ImmunogeneticsPub Date : 2025-03-31DOI: 10.1007/s00251-025-01376-w
Alessia Rota, Ana Veríssimo, Arnaud Gaigher
{"title":"Allele co-segregation and haplotype diversity of MHC IIβ genes in the small-spotted catshark Scyliorhinus canicula.","authors":"Alessia Rota, Ana Veríssimo, Arnaud Gaigher","doi":"10.1007/s00251-025-01376-w","DOIUrl":"10.1007/s00251-025-01376-w","url":null,"abstract":"<p><p>The major histocompatibility complex (MHC) constitutes a functionally relevant multigene family playing an essential role in the adaptive immune responses of jawed vertebrates, being directly involved in pathogen recognition. MHC diversity, driven by pathogen-mediated selection, is vital for species survival and is characterized by high genetic diversity in many taxa, namely at the sequence, allelic and haplotype levels. Chondrichthyans, the most basal jawed vertebrates with an adaptive immune system, exhibit a high diversity of MHC gene lineages conservatively organized in a compact region of the genome. Such genomic architecture suggests linkage among MHC genes, where alleles from different genes possibly co-segregate together. Such condition may have major implications on immune response, individual fitness and evolution. In this study, we examine MHC IIβ haplotype diversity in a model shark species, the small spotted catshark, Scyliorhinus canicula. Making use of pedigree data, we reconstructed MHC IIβ haplotypes to understand allele transmission from parent to offspring. Results indicate allele co-segregation consistent with tight linkage among MHC IIβ genes, suggesting the presence of functional stable haplotypes inherited from parents to offspring. The reconstructed haplotypes suggested extensive haplotype diversity characterized by variable allele numbers and allelic lineage composition, as well as marked allelic divergence, consistent with previous population-level data on this species. These findings underscore the complexity of MHC genetics (and of MHC evolution) in chondrichthyans. Accurate reconstruction of MHC haplotypes and assessment of its functional significance are crucial for better understanding adaptive immune responses and MHC evolutionary dynamics in chondrichthyans.</p>","PeriodicalId":13446,"journal":{"name":"Immunogenetics","volume":"77 1","pages":"19"},"PeriodicalIF":2.9,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11958417/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143752487","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Phylogenetic and structural insights into the origin of C-type lectin Mincle in vertebrates.","authors":"Taiki Ito, Carla Guenther, Eri Ishikawa, Takae Yabuki, Masamichi Nagae, Yoichiro Nakatani, Sho Yamasaki","doi":"10.1007/s00251-025-01375-x","DOIUrl":"10.1007/s00251-025-01375-x","url":null,"abstract":"<p><p>Our bodies are continuously exposed to injurious insults by infection and tissue damage, which are primarily sensed by innate immune receptors to maintain homeostasis. Among such receptors is macrophage-inducible C-type lectin (Mincle, gene symbol CLEC4E), a member of the C-type lectin receptor (CLR) family, which functions as an immune sensor for both pathogens and damaged self. To monitor these injurious stimuli, Mincle recognizes disaccharide-based pathogen-derived glycolipids and monosaccharide-based intracellular metabolites, such as β-glucosylceramide. Mincle is well-conserved among mammals; however, there are questions that remain unclear, such as from which lower vertebrate did it arise and whether the original ligand was self or non-self. Here, we found homologues of Mincle and its signaling subunit Fc receptor γ chain (FcRγ) in lower vertebrates, such as reptiles, amphibians, and fishes. The crystal structure of a Mincle homologue revealed that fish Mincle possesses a narrower sugar-binding pocket than that of mammalian Mincle, and accommodates only monosaccharide moieties. These results suggest that Mincle may have evolved from a self-recognizing receptor, and its sugar-binding pocket widened during evolution, presumably to adapt to disaccharide-based glycolipids derived from life-threatening pathogens.</p>","PeriodicalId":13446,"journal":{"name":"Immunogenetics","volume":"77 1","pages":"18"},"PeriodicalIF":2.9,"publicationDate":"2025-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11929736/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143691984","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ImmunogeneticsPub Date : 2025-02-28DOI: 10.1007/s00251-025-01374-y
Berkay Tokcan, Esra Nur Demirtaş, Selçuk Sözer
{"title":"Suppressed activation of the IRF7 and TLR9 by JAK2V617F gold nanoparticles.","authors":"Berkay Tokcan, Esra Nur Demirtaş, Selçuk Sözer","doi":"10.1007/s00251-025-01374-y","DOIUrl":"10.1007/s00251-025-01374-y","url":null,"abstract":"<p><p>Philadelphia chromosome-negative myeloproliferative neoplasms (Ph-MPNs) are characterized by the overproduction of myeloid cells and a lack of response to cytokine signaling, along with genomic instability and the accumulation of nucleic acids in the cytoplasm. In this study, we investigated the effects of oligonucleotide-gold nanoparticle conjugates (ON-GNPs) targeting JAK2 or JAK2V617F mRNAs on nucleic acid-sensing pathways in HEL, SET2, and K562 cell lines. We evaluated changes in gene expression related to TLR9 and cGAS/STING pathways, RAGE/TLR9 receptor dynamics, and inflammatory cytokine release over short-term (0.5-2 h) and long-term (24-72 h) exposures. Our results demonstrated that ON-GNPs transiently suppressed TLR9, IRF7, and NFKB1 expression during the short term, followed by significant upregulation after 24 h, persisting up to 72 h. Notably, JAK2V617F-targeting ON-GNPs induced heightened IRF7 activation in HEL and SET2 cells after 24 h without affecting TLR9/RAGE expression. Additionally, IL-8 secretion increased in HEL and SET2 culture media after 72 h, correlating with interferon pathway activation. This study reveals that complementary ON-GNPs can modulate nucleic acid-sensing pathways, suppressing IL-8 and inflammatory signaling in the short term while inducing delayed activation of TLR9 and IRF7 in the presence of JAK2V617F. These findings provide a promising foundation for developing ON-GNP-based therapeutic strategies to manage inflammation and disease progression in Ph-MPNs.</p>","PeriodicalId":13446,"journal":{"name":"Immunogenetics","volume":"77 1","pages":"16"},"PeriodicalIF":2.9,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11868351/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143523327","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ImmunogeneticsPub Date : 2025-02-13DOI: 10.1007/s00251-025-01372-0
Rebecca A Clemons, Chase H Smith, Kelly R Zamudio
{"title":"Primary regulatory T cell activator FOXP3 is present across Amphibia.","authors":"Rebecca A Clemons, Chase H Smith, Kelly R Zamudio","doi":"10.1007/s00251-025-01372-0","DOIUrl":"10.1007/s00251-025-01372-0","url":null,"abstract":"<p><p>The overall structure of the immune system is highly conserved across jawed vertebrates, but characterization and description of the immune system is heavily biased toward mammals. One arm of the vertebrate immune system, the adaptive immune system, mounts pathogen-specific responses that tend to be robust and effective at clearing pathogens. This system requires selection against self-recognition and modulation of the immune response. One of the mechanisms of immune modulation is the presence of regulatory T cells that suppress other effector immune cells. Regulatory T cells and their primary activator forkhead box protein P3 (FOXP3) have been well characterized in mammalian models but unexplored in most other vertebrate taxa. Amphibians are a good focal group for the characterization of FOXP3 due to their phylogenetic position on the vertebrate tree of life, and their susceptibility to emerging pathogens. In this study, we mined available transcriptomic and genomic data to confirm the presence of FOXP3 across the amphibian tree of life. We find that FOXP3 is present in all major clades of amphibians. We also test whether selection on FOXP3 shows signatures of intensification among the three main clades of amphibians, which may reflect shifts in the stringency of natural selection on this gene. Our findings provide insights into the evolutionary history of the vertebrate immune system and confirm the conservation of vertebrate immune genes within amphibians.</p>","PeriodicalId":13446,"journal":{"name":"Immunogenetics","volume":"77 1","pages":"15"},"PeriodicalIF":2.9,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143407037","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ImmunogeneticsPub Date : 2025-02-05DOI: 10.1007/s00251-025-01371-1
Cassandra R Woolley, Julia H Chariker, Eric C Rouchka, Easton E Ford, Elizabeth Hudson, Kamille M Rasche, Caleb S Whitley, Zachary Vanwinkle, Carolyn R Casella, Melissa L Smith, Thomas C Mitchell
{"title":"Full-length mRNA sequencing resolves novel variation in 5' UTR length for genes expressed during human CD4 T-cell activation.","authors":"Cassandra R Woolley, Julia H Chariker, Eric C Rouchka, Easton E Ford, Elizabeth Hudson, Kamille M Rasche, Caleb S Whitley, Zachary Vanwinkle, Carolyn R Casella, Melissa L Smith, Thomas C Mitchell","doi":"10.1007/s00251-025-01371-1","DOIUrl":"10.1007/s00251-025-01371-1","url":null,"abstract":"<p><p>Isoform sequencing (Iso-Seq) uses long-read technology to produce highly accurate full-length reads of mRNA transcripts. Visualization of individual mRNA molecules can reveal new details of transcript variation within understudied portions of mRNA, such as the 5' untranslated region (UTR). Differential 5' UTRs may contain motifs, upstream open reading frames (uORFs), and secondary structures that can serve to regulate translation or further indicate changes in promoter usage, where transcriptional control may impact protein expression levels. To begin to explore isoform variation during T-cell activation, we generated the first Iso-Seq reference transcriptome of activated human CD4 T cells. Within this dataset, we discovered many novel splice- and end-variant transcripts. Remarkably, one in every eight genes expressed in our dataset was found to have a notable proportion of transcripts with 5' UTR lengthened by over 100 bp compared to the longest corresponding UTR within the Gencode dataset. Among these end-variant transcripts, two novel isoforms were identified for CXCR5, a chemokine receptor associated with T follicular helper cell (Tfh) function and differentiation. When investigated in a model cell system, these lengthened UTR conferred reduced transcript stability and, for one of these isoforms, short uORFs introduced by the added length altered protein expression kinetics. This study highlights instances in which current reference databases are incomplete relative to the information obtained by long-read sequencing of intact mRNA. Iso-Seq is thus a promising approach to better understanding the plasticity of promoter usage, alternative splicing, and UTR sequences that influence RNA stability and translation efficiency.</p>","PeriodicalId":13446,"journal":{"name":"Immunogenetics","volume":"77 1","pages":"14"},"PeriodicalIF":2.9,"publicationDate":"2025-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11794378/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143188960","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ImmunogeneticsPub Date : 2025-01-31DOI: 10.1007/s00251-025-01370-2
Laura Cardoso Corrêa-Dias, Ágata Lopes-Ribeiro, Geovane Marques-Ferreira, Letícia Gomes-de-Pontes, Thaiza Aline Pereira-Santos, Erik Vinicius de Sousa Reis, Thaís de Fátima Silva Moraes, Olindo Assis Martins-Filho, Edel Figueiredo Barbosa-Stancioli, Flávio Guimarães da Fonseca, Jordana Grazziela Coelho-Dos-Reis
{"title":"HCV immunodominant peptide mapping reveals unique HLA-A*02-restricted signatures: insights for CD8<sup>+</sup> T-cell-based vaccines and immunotherapies.","authors":"Laura Cardoso Corrêa-Dias, Ágata Lopes-Ribeiro, Geovane Marques-Ferreira, Letícia Gomes-de-Pontes, Thaiza Aline Pereira-Santos, Erik Vinicius de Sousa Reis, Thaís de Fátima Silva Moraes, Olindo Assis Martins-Filho, Edel Figueiredo Barbosa-Stancioli, Flávio Guimarães da Fonseca, Jordana Grazziela Coelho-Dos-Reis","doi":"10.1007/s00251-025-01370-2","DOIUrl":"10.1007/s00251-025-01370-2","url":null,"abstract":"<p><p>Several barriers for the development of an HCV vaccine still exist, including the genetic diversity of the virus, and the shortage of assessable models for in vitro and in vivo assays. Therefore, in this study, HCV epitope mapping was performed for 59 polyprotein sequences from 7 HCV genotypes. Around 2,880 peptides were considered epitopes for CD8<sup>+</sup> T cells. The peptide induction of cytokines from Th1 and/or Th2 axes of the cellular immune response was assessed, indicating a tendency for Th2 axis. In vitro evaluation was performed using peptide microarray and a recombinant HLA-A*02:01 molecule. A total of 615 peptides of high reactivity to HLA-A*02:01 were identified, with predominance of leucine and tryptophan residues, highlighting their importance for TCR-epitope binding and CD8<sup>+</sup> T activation. Finally, HCV-derived peptide patterns restricted to HLA-A2*02:01 observed in this study provide important information for the development of a multi-epitope-based pan-genotypic vaccine against the virus.</p>","PeriodicalId":13446,"journal":{"name":"Immunogenetics","volume":"77 1","pages":"13"},"PeriodicalIF":2.9,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143074305","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ImmunogeneticsPub Date : 2025-01-17DOI: 10.1007/s00251-024-01369-1
Griffin Kutler Dodd, Can Keşmir
{"title":"In silico functional analysis of the human, chimpanzee, and gorilla MHC-A repertoires.","authors":"Griffin Kutler Dodd, Can Keşmir","doi":"10.1007/s00251-024-01369-1","DOIUrl":"10.1007/s00251-024-01369-1","url":null,"abstract":"<p><p>T cells recognize peptides displayed on the surface of cells on MHC molecules. Genetic variation in MHC genes alters their peptide-binding repertoire and thus influences the potential immune response generated against pathogens. Both gorillas and chimpanzees show reduced diversity at their MHC class I A (MHC-A) locus compared to humans, which has been suggested to be the result of a pathogen-mediated selective sweep. More specifically, gorillas lack A3 lineage alleles while chimpanzees seem to have lost the A2 lineage. While previous studies showed this using phylogenetic analysis, here, we take an in silico functional approach and use the peptide-MHC binding prediction software NetMHCpan to examine the peptide-binding repertoires of common human, chimpanzee, and gorilla MHC-A molecules. We find that both gorillas and chimpanzees lack the A02 peptide binding specificity (supertype) despite gorillas being expected to have this specificity since they kept the A2 lineage. Additionally, we show that human MHC molecules with the A02 specificity bind fewer virus-derived peptides than other MHC molecules. We also do not find differential presentation of self-peptides by the A02 supertype, making the purpose of maintaining this specificity in high frequencies in the human population unclear. Taken together, we hypothesize that poor presentation of viral peptides by A02 supertype MHC molecules could have resulted in a selective sweep in chimpanzees and/or gorillas, though we could not identify a specific virus that may have caused this sweep.</p>","PeriodicalId":13446,"journal":{"name":"Immunogenetics","volume":"77 1","pages":"12"},"PeriodicalIF":2.9,"publicationDate":"2025-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11741996/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143004617","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ImmunogeneticsPub Date : 2025-01-08DOI: 10.1007/s00251-024-01368-2
Cleopatra Petrohilos, Emma Peel, Luke W Silver, Katherine Belov, Carolyn J Hogg
{"title":"AMPed up immunity: 418 whole genomes reveal intraspecific diversity of koala antimicrobial peptides.","authors":"Cleopatra Petrohilos, Emma Peel, Luke W Silver, Katherine Belov, Carolyn J Hogg","doi":"10.1007/s00251-024-01368-2","DOIUrl":"10.1007/s00251-024-01368-2","url":null,"abstract":"<p><p>Characterising functional diversity is a vital element to understanding a species' immune function, yet many immunogenetic studies in non-model organisms tend to focus on only one or two gene families such as the major histocompatibility complex (MHC) or toll-like receptors (TLR). Another interesting component of the eukaryotic innate immune system is the antimicrobial peptides (AMPs). The two major groups of mammalian AMPs are cathelicidins and defensins, with the former having undergone species-specific expansions in marsupials. Here, we utilised data from 418 koala whole genomes to undertake the first comprehensive analysis of AMP diversity across a mammalian wildlife species' range. Overall, allelic diversity was lower than other immune gene families such as MHC, suggesting that AMPs are more conserved, although balancing selection was observed in PhciDEFB12. Some non-synonymous SNPs in the active peptide are predicted to change AMP function through stop gains, change in structure, and increase in peptide charge. Copy number variants (CNVs) were observed in two defensins and one cathelicidin. Interestingly, the most common CNV was the duplication of PhciCATH5, a cathelicidin with activity against chlamydia, which was more common in the southern part of the species range than the north. AMP copy number is correlated with expression levels, so we hypothesise that there is a selective pressure from chlamydia for duplications in PhciCATH5. Future studies should use phenotypic metadata to assess the functional impacts of this gene duplication.</p>","PeriodicalId":13446,"journal":{"name":"Immunogenetics","volume":"77 1","pages":"11"},"PeriodicalIF":2.9,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11711154/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142948212","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ImmunogeneticsPub Date : 2025-01-07DOI: 10.1007/s00251-024-01367-3
Edgar G Gutierrez, Jorge Ortega
{"title":"Uncovering selection pressures on the IRF gene family in bats' immune system.","authors":"Edgar G Gutierrez, Jorge Ortega","doi":"10.1007/s00251-024-01367-3","DOIUrl":"10.1007/s00251-024-01367-3","url":null,"abstract":"<p><p>Unlike other mammals, bats serve as natural reservoirs for several highly pathogenic viruses without exhibiting symptoms of infection. Recent research has explored the complex mechanisms underlying the balance between bats' antiviral defenses and their pathological responses. However, the evolution of the molecular drivers behind bats' antiviral strategies remains largely unknown. Interferon regulatory factors (IRFs) are essential transcription factors that bind to DNA and regulate the expression of numerous genes involved in antiviral defense, inflammation, immune cell differentiation, apoptosis, and oncogenesis. Our research focused on members of the IRF family, using 17 bat species and four terrestrial mammals available in GenBank. We employed CodeML to detect signs of positive selection through three different models. Statistically significant results were obtained for the IRF-1, IRF-4, IRF-5, IRF-6, and IRF-9 genes, which are known to play pivotal roles in various regulation mechanisms. Specifically, IRF-4 and IRF-5 are key in modulating the inflammatory response, while IRF-1 is essential for antiviral defense in bats, and IRF-9 regulates genes activated by type I interferon. Although the role of IRF-6 in these mechanisms requires further investigation in bats, all these genes show signs of positive selection, suggesting an optimization of the processes they regulate. These findings highlight the adaptive role of IRF elements in enhancing, among other things, the bat immune system, potentially improving their resilience and efficacy. Our study not only provides new genetic insights into bats but also underscores the remarkable molecular evolution within this unique group of mammals.</p>","PeriodicalId":13446,"journal":{"name":"Immunogenetics","volume":"77 1","pages":"10"},"PeriodicalIF":2.9,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142948213","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}