Article
Immunology
Reut Levi, Yoram Louzoun
Summary: This study reveals that beta chain rearrangement in T cells is a two-step process, where D-beta and J(beta) bind first and then V-beta is joined to the complex. The frequency of V(beta)J(beta) combinations in human and mouse deviates from the expected values based on gene usage frequency. This bias is mainly observed in functional rearrangements but also slightly in non-functional rearrangements. Preferred V(beta)J(beta) combinations in functional clones are shared between donors and samples, suggesting a common structural mechanism for these biases.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Oncology
Yi-Lin Chen, Chung-Liang Ho, Chen-Yan Hung, Wan-Li Chen, Chen Chang, Yi-Hsin Hou, Jian-Rong Chen, Pin-Jun Chen, Nan-Haw Chow, Wenya Huang, Ya-Ting Hsu, Tsai-Yun Chen, Tsunglin Liu
Summary: This study analyzed TCR beta sequences in Taiwanese TCL patients and found differences in sensitivity compared to European TCL patients using the BIOMED-2 test. Genetic variations in the BIOMED-2 primer sites were not the reason for this difference. The study suggests that non-recombined TCR beta sequences may be a new target for enhancing TCL diagnosis, and the proposed digital PCR assay showed positive results in TCL patients.
FRONTIERS IN ONCOLOGY
(2022)
Review
Oncology
Nicla Porciello, Ornella Franzese, Lorenzo D'Ambrosio, Belinda Palermo, Paola Nistico
Summary: Profiling the T-cell receptor repertoire allows for the investigation of antitumor immune response. By tracking the spatiotemporal variation of T-cell populations, the key cells responsible for tumor eradication can be identified. Furthermore, improvements in T-cell sequencing provide new opportunities and challenges for research.
JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH
(2022)
Article
Immunology
Mikiya Tsunoda, Hiroyasu Aoki, Haruka Shimizu, Shigeyuki Shichino, Kouji Matsushima, Satoshi Ueha
Summary: Temporal analysis of T cell receptor (TCR) repertoire is important for monitoring changes in antigen-specific T cells in cancer patients. However, lack of experimental models for temporal analysis within a homogeneous population limits understanding of the relationship between TCR repertoire changes and antitumor responses. Bilateral tumor model showed highly similar T-cell clones in bilateral tumors and different patterns in draining lymph nodes, suggesting independent induction of tumor-reactive T cell clones in each lymph node.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Multidisciplinary Sciences
Sabrina Giampaolo, Cristina M. Chiarolla, Konrad Knoepper, Martin Vaeth, Matthias Klein, Azeem Muhammad, Tobias Bopp, Friederike Berberich-Siebelt, Amiya K. Patra, Edgar Serfling, Stefan Klein-Hessling
Summary: In the thymus, the deletion of NFATc1 or its inducible isoforms during the DN stages of thymocyte development leads to an increase in gamma delta thymocytes while alpha beta thymocytes are mostly unaffected. These gamma delta thymocytes upregulate PLZF, the master regulator of NKT cell development, acquiring an NKT gamma delta cell phenotype with higher survival rates. The enhancer E2 is crucial for NFATc1's suppressive function in NKT gamma delta cell formation, translating a strong gamma delta TCR signal into inducible expression of NFATc1 isoforms to control the numbers of NKT gamma delta cells.
Review
Immunology
Mitchell N. Lefebvre, Nicholas Borcherding, Ryan J. Reis, Eric Mou, Vincent Liu, Ali Jabbari
Summary: Currently, diagnosis of CTCL is limited by clinical presentation, histopathology, and immunohistochemistry. However, recent advances in flow cytometry, polymerase chain reaction, high throughput sequencing, and other molecular techniques have shown promise in improving diagnosis and treatment of CTCL.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Immunology
Maria Eschke, Peter F. Moore, Haiyang Chang, Gottfried Alber, Stefan M. Keller
Summary: In this study, a detailed atlas of peripheral blood TCR alpha beta(+) T cell populations in healthy dogs was generated using single-cell RNA sequencing and immune repertoire sequencing. The researchers identified 22 T cell clusters, classified into CD4-dominant, CD8A-dominant, and CD4/CD8A-mixed groups. They also discovered several T cell populations not previously described in dogs, including mucosa-associated invariant T cell (MAIT)-like cells. This study provides important reference data for future research and has implications for T cell-specific therapies.
FRONTIERS IN IMMUNOLOGY
(2023)
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)
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
Biochemical Research Methods
Shirit Dvorkin, Reut Levi, Yoram Louzoun
Summary: The study introduces an autoencoder named ELATE to represent T cell receptors as real vectors for characterizing donors and specific receptors. By combining distance conserving autoencoders and Kernel Density Estimates, local repertoire density can be estimated to study repertoire properties.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Immunology
Jennifer Massey, Katherine Jackson, Mandeep Singh, Brendan Hughes, Barbara Withers, Carole Ford, Melissa Khoo, Kevin Hendrawan, John Zaunders, Benedicte Charmeteau-De Muylder, Remi Cheynier, Fabio Luciani, David Ma, John Moore, Ian Sutton
Summary: This study investigates T cell reconstitution in highly active MS patients for 36 months after AHSCT. The results show that AHSCT induces significant changes in the dominant T cell clones of CD4+ and CD8+ memory T cells. After lymphopenia-induced homeostatic proliferation, clonal attrition occurs. Recovery of thymically-derived CD4 naive T cell repertoire begins at 12 months and continues, but the diversity of the naive populations does not increase compared to baseline, indicating that the principal mechanism for durable remission from MS after AHSCT relates to depletion of putative auto-reactive clones.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Immunology
Mei Xia, Azra Blazevic, Andrew Fiore-Gartland, Daniel F. Hoft
Summary: In this study, the effects of BCG vaccination on γδ T cell responses were investigated. TCR repertoire sequencing revealed minimal changes in the diversity and distribution of TCR clones after vaccination, but identified specific clonotypes that significantly expanded or contracted. These findings provide new insights into the role of γδ T cells in Mycobacterium tuberculosis immunity.
FRONTIERS IN 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
Environmental Sciences
Lei Bao, Zihan Geng, Juan Wang, Liyi He, Aijuan Kang, Jianshi Song, Xiaoyan Huang, Yaling Zhang, Qingping Liu, Tao Jiang, Yaxian Pang, Yujie Niu, Rong Zhang
Summary: This study investigated the mechanisms by which silica nanoparticles (SiNPs) interact with T cells and affect their functions in the context of pulmonary fibrosis. The results showed that SiNPs could interfere with T cell activation by macrophage presentation via the LCK/Zap70 pathway and rearrange the TCR beta repertoire, leading to disruption of adaptive immunity and the pulmonary microenvironment.
ENVIRONMENTAL RESEARCH
(2022)
Review
Immunology
Rami Bechara, Alexia Feray, Marc Pallardy
Summary: Allergic reactions to drugs and chemicals are mediated by specific T cells and it is unclear whether there is a common occurrence of thymic selection of drug/chemical-specific T cells. Recent observations suggest that T-cell receptor recognition of hapten-modified peptides may play a crucial role in drug/chemical allergy. This understanding could lead to efficient strategies for allergy diagnosis and predicting the immunogenic potential of new chemicals.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Gastroenterology & Hepatology
Sascha Cording, Ludovic Lhermitte, Georgia Malamut, Sofia Berrabah, Amelie Trinquand, Nicolas Guegan, Patrick Villarese, Sophie Kaltenbach, Bertrand Meresse, Sherine Khater, Michael Dussiot, Marc Bras, Morgane Cheminant, Bruno Tesson, Christine Bole-Feysot, Julie Bruneau, Thierry Jo Molina, David Sibon, Elizabeth Macintyre, Olivier Hermine, Christophe Cellier, Vahid Asnafi, Nadine Cerf-Bensussan
Summary: The study identified mutations activating the JAK1-STAT3 pathway as the main drivers of enteropathy-associated T-cell lymphoma, potentially in combination with mutations in negative regulators of NF-kappa B. These mutations could promote the clonal emergence of malignant lymphocytes in the cytokine-rich coeliac intestine, and are attractive therapeutic targets for treating refractory celiac disease and blocking progression towards EATL.
Article
Medical Laboratory Technology
Christa Cobbaert, Ettore D. Capoluongo, Florent J. L. A. Vanstapel, Patrick M. M. Bossuyt, Harjit Pal Bhattoa, Peter Henrik Nissen, Matthias Orth, Thomas Streichert, Ian S. Young, Elizabeth Macintyre, Alan G. Fraser, Michael Neumaier
Summary: Laboratory medicine in the European Union is facing a regulatory revolution, and the unpreparedness of EU regulatory infrastructure may lead to negative consequences for the healthcare sector, patients, caregivers, and innovation in medical diagnostic care.
CLINICAL CHEMISTRY AND LABORATORY MEDICINE
(2022)
Review
Biochemistry & Molecular Biology
Thomas Lefeivre, Luke Jones, Amelie Trinquand, Antoine Pinton, Elizabeth Macintyre, Elisa Laurenti, Jonathan Bond
Summary: This review explores the relationship between the biology of acute leukaemia and normal blood cell development, focusing on T-lymphoid and myeloid cases. It discusses the potential for next-generation analytical tools to provide new perspectives that could enhance our understanding of immature blood cancer biology.
Letter
Oncology
Mary M. Taj, Anthony V. Moorman, Lina Hamadeh, Arnaud Petit, Vahid Asnafi, Fanny Alby-Laurent, Ajay Vora, Marc R. Mansour, Rosemary Gale, Sylvie Chevret, John Moppett, Andre Baruchel, Elizabeth Macintyre
Article
Oncology
Emeric Limagne, Lisa Nuttin, Marion Thibaudin, Elise Jacquin, Romain Aucagne, Marjorie Bon, Solene Revy, Robby Barnestein, Elise Ballot, Caroline Truntzer, Valentin Derangere, Jean-David Fumet, Charlene Latour, Cedric Rebe, Pierre-Simon Bellaye, Coureche-Guillaume Kaderbhai, Aodrenn Spill, Bertrand Collin, Mary B. Callanan, Aurelie Lagrange, Laure Favier, Bruno Coudert, Laurent Arnould, Sylvain Ladoire, Bertrand Routy, Philippe Joubert, Francois Ghiringhelli
Summary: Chemotherapy combined with MEK inhibitor enhances the sensitivity of lung cancer cells to immune checkpoint inhibitors by inducing CXCL10 expression and CD8(+) T cell recruitment. The study also highlights the role of TLR9- and OPTN-dependent mitophagy in enhancing the efficacy of chemoimmunotherapy.
Article
Hematology
Marina Lafage-Pochitaloff, Bastien Gerby, Veronique Baccini, Laetitia Largeaud, Vincent Fregona, Nais Prade, Pierre-Yves Juvin, Laura Jamrog, Pierre Bories, Sylvie Hebrard, Stephanie Lagarde, Veronique Mansat-De Mas, Oliver M. Dovey, Kosuke Yusa, George S. Vassiliou, Joop H. Jansen, Tobias Tekath, David Rombaut, Genevieve Ameye, Carole Barin, Audrey Bidet, John Boudjarane, Marie-Agnes Collonge-Rame, Carine Gervais, Antoine Ittel, Christine Lefebvre, Isabelle Luquet, Lucienne Michaux, Nathalie Nadal, Helene A. Poirel, Isabelle Radford-Weiss, Benedicte Ribourtout, Steven Richebourg, Stephanie Struski, Christine Terre, Isabelle Tigaud, Dominique Penther, Virginie Eclache, Michaela Fontenay, Cyril Broccardo, Eric Delabesse
Summary: This study investigated 113 cases of MDS and MDS/MPN with del(11q), revealing clinical features such as female predominance, similar survival prognosis to other MDS, low monocyte count, and abnormal megakaryopoiesis. The study also identified the common deleted region at 11q23.2, which is located between CADM1 and NXPE2 genes.
Review
Oncology
F. Nguyen-Khac, A. Bidet, A. Daudignon, M. Lafage-Pochitaloff, G. Ameye, C. Bilhou-Nabera, E. Chapiro, M. A. Collonge-Rame, W. Cuccuini, N. Douet-Guilbert, V Eclache, I Luquet, L. Michaux, N. Nadal, D. Penther, B. Quilichini, C. Terre, C. Lefebvre, M-B Troadec, L. Veronese
Summary: The complexity of karyotype has significant prognostic value in various malignancies, but there is no consensus on its definition and the prognostic impact varies among diseases. The GFCH has developed a practical document to aid cytogeneticists in assessing complex karyotypes in hematological disorders. Standardizing the evaluation of karyotype complexity and establishing consensus prognostic cut-offs for each disease is necessary.
Article
Pathology
Mona Phelippeau, Christine Lefebvre, Marie-Christine Jacob, Charlotte Syrykh, Julien Ghelfi, Sylvain Carras, Camille Laurent, Lysiane Molina, Severine Valmary-Degano
Summary: Follicular lymphoid hyperplasia induced by dasatinib is a recently described entity that is sometimes difficult to distinguish from small B-cell lymphoma. It is characterized by swollen lymph nodes with preserved follicular architecture, germinal centers with varied size and shape, a high number of mitoses, and tingible bodies macrophages. Follicular lymphoid hyperplasia can occur alone or in association with multiple reactive patterns. The immunohistochemical profile of germinal centers is CD20+, CD10+, BCL6+, BCL2-. Swollen lymph nodes disappear shortly after discontinuation of dasatinib. Clinicians and pathologists should be aware of this entity to avoid mistakenly suspecting lymphoma in patients with chronic myeloid leukemia treated with dasatinib. (c) 2022 Elsevier Masson SAS. All rights reserved.
ANNALES DE PATHOLOGIE
(2023)
Article
Medicine, General & Internal
Tatiana Raskovalova, Laura Scheffen, Marie-Christine Jacob, Simon Chevalier, Sylvie Tondeur, Benedicte Bulabois, Mathieu Meunier, Gautier Szymanski, Christine Lefebvre, Charlotte Planta, Chantal Dumestre-Perard, Nicolas Gonnet, Frederic Garban, Raymond Merle, Sophie Park, Jose Labarere
Summary: This study aims to compare the accuracy and agreement between a single-use dry reagent and a liquid reagent in quantifying peripheral blood neutrophil myeloperoxidase expression in suspected MDS patients.
Review
Oncology
Florian Renosi, Mary Callanan, Christine Lefebvre
Summary: This review discusses the differential diagnosis between Blastic pDC Neoplasm (BPDCN) and Acute Myeloid Leukemia with pDC expansion (pDC-AML) and their genomic features. Understanding the distinct characteristics of these two diseases is crucial for diagnosis and treatment.
Article
Family Studies
J. Grenier-Martin, M. Rivard, S. Patel, M. J. Lanovaz, C. Lefebvre
Summary: The purpose of this study was to evaluate the effectiveness of an online parent training for managing problem behaviors in families waiting for specialized services for children with intellectual and developmental disability. The results showed that the online training led to reductions in problem behavior frequency and parenting stress, while improving caregivers' self-efficacy.
JOURNAL OF CHILD AND FAMILY STUDIES
(2022)
Article
Oncology
Victor-Emmanuel Brett, Nicolas Lechevalier, Franck Trimoreau, Charles Dussiau, Sophie Dimicoli-Salazar, Lucie Coster, Isabelle Luquet, Nathalie Nadal, Benedicte Ribourtout, Elise Chapiro, Christine Lefebvre, Sylvie Tondeur, Estelle Balducci, Florence Nguyen-Khac, Claire Borie, Isabelle Radford-Weiss, Carole Barin, Virginie Eclache, Olivier Mansier, Audrey Bidet
Summary: In this study, a new entity called chromosomal abnormality with cytopenia of undetermined significance (CACtUS) was identified in some patients with cytopenias, absence of significant dysplasia, and presence of a chromosomal abnormality. Patients with CACtUS were found to have similar clinico-biological characteristics, overall survival, and risk of progression to high-risk MDS as low-risk MDS patients. Therefore, it is suggested that CACtUS patients be considered as high-risk CCUS and receive the follow-up regimen recommended for MDS patients.
GENES CHROMOSOMES & CANCER
(2023)
Letter
Oncology
Florence Nguyen-Khac, Audrey Bidet, Marie-Berengere Troadec, Lauren Veronese, Nathalie Auger, Agnes Daudignon, Nathalie Nadal, Dominique Penther, Lucienne Michaux, Marina Lafage-Pochitaloff, Christine Lefebvre
Editorial Material
Hematology
Christine Lefebvre, Gautier Szymanski
Article
Hematology
Nada Assaf, Christine Lefebvre, Victoria Raggueneau, Geoffroy Guignedoux, Alice Marceau-Renaut, Simon Chevalier, Sylvie Tondeur, Dominique Bories, Riad Benramdane, Philippe Rousselot, Christine Terre
Summary: This study investigated the characteristics and prognosis of patients with CBFB-MYH11 fusion gene and high-risk rearrangements. The results showed that the presence of high-risk abnormalities has a significant impact on the biological features and prognosis of inv(16) AML.
Article
Pathology
Juliana Mota Siqueira, Yoshitsugu Mitani, Camilla Oliveira Hoff, Flavia Bonini, Luana Guimaraes de Sousa, Mario L. Marques-Piubelli, Anurag Purushothaman, Mutsumi Mitani, Hui Dai, Shiaw-Yih Lin, Michael T. Spiotto, Ehab Y. Hanna, Daniel J. McGrail, Adel K. El-Naggar, Renata Ferrarotto
Summary: B7-H4 expression pattern varies among different types of salivary gland carcinomas, and high B7-H4 expression is associated with poor prognosis in adenoid cystic carcinoma.
Article
Pathology
Basile Tessier-Cloutier, Felix K. F. Kommoss, David L. Kolin, Kristyna Nemejcova, Dupreez Smith, Jennifer Pors, Colin J. R. Stewart, W. Glenn Mccluggage, William D. Foulkes, Andreas von Deimling, Martin Kobel, Cheng-Han Lee
Summary: This study provides a detailed analysis of the clinical, pathological, immunohistochemical, and molecular features of DDOC/UDOC. The majority of patients presented with extraovarian disease and had rapid disease progression resulting in high mortality rate.
Review
Pathology
Sophia J. Wagner, Christian Matek, Sayedali Shetab Boushehri, Melanie Boxberg, Lorenz Lamm, Ario Sada, Dominik J. E. Winter, Carsten Marr, Tingying Peng
Summary: Computational pathology research driven by deep learning faces challenges in reproducibility and reusability. Codebase with good documentation and robustness and generalizability of models are crucial. The reuse of computational pathology algorithms is limited, and their application in clinical settings is even rarer. This study evaluates 160 peer-reviewed articles, providing criteria for data and code availability and statistical analysis of results.
Article
Pathology
Andres M. Acosta, Lynette M. Sholl, Fiona Maclean, Chia-Sui Kao, Thomas M. Ulbright
Summary: This study assessed the clinicopathologic and genomic features of 14 cases of testicular sex cord-stromal tumors. The results showed that CTNNB1 mutations are rare in these tumors, and most of them have genomic alterations similar to testicular sex cord-stromal tumors with pure or predominant spindle cell components.
Article
Pathology
Toru Odate, Kaishi Satomi, Takashi Kubo, Yuko Matsushita, Toshihide Ueno, Akira Kurose, Kohei Shomori, Tokiko Nakai, Reiko Watanabe, Keiko Segawa, Shusa Ohshika, Naritomo Miyake, Sayaka Kudo, Tatsunori Shimoi, Eisuke Kobayashi, Motokiyo Komiyama, Seiichi Yoshimoto, Fumihiko Nakatani, Akira Kawai, Yasushi Yatabe, Shinji Kohsaka, Koichi Ichimura, Hitoshi Ichikawa, Akihiko Yoshida
Summary: Inflammatory rhabdomyoblastic tumors (IRMTs) are newly recognized skeletal muscle tumors with uncertain malignant potential. This study investigated 13 IRMTs using clinicopathologic, genetic, and epigenetic methods. The results showed specific histologic features and genetic mutations in these tumors, and most of them exhibited benign behavior.
Article
Pathology
Dale L. Davis, Adam C. Lechner, David B. Chapel, Jonathan C. Slack, Chrystalle Katte Carreon, Bradley J. Quade, Carlos Parra-Herran
Summary: The Amsterdam Consensus Statement introduced the term maternal vascular malperfusion (MVM) to classify a group of findings related to impaired maternal-placental circulation. The study found that features such as low placental weight, accelerated villous maturation, decidual arteriopathy, and infarcts are associated with adverse obstetrical outcomes, while the role of other features like distal villous hypoplasia, excess multinucleated trophoblast, and retroplacental hemorrhage needs further research.
Review
Pathology
Alain C. Borczuk
Summary: COVID-19 is an acute respiratory illness that can progress to acute respiratory distress syndrome. While most patients recover completely, some may experience persistent respiratory dysfunction, known as long COVID. The pathogenesis involves immune and cellular disturbances.
Article
Pathology
Annikka Weissferdt, Cheuk H. Leung, Heather Lin, Boris Sepesi, William N. William, Stephen G. Swisher, Tina Cascone, J. Jack Lee, Abujiang Pataer
Summary: Neoadjuvant treatment of non-small cell lung cancer challenges traditional processing of pathology specimens, and accurate evaluation of residual tumor is crucial for assessing treatment efficacy.