: Transient depletion of CD4(+) T cells in patients with gastrointestinal cancer induces remodeling of the T-cell repertoire, including clonal replacement and expansion of CD8(+) T-cell clones shared between the blood and tumor, deepening our understanding of tumor-specific CD8(+) T-cell responses.
CANCER IMMUNOLOGY RESEARCH
(2021)
Article
Biology
Peter C. de Greef, Theres Oakes, Bram Gerritsen, Mazlina Ismail, James M. Heather, Rutger Hermsen, Benjamin Chain, Rob J. de Boer
Article
Biology
Mariona Baliu-Pique, Vera van Hoeven, Julia Drylewicz, Lotte E. van der Wagen, Anke Janssen, Sigrid A. Otto, Menno C. van Zelm, Rob J. de Boer, Jurgen Kuball, Jose A. M. Borghans, Kiki Tesselaar
Summary: The study found that in patients after autologous hematopoietic stem cell transplantation (autoHSCT), the production rates of most T- and B-cell subsets increased significantly, but accompanied by an increase in cell loss rates, which persisted even after cell numbers normalized.
Article
Multidisciplinary Sciences
Peter C. de Greef, Rob J. de Boer
Summary: T cells with a diverse T cell receptor (TCR) protect the body from infection, with a substantial proportion of TCR beta rearrangements lacking a D segment. These sequences are more likely to be abundant within individuals and persist during fetal development and in the elderly.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Bettina Weigelin, Annemieke Th den Boer, Esther Wagena, Kelly Broen, Harry Dolstra, Rob J. de Boer, Carl G. Figdor, Johannes Textor, Peter Friedl
Summary: The study demonstrates that sublethal interactions from multiple CTL can accumulate over time and achieve tumor cell killing by additive cytotoxicity. Statistical modeling reveals that delivering three serial hits within decay intervals below 50 minutes can distinguish between tumor cell death or survival after recovery.
NATURE COMMUNICATIONS
(2021)
Article
Immunology
Juliane Schroter, Anet J. N. Anelone, Rob J. de Boer
Summary: In early-treated children with successful viral suppression, the CD4 depletion is typically mild and CD4(+) T cells tend to fully recover in numbers.
JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES
(2022)
Article
Immunology
Mariona Baliu-Pique, Julia Drylewicz, Xiaoyan Zheng, Lisa Borkner, Arpit C. Swain, Sigrid A. Otto, Rob J. de Boer, Kiki Tesselaar, Luka Cicin-Sain, Jose A. M. Borghans
Summary: Memory T cells play a crucial role in providing immune protection against reinfection and their long-term survival is still a subject of debate. This study suggests that memory phenotype CD8(+) T cells maintain themselves through cell division rather than individual cell longevity. CMV infection induces inflationary CD8(+) T cell responses that may result from the accumulation of long-lived CMV-specific memory CD8(+) T cells. The lifespans and production rates of CMV-specific CD8(+) T cells are similar to those of bulk memory-phenotype CD8(+) T cells.
JOURNAL OF IMMUNOLOGY
(2022)
Article
Immunology
Jason Cosgrove, Lucie S. P. Hustin, Rob J. de Boer, Leila Perie
Summary: Hematopoiesis is a dynamic process where stem and progenitor cells give rise to a vast number of blood and immune cells. Quantitative descriptions can help consolidate existing data, identify knowledge gaps, and generate new hypotheses.
TRENDS IN IMMUNOLOGY
(2021)
Letter
Biochemical Research Methods
Mario Castro, Rob J. de Boer
Summary: Despite the limitations pointed out by Villaverde and Massonis, the SIM method still holds value due to its applicability to various models, simplicity, and potential role in introducing identifiability issues to investigators with little mathematical training.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Microbiology
Sara P. H. A. van den Berg, Lyanne J. Derksen, Julia Drylewicz, Nening Nanlohy, Lisa Beckers, Josien Lanfermeijer, Stephanie Gessel, Martijn Vos, Sigrid Otto, Rob de Boer, Kiki Tesselaar, Jose A. M. Borghans, Debbie van Baarle
Summary: Cytomegalovirus (CMV) infection has a significant impact on the T-cell pool and is associated with immune system aging. However, the phenotypical differences between CMV-positive and CMV-negative individuals cannot be solely explained by the presence of large CMV-specific CD8(+) T-cell populations. CMV infection seems to have minimal effect on the dynamics of the T-cell pool, and the abundance of CMV-specific CD8(+) T-cells is not attributed to their longer lifespans.
Article
Immunology
Kaspar Bresser, Lianne Kok, Arpit C. Swain, Lisa A. King, Laura Jacobs, Tom S. Weber, Leila Perie, Ken R. Duffy, Rob J. de Boer, Ferenc A. Scheeren, Ton N. Schumacher
Summary: This study investigates the relationship between replicative history and the formation of distinct CD8(+) memory T cell subgroups. The researchers developed a genetic-tracing approach and found that central memory T (T-CM) cell pool has a higher number of prior divisions compared to the effector memory T cell pool. They also discovered that lowly divided T-CM cells display enriched expression of stem-cell-associated genes, exist in a relatively quiescent state, and are superior in eliciting a proliferative recall response upon activation.
Correction
Immunology
Kaspar Bresser, Lianne Kok, Arpit C. Swain, Lisa A. King, Laura Jacobs, Tom S. Weber, Leila Perie, Ken R. Duffy, Rob J. de Boer, Ferenc A. Scheeren, Ton N. Schumacher
Article
Immunology
Arpit C. Swain, Jose A. M. Borghans, Rob J. de Boer
Summary: The paper investigates the impact of resource competition on T-cell receptor diversity in the memory T-cell pool. It shows that cellular aging, along with a small continuous source, can increase TCR diversity and regulate chronic memory responses.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biology
Gerdien Mijnheer, Nila Hendrika Servaas, Jing Yao Leong, Arjan Boltjes, Eric Spierings, Phyllis Chen, Liyun Lai, Alessandra Petrelli, Sebastiaan Vastert, Rob J. de Boer, Salvatore Albani, Aridaman Pandit, Femke van Wijk, Di Chen
Summary: Autoimmune inflammation is characterized by tissue infiltration and expansion of antigen-specific T cells. In this study, the authors used CyTOF analysis and TCR sequencing to investigate the immune cell composition and expansion of specific T cell clones in juvenile idiopathic arthritis (JIA). They found that the infiltrates in different affected joints of the same patient were similar, and dominant T cell clones, including Tregs, persisted over time. These findings suggest the presence of autoantigen-driven expansion of T cell clones in localized autoimmune disease.
Article
Biology
Edward Schrom, Ann Kinzig, Stephanie Forrest, Andrea L. Graham, Simon A. Levin, Carl T. Bergstrom, Carlos Castillo -Chavez, James P. Collins, Rob J. de Boer, Adam Doupe, Roya Ensafi, Stuart Feldman, Bryan T. Grenfell, Alex Halderman, Silvie Huijben, Carlo Maley, Melanie Moses, Alan S. Perelson, Charles Perrings, Joshua Plotkin, Jennifer Rexford, Mohit Tiwari
Summary: Defending against various types of attacks and avoiding self-attacks are the common challenges faced by mammalian immune systems and computer systems. Despite extensive research, there has been limited exchange of information between the fields of biological immunity and cybersecurity. This paper proposes a conceptual framework to compare and evaluate different defensive strategies in both fields, aiming to identify general principles of optimal defense applicable to various defensive realms.
MATHEMATICAL BIOSCIENCES
(2023)
Article
Biophysics
Inge M. N. Wortel, Ioana Niculescu, P. Martijn Kolijn, Nir S. Gov, Rob J. de Boer, Johannes Textor
Summary: Cell migration is diverse, but a universal coupling between speed and persistence exists. An existing cellular Potts model shows how cell shape dynamics and local protrusion dynamics play a role in reproducing this speed-persistence coupling.
BIOPHYSICAL JOURNAL
(2021)