Article
Genetics & Heredity
Tina Fuchs, Kerstin Puellmann, Chunlin Wang, Jian Han, Alexander W. Beham, Michael Neumaier, Wolfgang E. Kaminski
Summary: Recent research shows the presence of T cell receptor-based combinatorial immune receptors in neutrophils and monocytes/macrophages. These cells exhibit highly complex TCR beta transcriptomes with unique repertoires, and individual-specific changes are observed during differentiation of monocytes into macrophages. The study reveals the complexity and plasticity of the immune systems based on phagocytes, shedding light on their role in immunity alongside T cells.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2021)
Article
Immunology
Shaima Al Khabouri, Robert A. Benson, Catriona T. Prendergast, Joshua I. Gray, Thomas D. Otto, James M. Brewer, Paul Garside
Summary: The study found that in the development of inflammatory arthritis, the clonality and diversity of CD4 T cell repertoire expands as the disease progresses, first reflected in lymph nodes and then in joints. Therefore, antigen-specific tolerogenic therapies targeted at the early stages of disease with less diverse CD4 T cell clonality may be more effective.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Brianne Edwards, Eli D. Hornstein, Nathan J. Wilson, Heike Sederoff
Summary: This study developed a simple method using T-DNA-specific primers and high-throughput sequencing to identify transgene insertion sites in the T-1 generation of any crop transformed via Agrobacterium. The example using allohexaploid oil-seed plant Camelina sativa demonstrated the feasibility of determining insertion site location of two transgenes. This new methodology allows for early selection of desirable transgene location and copy number to generate homozygous lines within two generations.
Article
Ecology
Lorna E. Drake, Jordan P. Cuff, Rebecca E. Young, Angela Marchbank, Elizabeth A. Chadwick, William O. C. Symondson
Summary: Metabarcoding offers a powerful tool for studying biodiversity and trophic interactions, but the use of MSCTs lacks consensus, and further research is needed to determine best practices.
METHODS IN ECOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Anielka Zehnaker, Amandine Vallet, Juliette Gourdon, Caterina Sarti, Vinesh Jugnarain, Maya Haj Hassan, Laetitia Mathias, Camille Gauthier, Pauline Raynaud, Thomas Boulo, Linda Beauclair, Yves Bigot, Livio Casarini, Pascale Crepieux, Anne Poupon, Benoit Piegu, Frederic Jean-Alphonse, Gilles Bruneau, Eric Reiter
Summary: Developing modulatory antibodies against G protein-coupled receptors is challenging. In this study, the researchers successfully identified a positive modulator VHH (PRC1) targeting the follicle-stimulating hormone receptor (FSHR), which has significant implications for reproduction regulation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Physical
Jingyu Qi, Haibin Zhu, Yijian Li, Xiangyu Guan, Ying He, Guanhua Ren, Qiang Guo, Longqi Liu, Ying Gu, Xuan Dong, Ya Liu
Summary: Cell-cell interaction is an important way for transmitting information and activating the effects of functional cells. Researchers propose a droplet-based microfluidic platform for cell-cell interaction sequencing and screening, which allows for efficient analysis and interpretation of single-cell transcriptomes in cell interactions. This work fills a gap in the current experimental platform for cell-cell interaction research and has significant practical implications in biomedicine.
Article
Gastroenterology & Hepatology
Yipeng Ma, Jiayu Ou, Tong Lin, Lei Chen, Junhui Chen, Mingjun Wang
Summary: This study presents an HBV-specific TCR identification method that does not require the TCR singularization process, using ranking-based and alpha-beta chain mixture-based strategies. These strategies are effective for identifying HBV-specific TCRs and may be used for treating HBV-related HCC.
HEPATOLOGY COMMUNICATIONS
(2021)
Article
Medicine, Research & Experimental
Hongmei Liu, Wenjing Pan, Congli Tang, Yujie Tang, Haijing Wu, Akihiko Yoshimura, Yan Deng, Nongyue He, Song Li
Summary: The adaptive immune response recognizes and neutralizes threats through T or B lymphatic receptors. High-throughput sequencing and bioinformatics offer research opportunities. Analyzing immune repertoire data reveals biological information and aids in improving experimental and computational methods.
Article
Biochemical Research Methods
Connor S. Dobson, Anna N. Reich, Stephanie Gaglione, Blake E. Smith, Ellen J. Kim, Jiayi Dong, Larance Ronsard, Vintus Okonkwo, Daniel Lingwood, Michael Dougan, Stephanie K. Dougan, Michael E. Birnbaum
Summary: Deciphering immune recognition is crucial for understanding diseases and developing vaccines and immunotherapies. However, current technologies lack the capability to capture the complexity of immune receptor repertoires and potential antigens simultaneously, limiting research progress. RAPTR combines viral pseudotyping and molecular engineering to enable interaction screens between antigens and immune receptors, providing a suite of tools with broad applications.
Article
Respiratory System
Qiao-Yan Lian, Ao Chen, Jian-Heng Zhang, Wei-Jie Guan, Xin Xu, Bing Wei, Dan-Xia Huang, Jian-Xing He, Chun-Rong Ju
Summary: HT-NGS has a higher pathogen detection rate and sensitivity for diagnosing pulmonary infections in LTx recipients compared to conventional microbiological testing, providing diagnostic advantages and helping optimize treatment regimens, including identification of uncommon pathogens.
BMC PULMONARY MEDICINE
(2021)
Article
Oncology
Tao Dao, Martin G. Klatt, Tatyana Korontsvit, Sung Soo Mun, Sean Guzman, Marissa Mattar, Oliver Zivanovic, Chrisann K. Kyi, Nicholas D. Socci, Roisin E. O'Cearbhaill, David A. Scheinberg
Summary: Identification of mutated HLA ligands with potential immunotherapy targets for ovarian cancer was conducted through mass spectrometry and sequencing; although these mutated epitopes induced T cell responses in healthy donors' blood, they did not elicit autologous responses in the patient; further research on T cell responses to p53 Y220C mutation in ovarian cancer is warranted.
CANCER IMMUNOLOGY IMMUNOTHERAPY
(2021)
Review
Immunology
Jianing Fu, Mohsen Khosravi-Maharlooei, Megan Sykes
Summary: Recent advances in high throughput sequencing and transcriptomic analysis, particularly at the single cell level, have provided new insights into human immunology and immune-related diseases. The use of HTS of TCRs has allowed assessment of the human alloresponse development, magnitude, and nature at a new level, and has provided a tool for tracking the fate of pre-transplant-defined TCRs. Studies combining high throughput TCR sequencing with single cell transcriptional analyses have shed light on human allograft rejection and tolerance.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Hao Xiong, Liyan Ji, Jin Yang, Jianji Wan, Mengmeng Song, Guangren Liu, Ling Yang, Xiuqin Dong
Summary: This study assessed the TCRβ repertoire diversity and composition of CD8+ T cells in blood of 9 nonsegmental vitiligo patients via high-throughput sequencing. Vitiligo patients showed low TCRβ diversity with highly expanded clones. Differential usage of TRBV, the TRBJ gene, and the TRBV/TRBJ combination were observed between vitiligo patients and healthy controls. A set of TRBV/TRBJ combinations could differentiate vitiligo patients from healthy controls. This study revealed distinct TCRβ repertoires of CD8+ T cells in vitiligo and may contribute to the exploration of immune biomarkers and therapeutic targets.
MOLECULAR IMMUNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Robert Dixon, Stephen G. Preston, Stefan Dascalu, Patrik G. Flammer, Steven R. Fiddaman, Kirstie McLoughlin, Amy Boyd, Jiri Volf, Ivan Rychlik, Michael B. Bonsall, Bernd Kaspers, Adrian L. Smith
Summary: This study reveals that chicken TCR gamma locus has undergone tandem duplication events that have shaped its evolution. Repertoire sequencing shows large differences in the usage of individual TRGV genes across various tissues, with TRGV3.3 dominating every tissue. The application of repertoire analysis in chickens with a high circulating gamma delta phenotype is important for understanding the functional diversity of these cells and their potential in improving health.
Article
Cell Biology
Xi Jia, Tian-Yu Zhai, Bing Wang, Jin-An Zhang, Rong-Hua Song
Summary: The TCR repertoire in patients with autoimmune thyroid diseases (AITDs) is expanded and has many upregulated TRBV genes. The differences in TCR profiles become more pronounced in patients with refractory Graves' disease (RGD) as the disease progresses.
MOLECULAR AND CELLULAR ENDOCRINOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Stefan A. Schattgen, Kate Guion, Jeremy Chase Crawford, Aisha Souquette, Alvaro Martinez Barrio, Michael J. T. Stubbington, Paul G. Thomas, Philip Bradley
Summary: Integrating T cell sequences and gene expression profiles uncovers functional subsets in single-cell datasets, revealing relationships between TCR sequences and phenotypes. The CoNGA approach identifies correlations between TCR sequence and GEX profiles through statistical analysis, helping elucidate complex relationships in large single-cell datasets.
NATURE BIOTECHNOLOGY
(2022)
Review
Immunology
Janet Chou, Paul G. Thomas, Adrienne G. Randolph
Summary: Children are generally resistant to severe disease resulting from SARS-CoV-2 infection, but cases of pediatric COVID-19 and a new syndrome called MIS-C can occur. Studies have identified immunological differences between children and adults in their response to SARS-CoV-2, which helps to understand the pediatric immune mechanisms to the infection.
Review
Immunology
Robert C. Mettelman, Kaitlynn E. Allen, Paul G. Thomas
Summary: The lungs are constantly exposed to various substances and pathogens, thus requiring regulation of immune responses in the respiratory tract with understanding of the interactions between structural and immune cells. Studying immune responses in the lungs is crucial for treating pulmonary diseases and infections, as well as next-generation vaccine design.
Article
Immunology
Zion Congrave-Wilson, Wesley A. Cheng, Yesun Lee, Stephanie Perez, Lauren Turner, Carolyn Jennifer Marentes Ruiz, Shirley Mendieta, Adam Skura, Jaycee Jumarang, Jennifer Del Valle, John Kubale, Emma Kaitlynn Allen, Paul G. Thomas, Aubree Gordon, Pia S. Pannaraj
Summary: This study compared the serological responses following natural infection and vaccination, finding that responses after natural infection were more variable while antibody levels after vaccination remained durable for up to 12 months. Individuals with both infection and vaccination had more robust and slower declining SARS-CoV-2-specific antibody levels.
Letter
Biochemical Research Methods
Mikhail Goncharov, Dmitry Bagaev, Dmitrii Shcherbinin, Ivan Zvyagin, Dmitry Bolotin, Paul G. Thomas, Anastasia A. Minervina, Mikhail V. Pogorelyy, Kristin Ladell, James E. McLaren, David A. Price, Thi H. O. Nguyen, Louise C. Rowntree, E. Bridie Clemens, Katherine Kedzierska, Garry Dolton, Cristina Rafael Rius, Andrew Sewell, Jerome Samir, Fabio Luciani, Ksenia V. Zornikova, Alexandra A. Khmelevskaya, Saveliy A. Sheetikov, Grigory A. Efimov, Dmitry Chudakov, Mikhail Shugay
Article
Microbiology
Sinead E. Morris, Renate Strehlau, Stephanie Shiau, Elaine J. Abrams, Caroline T. Tiemessen, Louise Kuhn, Andrew J. Yates
Summary: This study highlights the importance of combining mathematical modeling with clinical data to understand the dynamics of HIV suppression and rebound in infants. The researchers found that a deterministic model used for adults could not fully explain the diverse trajectories of HIV infection in infants. They also discovered that infants with faster CD4 reconstitution rates on antiretroviral treatment were more likely to experience resurgences in viral load.
Article
Biology
Sanket Rane, Thea Hogan, Edward Lee, Benedict Seddon, Andrew J. Yates
Summary: In this study, a unified model of naive CD4 and CD8 T cell population dynamics in mice was identified using multiple modelling and experimental approaches. It was found that both subsets divide rarely and progressively increase their survival capacity with cell age. Newly generated naive CD8 T cells were found to be lost more rapidly during the first 3-4 weeks of life. No evidence for elevated division rates in neonates or feedback regulation of naive T cell numbers at any age was found.
Editorial Material
Multidisciplinary Sciences
Douglas R. Green, Paul G. Thomas
Article
Immunology
Timothy A. A. Gondre-Lewis, Chao Jiang, Mandy L. Ford, David M. Koelle, Alessandro Sette, Alex K. Shalek, Paul G. Thomas
Summary: On June 15-16, 2022, the National Institute of Allergy and Infectious Diseases organized a virtual workshop to discuss T cell technologies including assays, development of novel technologies, their applications in both laboratory and clinical settings, as well as the challenges and innovations in the field.
Article
Biochemical Research Methods
Branden J. Olson, Stefan A. Schattgen, Paul G. Thomas, Philip Bradley, Frederick A. Matsen
Summary: This paper introduces a nonparametric approach for comparing TCR repertoires using the Sinkhorn distance as an optimal transport method and the recently-created TCR distance called TCRdist. The authors demonstrate that their methods can identify meaningful differences between TCR distributions and compete with more complicated methods.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Virology
Sherri L. L. Surman, Bart G. G. Jones, Rhiannon R. R. Penkert, Robert E. E. Sealy, Tony Marion, Paul G. G. Thomas, Geoffrey Neale, Beisi Xu, Julia L. L. Hurwitz
Summary: Females generally have stronger immune responses compared to males, which may be attributed to higher estrogen levels. Experiments on animals and humans have shown that supplementation of estrogen can improve immune responses. These findings are important for the optimization of vaccines and drugs for both male and female hosts.
Review
Medicine, Research & Experimental
Mohamed A. Ghonim, David F. Boyd, Tim Flerlage, Paul G. Thomas
Summary: In recent years, the role of fibroblasts in inflammation has attracted increasing interest. Fibroblasts exhibit diverse functionality and subsets, with phenotypes that depend on their spatial distribution within tissues and immunopathologic cues. In addition to their structural support and tissue remodeling roles, fibroblasts mediate crucial interactions with immune cells, which have significant implications for disease mechanisms and therapeutic targets. Fibroblasts in the respiratory tract play a pivotal role in determining the severity and outcome of various acute and chronic lung diseases.
JOURNAL OF CLINICAL INVESTIGATION
(2023)
Article
Cell Biology
Mikhail V. Pogorelyy, Elisa Rosati, Anastasia A. Minervina, Robert C. Mettelman, Alexander Scheffold, Andre Franke, Petra Bacher, Paul G. Thomas
Summary: This study conducted a meta-analysis of large, publicly available TCR datasets from SARS-CoV-2-infected individuals to identify public CD4(+) responses. The results revealed over 1,200 abTCRs forming six prominent similarity clusters, and the validation of HLA restriction and epitope specificity predictions for five clusters using transgenic T cell lines. Overall, these findings provide insights into immunodominant CD4(+) T cell responses to SARS-CoV-2 and demonstrate the utility of the reverse epitope discovery approach.
CELL REPORTS MEDICINE
(2022)
Article
Medical Laboratory Technology
Edward S. Lee, Thomas J. S. Durant
Summary: With the increasing demand for laboratory testing by mass spectrometry, automated methods for data analysis are needed. Clinical mass spectrometry data is well-suited for machine learning methods, offering optimization of workflows, improved result quality, and enhanced understanding of high-dimensional datasets and their relationship with disease. There is an opportunity to improve technological literacy of ML-based software in the clinical laboratory scientist community.
JOURNAL OF MASS SPECTROMETRY AND ADVANCES IN THE CLINICAL LAB
(2022)