Urochordates, the closest relatives of vertebrates, lack adaptive immunity. However, some taxa, such as the colonial species Botryllus schlosseri, provide a unique model for studying innate self/non-self recognition through natural allogeneic transplantation responses. In this species, interactions between colonies are controlled by a highly polymorphic locus, with the Botryllus histocompatibility factor (BHF) being the only gene known to predict tissue fusion or rejection outcomes with complete accuracy. Here, we analyzed full-length BHF alleles from 19 laboratory-born and wild colonies and found that highly divergent alleles tend to coexist within individuals, whereas identical alleles can be shared across continental-scale distances. Despite extensive length variation, evidence of intragenic recombination, and pronounced nucleotide diversity, BHF exhibits limited protein divergence, with 33 alleles encoding only 17 distinct protein variants. Contrary to expectations for polymorphic recognition genes, no evidence of balancing or directional selection was detected. Instead, signatures of purifying selection were observed. We propose that this contrast between nucleotide and protein diversity arises from the combined effects of recombination, human-mediated gene flow, and linkage to nearby loci under balancing selection, while functional constraints maintain protein stability. These findings suggest that extensive protein diversification may not be a universal driver of allorecognition gene evolution.

The adaptive immune receptor repertoire (AIRR) - the collection of an individual's B-cell and T-cell receptors (BCRs and TCRs, respectively) - encodes cumulative immune history and is shaped by both germline genetics and environmental exposures. Skewed repertoires have been linked to infections, vaccination responses and autoimmune diseases such as celiac disease (CeD) where biased usage of immunoglobulin and T-cell receptor genes reactive to disease relevant antigens has been reported. Motivated by evidence that germline variation, notably human leukocyte antigen (HLA), influences naïve AIRRs and by prior machine-learning studies that classified CeD using naïve BCR AIRR-sequencing (AIRR-seq) data, we applied machine learning analysis to naïve CD4[+] TCR and naïve BCR AIRR-seq repertoires to test whether repertoire features can distinguish subjects with CeD from controls and to identify drivers of such classification. Naïve CD4[+] TCR repertoires yielded moderate diagnosis classification, but this signal was largely explained by enrichment of the HLA-DQ2.5 allotype. TCR variable gene frequencies predicted HLA-DQ2.5 status with high accuracy and controlling for HLA-DQ2.5 abolished TCR-based diagnosis classification. In contrast, naïve BCR repertoires could not be used to classify CeD. Overall, our findings show that germline HLA variation significantly affects naïve TCR composition and thereby indirectly facilitates moderately successful CeD status classification.

Immunosenescence is a complex biological process characterized by progressive remodeling of immune function during aging, leading to increased susceptibility to infections, chronic inflammatory diseases, cancer, and reduced vaccine efficacy. While cumulative antigen exposure, infections, lifestyle factors, environmental exposures, and epigenetic influences contribute to immune decline, a growing body of evidence suggests that genetic predisposition also plays an important modulatory role in shaping the molecular trajectory of immune aging. This review discusses how inherited variation in cytokine-regulatory pathways may influence IL-6, TNF-α, interferon, and TGF-β signaling, thereby contributing to inflammatory set points that favor chronic immune activation and inflammaging. Inherited differences in innate and adaptive immune signaling, including KIR-HLA interactions, DNA-sensing pathways, and downstream JAK-STAT and NF-κB cascades, may alter activation thresholds and immune-cell differentiation. Variants affecting mitochondrial redox balance and autophagy may enhance reactive oxygen species accumulation and metabolic exhaustion, thereby potentially contributing to immune-cell senescence. Genetic factors affecting folate metabolism, epigenetics, telomeres, and DNA repair drive epigenetic drift, cellular aging, and clonal instability in immune cells. These mechanisms appear as measurable molecular and cellular biomarkers, including inflammatory signals, immune cell activation, oxidative stress, telomere shortening, and multi-omic indicators. Understanding this molecular architecture provides a foundation for identifying predictive biomarkers and developing precision strategies to preserve immune competence and promote healthy aging.

Breast cancer (BC) is closely linked to coronary heart disease (CHD), yet the genetic causal relationship and common driving mechanism between the two have not been fully elucidated. The purpose of this study is to infer the causal relationship between BC and CHD at the genetic level and identify the cross-omic molecular characteristics of them through the integrated analysis of multiple genomics. Firstly, large-scale Genome Wide Association Study (GWAS) data were used for bidirectional Mendelian randomization (MR) analysis. Secondly, multi-center transcriptome data were integrated and combined with differential expression analysis (DEGs) and weighted gene co-expression network analysis (WGCNA) to screen for key comorbidity genes. Univariate, Least Absolute Shrinkage and Selection Operator (LASSO), and multivariate Cox regression analyses were used to construct a prognostic model. The Benjamin Hochberg method was used for False Discovery Rate (FDR) correction. Finally, molecular pathways were explored through Gene Set Enrichment Analysis (GSEA), and key genes were validated using quantitative real-time polymerase chain reaction (qRT-PCR) in independent clinical samples. MR analysis revealed a significant positive correlation between BC and CHD in Asian populations (OR = 1.095, 95% CI: 1.005-1.192, P = 0.037). However, no significant association was observed in European populations. Transcriptome analysis identified a prognostic risk score composed of 5 CHD-related genes (HES1, MLPH, TRIB3, HSPBP1, and STARD3), which can independently predict the prognosis of BC patients. GSEA analysis indicated that the comorbidity mechanism involved dysregulation of cell cycle, immune inflammation, and metabolism-related pathways. qRT-PCR verification confirmed that compared with patients with BC, the expression levels of HES1, TRIB3, HSPBP1, and STARD3 in the peripheral blood of BC combined with CHD patients were significantly upregulated (P < 0.05). This study established for the first time the genetic causal relationship between BC and CHD in Asian populations, and revealed the inflammation-immune-metabolism molecular axis mediating comorbidities. The identified key genes not only serve as biomarkers for BC prognosis, but also provide a new perspective for understanding the pathological mechanisms and precise diagnosis and treatment of tumor cardiovascular comorbidities.

ObjectiveAutoimmune and autoinflammatory diseases (AIDs) represent a heterogeneous group of immune-mediated disorders characterized by dysregulated innate and adaptive immune responses. This study aimed to investigate the immunogenetic background of AIDS by assessing the distribution of genetic variants identified by a targeted next-generation sequencing (NGS) panel and elucidating genotype-phenotype correlations in the context of systemic immune dysregulation.Materials and methodsA targeted NGS panel encompassing 19 genes involved in immune regulation, inflammatory signaling pathways, and immune tolerance was utilized to evaluate a cohort of 110 patients presenting with clinical manifestations suggestive of autoinflammatory disease. Clinical severity was quantitatively assessed using longitudinal serum C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR) measurements across acute and baseline periods. Detected variants were classified according to the American College of Medical Genetics and Genomics (ACMG) guidelines and correlated with patient clinical phenotypes and established immunogenetic literature.ResultsA total of 55 genetic variants were identified across 41 patients. Alterations predominantly clustered in MEFV (38.2%), HFE (29.1%), and SLC29A3 (21.8%), followed by NOD2, MVK, CARD14, IL10RB, and PLCG2 (1.8% each). According to ACMG criteria, 61.8% of the variants were pathogenic, 25.5% were likely pathogenic, and 12.7% were VUS. Genotype-phenotype correlation analyses successfully linked rare variants (including PLCG2, IL10RB, and CARD14) and oligogenic combinations to specific laboratory profiles. These findings revealed unexpected penetrance, variable expressivity, and distinct biomarker disassociations, most notably highlighted by isolated ESR elevations reaching 91 mm/h.ConclusionOur findings underscore the immunogenetic heterogeneity of autoinflammatory diseases and substantiate the diagnostic value of NGS-based profiling in deciphering complex genotype-phenotype associations. The integration of specific quantitative biomarkers and downstream mechanisms highlights how non-HLA regulatory variants reshape the chronic inflammatory immune microenvironment, lowering the threshold for inflammasome activation and systemic autoimmunity.

Cytokines are crucial in regulating hypertension and vascular inflammation. The clinical significance of circulating IL-36γ levels and IL36G gene variants in relation to essential hypertension risk was assessed because IL-36γ has been associated with several cardiovascular diseases, while its role in essential hypertension is still unknown. Serum IL-36γ levels were determined by enzyme-linked immunosorbent assay, while IL36G polymorphisms were assessed by PCR-RFLP method in 264 patients with essential hypertension and 264 normotensive controls. Patients showed significantly elevated serum IL-36γ levels (p < 0.0001) when compared with the controls. Significant association between IL36G rs11690399 and rs11683399 polymorphisms and essential hypertension susceptibility were found through genotyping analysis, with combination genotypes (GT + TT) and (TG + GG) conferring an elevated risk of a disease. A 2.6-fold and a 1.9-fold increased risk of essential hypertension was observed to the T allele of rs11690399 and the G allele of rs11683399, respectively. Significantly higher levels of IL-36γ were associated with variant genotypes, suggesting a genotype-phenotype correlation. T-T and T-G were found to be a risk haplotype for essential hypertension by haplotype analysis. A causal relationship between increased IL-36γ and the risk of hypertension was shown by Mendelian randomization (OR = 1.0066; 95% CI: 1.0028-1.0104, p < 0.0001). A diagnostic performance for IL-36γ (AUC = 0.862) was found by ROC analysis, indicating its potential as a clinical biomarker. In conclusion, there is a significant association between essential hypertension and higher IL-36γ levels and IL36G polymorphisms. These results suggest that elevated circulatory IL-36γ may play a role in the pathophysiology of essential hypertension.

Defensins are key innate immune proteins exhibiting pleiotropic functions such as antibacterial activity, antiviral activity, anti-inflammatory activity, immunomodulatory functions, and roles in reproduction. Genomic information inadequately explains the whole gamut of the landscape of β-defensin in Bubalus bubalis and Ovis aries genomes. This study investigates the sequence evaluation and evolutionary relationships of β-defensin with 131 complete sequences in buffalo, sheep, and human. Sequence and domain-based analyses revealed diverse patterns of disulfide bridges and multiple signature patterns, including N- and O-glycosylation sites, N-myristoylation sites, and protein kinase C phosphorylation sites, indicating extensive post-translational regulation involved in various antimicrobial activities, signaling pathways, and reproduction. Phyre2-based 3D structural modeling, followed by PyMOL visualization, revealed β-strands stabilized by cysteine disulfide bonds and a short N-terminal α-helix. Variation analysis of β-defensin sequences identified unique allelic variants with several conserved amino acid positions. All sequences shared the characteristic six conserved cysteine residues, along with conserved glycine (G) in the GXC motif and glutamic acid (E), which contribute to structural stability and proper protein folding. We report sixteen amino acid sites depicting 9 distinct types of mutations within the cysteine residues, with most frequent substitutions of C→S (5/16) and C→P (3/16) amino acids. Phylogenetic and domain-based analyses across humans, sheep, and buffalo revealed eight major clusters, of which cluster I was found to be most diverse (36/131). Altogether, we provide a comprehensive analysis of β-defensin protein sequences revealing conserved features, functional motifs, and evolutionary relationships underpinning the functional role of β-defensins.

TAPBP is a key chaperone of the peptide-loading complex that facilitates peptide loading onto major histocompatibility complex class I (MHC I) molecules. This study characterized TAPBP alleles in Korean Native Chickens (KNCs), identified novel variants, and evaluated allelic associations with BF2. Thirty-six samples representing six KNC lines were genotyped using LEI0258 and the MHC-B SNP panel, and individuals homozygous at both markers were classified into 16 groups. The same samples were subjected to Sanger sequencing of TAPBP exons 3-8. Sequences were assembled and aligned against MHC-B reference alleles of the TAPBP gene and the Red Junglefowl reference. Additional comparisons with "tapasin allele" datasets enabled the identification of novel variants. Six novel nucleotide variants were detected across exons 3-6, including one nonsynonymous substitution in exon 4 (D251H). This residue corresponds to position Q265 in human TAPBP and lies adjacent to residues involved in MHC I interaction, suggesting potential functional relevance. Furthermore, TAPBP exhibited high haplotype diversity (Hd = 0.93) and moderate nucleotide diversity (π = 0.00892), with exon 5 showing the highest diversity (π = 0.01). B9 was the most frequent allele at the nucleotide level, whereas B6/B24 predominated at the amino acid level. Comparison with BF2 data revealed allele-dependent pairing patterns: BF2-B9 consistently matched TAPBP-B9, whereas BF2-B6 was associated with distinct TAPBP nucleotide variants, indicating allelic diversification. Homozygosity at LEI0258 and the SNP panel corresponded with TAPBP homozygosity, supporting marker-based prediction. These findings highlight potential BF2-TAPBP associations and provide a foundation for understanding variation in MHC I peptide loading.

The evolutionary relationship between amphibian IgM, IgY, and IgX/A-like antibodies has remained difficult to resolve, largely because repetitive heavy-chain loci are often incompletely or inconsistently annotated. In this study, I re-analyzed reconstructed four-domain heavy-chain constant regions from amphibian loci to test whether the evolution of IgXA is better explained by uniform divergence or by a mosaic history involving partial exon replacement. The reconstructed dataset comprised 86 complete antibodies from 29 species (29 IgM, 33 IgY, and 24 IgXA). Exact nucleotide matching against the reconstructed exon set yielded 79 antibodies, allowing the identification of 21 strictly microsyntenic species-level IgM/IgY/IgXA trios for recombination analyses. Domain alignments, Poisson-corrected amino-acid distances, and UMAP embeddings revealed a clear structural transition: IgXA clustered closer to IgY in CH1 and CH2, remained nearly intermediate in CH3, and shifted decisively toward IgM in CH4. Mean inter-class distances (IgY-IgXA vs. IgM-IgXA) reflected this pattern: 0.964 vs. 1.275 in CH1, 1.254 vs. 1.477 in CH2, 1.242 vs. 1.248 in CH3, and 1.220 vs. 0.962 in CH4. Within-species trio comparisons reinforced this polarity: 16 of 21 trios displayed an IgY-like CH1-CH2, 16 exhibited an IgM-like CH4, and 12 combined both features. Furthermore, GARD detected recombination breakpoints close to the CH3/CH4 boundary in 6 of the 21 trios, including three cases within 30 nucleotides of the exon junction. Maximum-likelihood domain trees confirmed that the strongest IgXA-IgM sister relationship occurred in CH4, where the largest relevant clade showed 91.7/89.0 SH-aLRT/UFBoot support. Together, these reconstructed sequence data support a mosaic origin for amphibian IgXA, most parsimoniously explained by partial exon shuffling or replacement within a conserved constant-region genomic block.

Understanding how environmental heterogeneity drives spatially varying selection is key to deciphering adaptive evolution. The Major Histocompatibility Complex (MHC) provides an ideal model to study this process. We investigated the MHC class II DQA gene across seven subspecies of wild argali sheep (Ovis ammon) in China. High-throughput sequencing of 98 individuals revealed high diversity (25 alleles), with balancing selection maintaining allelic richness and trans-species polymorphism indicating long-term balancing selection. Molecular evolutionary analyses uncovered heterogeneous positive selection on antigen-binding sites among subspecies (ω = 1.181-3.000), mirroring variable pathogen-driven pressures. Mantel tests detected no significant isolation-by-distance or isolation-by-environment. However, Spearman correlations identified significant associations between specific alleles (e.g., Ovam-DQA*08) and climatic variables, as well as between allele frequencies and MaxEnt-predicted suitability. Redundancy analysis showed that temperature and precipitation explained 54.7% of allele frequency variance. Ecological niche modeling suggested that annual mean temperature was associated with allele distribution, indicating that abiotic factors may shape immunogenetic variation, likely by structuring pathogen communities. Our study provides the first MHC characterization in argali and elucidates how balancing and positive selection interact to maintain functional diversity, offering a foundation for predicting evolutionary responses to environmental change.

In vertebrates, cytidine-to-uracil (C-to-U) editing is mediated by the AID/APOBEC family of deaminases, with APOBEC1 (A1) known to catalyse precise RNA editing of apolipoprotein B (apoB) transcripts in mammals. Despite its well-characterised role in mammals, the evolutionary history and functional divergence of A1 across birds remain underexplored. Here, we investigate the evolutionary trajectory of A1 in birds, where both the presence of the gene and apoB RNA editing activity have been questioned. Through a comprehensive in silico analysis of 81 avian genomes, we identify recurrent disruptions and catalytic inactivation of A1 in multiple lineages. Comparative sequence and structural analyses reveal a lack of domains and key residues essential for RNA binding, dimerisation, and cofactor interaction, suggesting a role in DNA editing. Furthermore, genome-wide screening for A1-associated G-to-A mutations in long terminal repeat (LTR) retrotransposons demonstrates that species with higher endogenous retrovirus (ERV) loads retain more DNA editing signatures, consistent with a defensive role of A1 against retroelements. In contrast, species with low ERV content exhibit relaxed selection and frequent A1 pseudogenisation. Together, these findings support the hypothesis that DNA editing represents the ancestral function of A1, with RNA editing in mammals evolving later as an exaptation following the expansion of A3 and changes in retroviral pressures.

The major histocompatibility complex (MHC) plays a central role in vertebrate adaptive immunity by encoding receptors that recognize pathogen-derived antigens. Migratory shorebirds, such as the Hudsonian Godwit (Limosa haemastica), encounter diverse pathogen landscapes across a wide range of habitats along their migratory routes. Therefore, migratory birds are expected to maintain a robust and effective immune system that minimizes the effects of infection without compromising their migration performance. We examined the genetic diversity of MHC class I exon 3 and MHC class IIB exon 2 across the species range. A total of 57 MHC-I and 13 MHC-IIB alleles were identified, with high polymorphisms observed in the peptide-binding regions (PBR). Signatures of positive selection were more pronounced in PBR sites from MHC-I than from MHC-IIB, suggesting stronger selective pressure from intracellular pathogens. In contrast, the relatively low allelic diversity and weaker selection signatures of MHC-IIB may reflect reduced exposure to extracellular pathogens. Despite broad geographic sampling, no evidence of an adaptive population structure was detected, indicating limited local adaptation and the likely influence of gene flow or neutral processes. Phylogenetic analyses revealed that some L. haemastica alleles clustered with those from closely related Scolopacidae species. These findings highlight the importance of pathogen-mediated selection in shaping MHC variation, providing valuable insights into the variability of a key group of adaptive immune genes in exceptional avian migratory species facing growing environmental pressure.

Pemphigus vulgaris (PV) is a rare autoimmune blistering disease mediated by pathogenic autoantibodies. Although both HLA and non-HLA loci contribute to disease susceptibility, their combined roles in immune regulation remain incompletely understood. This study investigated the joint contribution of HLA-DRB1 and FCGR2B variants to PV susceptibility within an integrative immunogenetic framework. Genotype data from 286 individuals (200 controls and 86 PV patients) were analyzed using bias-reduced association models, two-locus genotype combination analyses, and cumulative genetic risk modeling. Gene-gene relationships were explored through epistasis testing, while functional relevance was examined using biological annotation approaches. HLA-DRB1*04:02 and *14:01 were significantly associated with increased PV risk, whereas *11:01 and *16:01 demonstrated protective effects after multiple testing correction (q < 0.05). The FCGR2B c.671T > C (I232T) variant showed a modest effect in single-locus analyses but did not remain statistically significant after correction for multiple testing. Several two-locus genotype combinations involving FCGR2B and HLA-DRB1 were enriched among patients; however, interaction analyses supported an additive immunogenetic architecture rather than epistasis. Genetic risk modeling demonstrated improved discrimination with weighted scores, and explainable machine-learning analysis identified HLA-DRB1 as the dominant predictor, with FCGR2B contributing a secondary modulatory signal. These findings delineate an additive immunogenetic framework underlying PV susceptibility, emphasizing the central role of HLA-DRB1. Although FCGR2B did not retain independent statistical significance after multiple-testing correction, the results suggest a potential modulatory contribution within the broader immunogenetic architecture of PV.

The humoral immune response relies on a diverse antibody repertoire, which is expanded through processes such as somatic hypermutation, class-switch recombination and gene conversion. These processes are primarily mediated by activation-induced cytidine deaminase (AID). Gene conversion generates diversity in immunoglobulin heavy and light chains (IGHVs) in species such as chickens and rabbits, though it has not been widely studied. Since 80% of the equine IGHV repertoire originates from only three functional gene segments, we examined gene conversion events in horses to assess their role in antibody diversification. Using a modified version of BrepConvert, which optimized analysis time, we identified gene conversion events in 6.9% of immunoglobulin sequences. The results showed a local preference, with most events occurring at the beginning of framework region 1 (FR1) and within complementarity-determining region 2 (CDR2). Pseudogenes IGHV4-35, IGHV4-53, and IGHV4-38 were utilized most frequently, while functional genes IGHV4-21, IGHV4-22, and IGHV4-29 exhibited the highest event frequencies. Interestingly, while most mismatched regions were only three nucleotides long, 91% of these events are flanked by specific sequences (six nucleotides at the 5' end and one nucleotide at the 3' end). Furthermore, functional pseudogene pairs often share identical leader regions of 5-26 nucleotides, suggesting expanded events. We also identified a potential association between these events and local non-B DNA conformations, as well as with the zinc finger protein ZNF691, which supports the involvement of DNA-binding factors. Together, these findings demonstrate that gene conversion significantly contributes to equine antibody diversity by targeting specific IGHV regions.

Major histocompatibility complex class II beta (MHC-class IIB) genes are highly polymorphic and play important roles in immune function, making them valuable DNA markers for efficient animal breeding and conservation management programs. However, MHC genetic information on king penguins (Aptenodytes patagonicus; Appa) in captivity remains limited. Here, we developed a Next Generation Sequencing (NGS)-based genotyping method to characterize MHC class IIB (Appa-CIIB) polymorphisms in 99 king penguins housed at Adventure World (Wakayama, Japan), identifying 72 novel Appa-CIIB alleles, each encoding a distinct amino acid sequence. Phylogenetic analysis classified these alleles into two major and one minor lineage, with peptide-binding regions in the main lineages showing signatures of positive selection. Thirty-four Appa-CIIB haplotypes composed of one to three Appa-CIIB loci, were inferred using individual management records (IMRs) from 123 individuals. Pedigree analysis revealed that 114 individuals belonged to a single extended family encompassing up to five generations, with the founders representing the first generation. Despite over 30 years of captive maintenance, population genetic analyses indicated that this population has retained high genetic diversity. The identification of multiple Appa-CIIB loci and copy number variations suggests that the Appa-CIIB region has undergone gene duplication and recombination events during evolution. These findings provide valuable insights into the genetics and evolutionary characteristics of Appa-CIIB genes and offer a practical framework for managing king penguin gene diversity in captivity, supporting future breeding programs that minimize inbreeding depression and maintain healthy populations.