Immunoinformatics (Amsterdam, Netherlands)最新文献

Is the vaccination-induced B cell receptor repertoire predictable? 疫苗诱导的B细胞受体库可预测吗？

Immunoinformatics (Amsterdam, Netherlands) Pub Date : 2025-09-01 DOI: 10.1016/j.immuno.2025.100057

Eve Richardson , Lisa Willemsen , Pramod Shinde , Morten Nielsen , Bjoern Peters

{"title":"Is the vaccination-induced B cell receptor repertoire predictable?","authors":"Eve Richardson , Lisa Willemsen , Pramod Shinde , Morten Nielsen , Bjoern Peters","doi":"10.1016/j.immuno.2025.100057","DOIUrl":"10.1016/j.immuno.2025.100057","url":null,"abstract":"<div><div>Vaccines trigger an immune response that results in a population of memory cells that can quickly respond to subsequent antigen re-encounters. Most vaccines are designed to induce memory B cells with vaccine-specific B cell receptors (BCRs). Post-vaccination, clonal expansion of B cells results in measurably expanded vaccine-specific BCR clonotypes. We set out to determine to what extent it is predictable which specific BCR clonotypes are vaccine-induced in an individual. We sequenced the BCR heavy chain repertoire in a cohort of 19 individuals prior- and 7 days post Tdap booster vaccination. We tested two modalities to predict which clonotypes were expanded post-vaccination: first, we utilized a small database of monoclonal antibodies with known specificity to Tdap vaccine antigens and tested various sequence look-up methods, identifying clonal look-up as the best method. We then utilized a leave-one-out approach in which expanded clonotypes in one individual were predicted using data from other members of the cohort. The second approach significantly outperformed the first, indicating that BCR clonotype expansion can be learned across subjects. These results support the utility of systematically collecting BCR specificity data through efforts like the Immune Epitope database and highlight the limitations on general prediction approaches resulting from relatively small dataset sizes for BCRs with known specificities. Additionally, our study provides 1) a comparison of several BCR specificity prediction methods, 2) a dataset that can be used for benchmarking of subsequent methods, and 3) a methodological framework for comparing BCR repertoires pre- and post-vaccination.</div></div>","PeriodicalId":73343,"journal":{"name":"Immunoinformatics (Amsterdam, Netherlands)","volume":"19 ","pages":"Article 100057"},"PeriodicalIF":0.0,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144925402","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The gremlin in the works: why T cell receptor researchers need to pay more attention to germline reference sequences 工作中的小妖精：为什么T细胞受体研究人员需要更多地关注种系参考序列

Immunoinformatics (Amsterdam, Netherlands) Pub Date : 2025-08-28 DOI: 10.1016/j.immuno.2025.100058

James M. Heather , Ayelet Peres , Gur Yaari , William Lees

{"title":"The gremlin in the works: why T cell receptor researchers need to pay more attention to germline reference sequences","authors":"James M. Heather , Ayelet Peres , Gur Yaari , William Lees","doi":"10.1016/j.immuno.2025.100058","DOIUrl":"10.1016/j.immuno.2025.100058","url":null,"abstract":"<div><div>The rise of T cell receptor (TCR) sequencing technologies is driving both new understandings of the immune system and the development of novel clinical platforms. Such analyses rely on comparing recombined TCR sequences to unrearranged germline reference sequences during V(D)J annotation. In this study we observed that, despite the importance of this step in TCR analysis, most published studies do not properly report the reference used. We use public datasets to illustrate why references should be explicitly specified: using IMGT/GENE-DB as an example, we document how the reference set changes over time. Furthermore we illustrate how prescriptivist interpretations of reference metadata may be obscuring rather than illuminating TCR biology, and demonstrate the need to perform full V gene sequencing in order to unambiguously determine the final translated TCR polypeptide sequence. In summary, we argue that in order to ensure the accuracy and reproducibility of TCR sequencing – an ever more pressing task as more TCR-based diagnostics and therapeutics are developed – we should all take more care with the development, use, and reporting of the TCR germline references used in our science.</div></div>","PeriodicalId":73343,"journal":{"name":"Immunoinformatics (Amsterdam, Netherlands)","volume":"20 ","pages":"Article 100058"},"PeriodicalIF":0.0,"publicationDate":"2025-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145109926","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Building immunoglobulin and T cell receptor gene databases for the future 未来建立免疫球蛋白和T细胞受体基因数据库

Immunoinformatics (Amsterdam, Netherlands) Pub Date : 2025-08-27 DOI: 10.1016/j.immuno.2025.100059

Corey T. Watson , Andrew M. Collins , Mats Ohlin , James M. Heather , Ayelet Peres , William D. Lees , Gur Yaari

引用次数: 0

Challenges and future directions of AIRR-seq-based diagnostics 基于airr -seq的诊断的挑战和未来方向

Immunoinformatics (Amsterdam, Netherlands) Pub Date : 2025-07-17 DOI: 10.1016/j.immuno.2025.100056

Ulrik Stervbo , Paraskevas Filippidis , Felix Breden , Lindsay G. Cowell , Frederic Davi , Victor Greiff , Anton W. Langerak , Eline T. Luning Prak , Alexandra F. Sharland , Enkelejda Miho , Pieter Meysman

{"title":"Challenges and future directions of AIRR-seq-based diagnostics","authors":"Ulrik Stervbo , Paraskevas Filippidis , Felix Breden , Lindsay G. Cowell , Frederic Davi , Victor Greiff , Anton W. Langerak , Eline T. Luning Prak , Alexandra F. Sharland , Enkelejda Miho , Pieter Meysman","doi":"10.1016/j.immuno.2025.100056","DOIUrl":"10.1016/j.immuno.2025.100056","url":null,"abstract":"<div><div>Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) is a promising diagnostic method across various clinical conditions, yet its widespread implementation faces several challenges. This perspective examines the current landscape of AIRR-seq diagnostics and outlines key obstacles and opportunities for advancement. Critical challenges include the need for standardized quality controls, privacy protection under General Data Protection Regulation (GDPR) and Health Insurance Portability and Accountability Act (HIPAA) frameworks, and the development of clinically compatible bioinformatics pipelines. Machine learning approaches offer potential solutions for interpreting complex repertoire signatures, though these models must balance accuracy with interpretability for clinical adoption. Future applications may include early disease detection, prognosis, and monitoring of treatment and vaccine responses. However, successful clinical integration will require sustained collaboration among funding bodies, regulatory agencies, researchers, diagnosticians, and clinicians to establish clear guidelines and expand existing repositories with well-characterized patient samples. The collaborative efforts of the AIRR Diagnostics Working Group and the AIRR Community's initiatives are working towards unlocking the potential of AIRR-seq in precision medicine and enhancing diagnostic capabilities.</div></div>","PeriodicalId":73343,"journal":{"name":"Immunoinformatics (Amsterdam, Netherlands)","volume":"19 ","pages":"Article 100056"},"PeriodicalIF":0.0,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144723797","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Comparison of different substitution matrices for distance based T-cell receptor epitope predictions using tcrdist3 使用tcrdist3进行基于距离的t细胞受体表位预测的不同替代矩阵的比较

Immunoinformatics (Amsterdam, Netherlands) Pub Date : 2025-07-07 DOI: 10.1016/j.immuno.2025.100051

Marc Hoffstedt, Hermann Wätzig, Knut Baumann

{"title":"Comparison of different substitution matrices for distance based T-cell receptor epitope predictions using tcrdist3","authors":"Marc Hoffstedt, Hermann Wätzig, Knut Baumann","doi":"10.1016/j.immuno.2025.100051","DOIUrl":"10.1016/j.immuno.2025.100051","url":null,"abstract":"<div><div>Various methods, differing in complexity, have been developed to predict T-cell receptor epitopes. tcrdist3, which implements an easy-to-interpret distance-based approach, has demonstrated performance comparable to the best feature-based methods. Here, a new substitution matrix for tcrdist3 is proposed and its performance is compared to various other substitution matrices. Small performance gains were possible; however tcrdist3 was found to perform reliably well with most substitution matrices. Randomly generated substitution matrices were used as a baseline and resulted in good classification results. It was observed that the prediction quality was negatively correlated with the relative standard deviation of the matrix used (i.e. a larger variance of the weights resulted in poorer predictivity). The most important factor of the tcrdist3-distance between two sequences that could be singled out is the number of substitutions. tcrdist3 implicitly considers the number of substitutions and the type of substitution simultaneously. Using substitution matrices with larger variance penalizes certain substitutions more strongly, which blurs the clusters of sequences with the same number of substitutions. Since the number of substitutions was a key predictor, this resulted in decreased prediction performance.</div></div>","PeriodicalId":73343,"journal":{"name":"Immunoinformatics (Amsterdam, Netherlands)","volume":"19 ","pages":"Article 100051"},"PeriodicalIF":0.0,"publicationDate":"2025-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144634320","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Structural insights on the differentiation and reversion of conformational changes in SARS-CoV-2 spike protein models across variants occurring from December, 2019 to November, 2021 2019年12月至2021年11月发生变异的SARS-CoV-2刺突蛋白模型构象变化分化和逆转的结构见解

Immunoinformatics (Amsterdam, Netherlands) Pub Date : 2025-06-27 DOI: 10.1016/j.immuno.2025.100055

Marni E. Cueno, Kenichi Imai

{"title":"Structural insights on the differentiation and reversion of conformational changes in SARS-CoV-2 spike protein models across variants occurring from December, 2019 to November, 2021","authors":"Marni E. Cueno, Kenichi Imai","doi":"10.1016/j.immuno.2025.100055","DOIUrl":"10.1016/j.immuno.2025.100055","url":null,"abstract":"<div><div>Conformational changes in the SARS-CoV-2 spike protein are critical for understanding viral evolution. In this study, we provide comparative structural and electrostatic analyses across variants, revealing both differentiation and reversion patterns not previously described in locked and activated spike conformations. More specifically, we generated SARS2 spike protein models from the various recorded variants between December, 2019 and November 2021, and performed structural superimposition, dendrogram analyses, and electrostatic mapping. We confirmed which locked and activated conformations differed and reversed between the Original spike protein model and subsequent SARS2 variants and subvariants. Additionally, among the spike protein models of subsequent SARS2 variants and subvariants during December, 2019-November, 2021, we likewise established structural variations and reversions among the locked and activated conformations. Moreover, we established the structural relationship and clustering among the locked and activated conformations of the SARS2 spike protein models. Furthermore, we determined the electrostatic potential of all generated SARS2 spike protein models to establish the surface charge distribution. Taken together, we found that certain locked and activated conformations of the Original SARS2 spike protein models exhibited both structural differences and, surprisingly, reversion when compared to subsequent variants and subvariants. Similarly, structural differentiation and reversion were also observed in the locked and activated conformations across the spike protein models. Additionally, we identified distinct structural clusters within the locked and activated conformations, establishing a structural relationship among certain SARS2 spike protein models. Moreover, we found that during spike evolution reorganization of the surface charge distribution occurs during structural differentiation and reversion.</div></div>","PeriodicalId":73343,"journal":{"name":"Immunoinformatics (Amsterdam, Netherlands)","volume":"19 ","pages":"Article 100055"},"PeriodicalIF":0.0,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144523417","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Challenges for the immunoglobulin and T cell receptor gene nomenclatures in the modern genomics era 免疫球蛋白和T细胞受体基因命名在现代基因组学时代的挑战

Immunoinformatics (Amsterdam, Netherlands) Pub Date : 2025-06-27 DOI: 10.1016/j.immuno.2025.100053

Andrew M. Collins , Corey T. Watson , Henk-Jan van den Ham , Luc Teyton , Elisa Rosati , Yana Safonova

{"title":"Challenges for the immunoglobulin and T cell receptor gene nomenclatures in the modern genomics era","authors":"Andrew M. Collins , Corey T. Watson , Henk-Jan van den Ham , Luc Teyton , Elisa Rosati , Yana Safonova","doi":"10.1016/j.immuno.2025.100053","DOIUrl":"10.1016/j.immuno.2025.100053","url":null,"abstract":"<div><div>For over thirty years, an approach to the nomenclatures of human immunoglobulin (IG) and T cell receptor (TR) genes has operated successfully and has been widely supported by the research community. The principles behind the human nomenclatures were then applied to the development of nomenclatures for IG and TR genes in non-human species. More recently, however, genomic sequencing has highlighted the limitations of this historic approach to nomenclature. The sequencing of IG and TR gene loci from multiple individuals and from a number of species has unveiled an extraordinary level of structural variation within the loci of all species that have so far been studied in this way. The designated gene naming authority - the International Union of Immunological Societies (IUIS) IG and TR Nomenclature Sub-Committee - has determined that a more careful approach is required before the genes of any species are officially named. In this opinion piece, we outline the challenges of the IG and TR nomenclatures, hoping to stimulate dialogue within the research community. Such dialogue would help guide the formulation of official policies to determine the appropriate level of knowledge of a locus that should be required before official gene names can be assigned. Strategies are also presented that should allow the unambiguous reporting and discussion of IG and TR gene sequences if their official naming is delayed.</div></div>","PeriodicalId":73343,"journal":{"name":"Immunoinformatics (Amsterdam, Netherlands)","volume":"19 ","pages":"Article 100053"},"PeriodicalIF":0.0,"publicationDate":"2025-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144632699","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

AnalyzAIRR: A user-friendly guided workflow for AIRR data analysis AnalyzAIRR：一个用户友好的指导工作流，用于AIRR数据分析

Immunoinformatics (Amsterdam, Netherlands) Pub Date : 2025-06-25 DOI: 10.1016/j.immuno.2025.100052

Vanessa Mhanna , Gabriel Pires , Grégoire Bohl-Viallefond , Karim El Soufi , Nicolas Tchitchek , David Klatzmann , Adrien Six , Hang P. Pham , Encarnita Mariotti-Ferrandiz

{"title":"AnalyzAIRR: A user-friendly guided workflow for AIRR data analysis","authors":"Vanessa Mhanna , Gabriel Pires , Grégoire Bohl-Viallefond , Karim El Soufi , Nicolas Tchitchek , David Klatzmann , Adrien Six , Hang P. Pham , Encarnita Mariotti-Ferrandiz","doi":"10.1016/j.immuno.2025.100052","DOIUrl":"10.1016/j.immuno.2025.100052","url":null,"abstract":"<div><div>The analysis of bulk adaptive immune receptor repertoires (AIRR) enables the understanding of immune responses in both normal and pathological conditions. However, the complexity of AIRR calls for advanced, specialized methods to extract meaningful biological insights. These sophisticated approaches often present challenges for researchers with limited bioinformatics expertise, hindering access to comprehensive immune system analysis. To address this challenge, we developed AnalyzAIRR, an AIRR-compliant R package enabling advanced bulk AIRR sequencing data. The tool integrates state-of-the-art statistical and visualization methods applicable at various levels of granularity. It offers a platform for general data exploration, filtering and manipulation, and in-depth cross-comparisons of AIRR datasets, aimed at answering specific biological questions. We illustrate AnalyzAIRR functionalities using a published murine dataset of 18 T-cell receptor repertoires from three diferrent T cell subsets. We first detected and removed a major contaminant in a group of samples, before proceeding with the comparative analysis. Subsequent cross-sample analysis revealed differences in repertoire diversity that aligned with the respective cell phenotypes, and in repertoire convergence among the studied subsets. AnalyzAIRR’s set of analytical metrics is integrated into a Shiny web application and complemented with a tutorial to help users in their analytical strategy, making it user-friendly for biologists with little or no background in bioinformatics.</div></div>","PeriodicalId":73343,"journal":{"name":"Immunoinformatics (Amsterdam, Netherlands)","volume":"19 ","pages":"Article 100052"},"PeriodicalIF":0.0,"publicationDate":"2025-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144523416","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Corrigendum to “T-cell receptor binding prediction: A machine learning revolution” [ImmunoInformatics, Volume 15, September 2024, 100040] “t细胞受体结合预测：机器学习革命”的更正[免疫信息学，第15卷，2024年9月，100040]

Immunoinformatics (Amsterdam, Netherlands) Pub Date : 2025-06-01 DOI: 10.1016/j.immuno.2025.100049

Prof. María Rodríguez Martínez

引用次数: 0

Molecular mimicry impact of the COVID-19 pandemic: Sequence homology between SARS-CoV-2 and autoimmune diseases epitopes COVID-19大流行的分子模拟影响：SARS-CoV-2与自身免疫性疾病表位的序列同源性

Immunoinformatics (Amsterdam, Netherlands) Pub Date : 2025-03-13 DOI: 10.1016/j.immuno.2025.100050

Pablo Maldonado-Catala , Ram Gouripeddi , Naomi Schlesinger , Julio C. Facelli

引用次数: 0