Immunoinformatics (Amsterdam, Netherlands)最新文献

{"title":"Challenges and future directions of AIRR-seq-based diagnostics","authors":"Ulrik Stervbo ,&nbsp;Paraskevas Filippidis ,&nbsp;Felix Breden ,&nbsp;Lindsay G. Cowell ,&nbsp;Frederic Davi ,&nbsp;Victor Greiff ,&nbsp;Anton W. Langerak ,&nbsp;Eline T. Luning Prak ,&nbsp;Alexandra F. Sharland ,&nbsp;Enkelejda Miho ,&nbsp;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":"2025-09-01","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}

{"title":"AnalyzAIRR: A user-friendly guided workflow for AIRR data analysis","authors":"Vanessa Mhanna ,&nbsp;Gabriel Pires ,&nbsp;Grégoire Bohl-Viallefond ,&nbsp;Karim El Soufi ,&nbsp;Nicolas Tchitchek ,&nbsp;David Klatzmann ,&nbsp;Adrien Six ,&nbsp;Hang P. Pham ,&nbsp;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":"2025-09-01","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}

{"title":"Challenges for the immunoglobulin and T cell receptor gene nomenclatures in the modern genomics era","authors":"Andrew M. Collins ,&nbsp;Corey T. Watson ,&nbsp;Henk-Jan van den Ham ,&nbsp;Luc Teyton ,&nbsp;Elisa Rosati ,&nbsp;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":"2025-09-01","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}

{"title":"Building immunoglobulin and T cell receptor gene databases for the future","authors":"Corey T. Watson ,&nbsp;Andrew M. Collins ,&nbsp;Mats Ohlin ,&nbsp;James M. Heather ,&nbsp;Ayelet Peres ,&nbsp;William D. Lees ,&nbsp;Gur Yaari","doi":"10.1016/j.immuno.2025.100059","DOIUrl":"10.1016/j.immuno.2025.100059","url":null,"abstract":"<div><div>Genetic databases for immunoglobulin (IG) and T cell receptor (TR) genes have evolved from small catalogs to critical resources underpinning immunogenetic research. Accurate annotation enables the analysis of repertoire diversity, somatic hypermutation, clonal relationships, and lineage development. Recent advances in high-throughput repertoire sequencing and long-read genomics now allow for unprecedented discovery of germline variation across populations and species, but they also expose limitations of existing resources. Here, we discuss the historical evolution of IG/TR databases, highlight the challenges and opportunities presented by changing data landscapes, and outline strategies for building future databases that integrate genomic and expression data, support population diversity, and align with evolving nomenclature frameworks. Enhanced germline resources will be essential for accurate annotation, reproducible research, and the next generation of immunological discovery and clinical translation.</div></div>","PeriodicalId":73343,"journal":{"name":"Immunoinformatics (Amsterdam, Netherlands)","volume":"19 ","pages":"Article 100059"},"PeriodicalIF":0.0,"publicationDate":"2025-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144913119","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}

{"title":"Is the vaccination-induced B cell receptor repertoire predictable?","authors":"Eve Richardson ,&nbsp;Lisa Willemsen ,&nbsp;Pramod Shinde ,&nbsp;Morten Nielsen ,&nbsp;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}

{"title":"Corrigendum to “T-cell receptor binding prediction: A machine learning revolution” [ImmunoInformatics, Volume 15, September 2024, 100040]","authors":"Prof. María Rodríguez Martínez","doi":"10.1016/j.immuno.2025.100049","DOIUrl":"10.1016/j.immuno.2025.100049","url":null,"abstract":"","PeriodicalId":73343,"journal":{"name":"Immunoinformatics (Amsterdam, Netherlands)","volume":"18 ","pages":"Article 100049"},"PeriodicalIF":0.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144279474","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}

{"title":"Molecular mimicry impact of the COVID-19 pandemic: Sequence homology between SARS-CoV-2 and autoimmune diseases epitopes","authors":"Pablo Maldonado-Catala ,&nbsp;Ram Gouripeddi ,&nbsp;Naomi Schlesinger ,&nbsp;Julio C. Facelli","doi":"10.1016/j.immuno.2025.100050","DOIUrl":"10.1016/j.immuno.2025.100050","url":null,"abstract":"<div><div>Molecular mimicry is one mechanism by which an infectious agent may trigger an autoimmune disease in a human subject and occurs when foreign- and self-peptides contain similar epitopes that activate an autoimmune response in a susceptible individual. Here, we employ a scalable in-silico approach, to identify 861 pairs of known SARS-CoV-2 and autoimmune disease epitopes, out of more than one billion possible pairs. These SARS-CoV-2 epitopes show 1) sequence homology to human autoimmune disorder epitopes, 2) empirical binding data that predict that they bind the same major histocompatibility complex (MHC) molecule and 3) exhibit high empirical immunogenicity. Analysis of these epitope pairs reveals an association between autoimmune disorders, such as type 1 diabetes, autoimmune uveitis, ankylosing spondylitis, and SARS-CoV-2 infection. These associations are consistent with those reported in the literature from the analysis of clinical records.</div></div>","PeriodicalId":73343,"journal":{"name":"Immunoinformatics (Amsterdam, Netherlands)","volume":"18 ","pages":"Article 100050"},"PeriodicalIF":0.0,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143642266","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deciphering the role of molecular mimicry in the etiopathogenesis of Autoimmune Hemolytic Anemia using an immunoinformatics approach.","authors":"Pratyusha Patidar ,&nbsp;Arihant Jain ,&nbsp;Tulika Prakash","doi":"10.1016/j.immuno.2025.100047","DOIUrl":"10.1016/j.immuno.2025.100047","url":null,"abstract":"<div><div>Autoimmune hemolytic anemia (AIHA) is a chronic autoimmune disease characterized by the self-destruction of red blood cells (RBCs). For investigating the role molecular mimicry in the onset of AIHA manifestations, we identified the microbial epitopes as precipitating factors in the disease etiopathology using an integrated immunoinformatics pipeline which includes sequence homology search between microbial and RBC proteins, followed by B-cell and T-cell epitope prediction. These epitopes were further subjected to a homology search with the human gut microbial proteins. Eight out of the ten analysed infectious agents, including Hepatitis C Virus (HCV), Cytomegalovirus (CMV), Epstein-Barr Virus (EBV), Herpes Simplex Virus (HSV), Human Papillomavirus (HPV), Human Immunodeficiency Virus (HIV), <em>Mycoplasma pneumoniae</em> (MP), and <em>Treponema pallidum</em> (TP), possessed B-cell and T-cell epitopes. Interestingly, EBV, HSV, MP, and TP displayed conformational B-cell epitopes, which overlapped with their linear B-cell epitopes. HLA DRB1_0305 was found to exhibit binding with several bacterial epitopes indicating its predisposing potential to AIHA. Further, we report cross-reactive microbial epitopes against RBC proteins that have been experimentally proven to be associated with AIHA indicating a high possibility of those epitopes causing AIHA. Additionally, many B-cell and T-cell epitopes exhibited exact homologies with various human gut microbial proteins. The functional annotation highlighted the involvement of specialized RBC functions, such as cytoskeleton organization, ammonium homeostasis, signalling transduction, in the underlying disease mechanism. These findings suggest that infection-causing pathogens and gut microbes might have a plausible association with AIHA in the context of molecular mimicry.</div></div>","PeriodicalId":73343,"journal":{"name":"Immunoinformatics (Amsterdam, Netherlands)","volume":"17 ","pages":"Article 100047"},"PeriodicalIF":0.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143395696","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative analysis of SLA-1 and SLA-2 genetic diversity in exotic, hybrid, and local pig breeds of Cameroon in relation to adaptive immunity against African swine virus","authors":"Ebanja Joseph Ebwanga ,&nbsp;Jess Bouhuijzen Wenger ,&nbsp;Robert Adamu Shey ,&nbsp;Nadine Buys ,&nbsp;Rob Lavigne ,&nbsp;Stephen Mbigha Ghogomu ,&nbsp;Jan Paeshuyse","doi":"10.1016/j.immuno.2025.100048","DOIUrl":"10.1016/j.immuno.2025.100048","url":null,"abstract":"<div><div>African swine fever is a severe hemorrhagic swine disease that greatly affects smallholder pig farm productivity in low-income countries as well as some developed countries. Research has shown that the indigenous pigs and wild suids in Africa are either tolerant or resistant to the disease. Also, resistance to disease and favourable production traits are attributed to polymorphism within the major histocompatibility complex (MHC), which is crucial for the vertebrate's adaptive immune response. The polymorphism within the swine leukocyte antigen (SLA) is attributable to host-pathogen co-evolution which results in improved resistance to disease as well as adaptation to diverse environments. While this makes the SLA essential for comparative diversity studies, comparative SLA studies are absent in this context. We undertook SLA-1 and SLA-2 exon-2 comparative genetic diversity study within the locally adapted (local) breed, hybrid (a cross between local and exotic), and the exotic breed of pigs in Cameroon using the polymerase chain reaction sequence-based typing method on 41 animals. Our data analyses provide evidence of positive balancing selection as well as conserved private alleles within the local breeds, the highest expected heterozygosity within the tolerant population while the exotic population had the highest number of haplotypes for both SLA-1 and SLA-2 . The results from this study contribute to our expanding knowledge of SLA genetic diversity while providing the first SLA data for the indigenous and exotic breeds of pigs in Cameroon.</div></div>","PeriodicalId":73343,"journal":{"name":"Immunoinformatics (Amsterdam, Netherlands)","volume":"17 ","pages":"Article 100048"},"PeriodicalIF":0.0,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143453878","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multicohort analysis identifies conserved transcriptional interactions between humans and Plasmodium falciparum","authors":"Bárbara Fernandes Silva ,&nbsp;Nágila Isleide Silva ,&nbsp;Pedro Felipe Loyola Souza ,&nbsp;Tiago Paiva Guimarães ,&nbsp;Luiz Gustavo Gardinassi","doi":"10.1016/j.immuno.2024.100044","DOIUrl":"10.1016/j.immuno.2024.100044","url":null,"abstract":"<div><p>Malaria is caused by <em>Plasmodium</em>, a parasite that replicates inside and ruptures erythrocytes, causing an intense inflammatory response. Advances in high-throughput sequencing technologies have enabled the simultaneous study of the gene expression in humans and <em>P. falciparum</em>. However, the high-dimensional correlational networks generated in previous studies challenge the interpretation of the underlying biology, whereas associations found in one cohort might not replicate in independent samples due confounding factors affecting gene expression. We combined multicohort analysis of correlations with a hierarchical grouping approach to improve the discovery and interpretation of transcriptional associations between humans and <em>P. falciparum</em>. We analyzed nine public dual-transcriptomes acquired from whole blood of individuals infected with <em>P. falciparum</em>. Blood Transcription Modules (BTM) were used to reduce the dimension of host transcriptomes and Spearman's correlation analysis was used to identify host-parasite associations. Following, we performed meta-analysis of correlations with Stouffer's method and Bonferroni correction that resulted in a major transcriptional meta-network between humans and <em>P. falciparum</em>. We identified, for example, positive correlations between <em>PAK1, NFKBIA, BIRC2, NLRC4, TLR4, RIPK2</em> expression and <em>PF3D7_1205800</em>, a putative <em>P. falciparum</em> high mobility group protein B3 (HMGB3). We also applied a leave-one-out strategy to prevent influence of confounding factors, resulting in highly conserved associations between host genes related to inflammation, immune cells, and glycerophospholipid metabolism with <em>PF3D7_1223400</em>, which encodes a putative phospholipid-transporting ATPase. Paired metabolomics and transcriptomics data revealed negative correlation between <em>PF3D7_1223400</em> expression and the relative abundance of 1-linoleoyl-GPG. Collectively, our study provides data-driven hypotheses about molecular mechanisms of host-parasite interaction.</p></div>","PeriodicalId":73343,"journal":{"name":"Immunoinformatics (Amsterdam, Netherlands)","volume":"16 ","pages":"Article 100044"},"PeriodicalIF":0.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2667119024000144/pdfft?md5=0bb5fec5def6b5a092876014fea42924&pid=1-s2.0-S2667119024000144-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142274294","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}