Corey T. Watson

Black-footed ferrets (Mustela nigripes) are among the world's most endangered mammals and remain highly vulnerable to sylvatic plague caused by Yersinia pestis, yet the genetic basis of this susceptibility has remained unknown. Current conservation strategies rely on vaccination of captive-bred animals and large-scale flea control with insecticides, approaches that are costly, labor-intensive, and difficult to implement across the species' natural range. Several closely related mustelid species, including the domestic ferret, are substantially more resistant to plague, providing an opportunity to identify naturally evolved immune mechanisms through comparative immunogenomics. Here we identify a conserved class of immunoglobulin lambda variable genes encoding unusually long antigen-binding loops with CCR5-mimicking sequence features that are widespread among Caniformia species. Because CCR5 has been implicated in host interactions with Yersinia species, we hypothesized that antibodies encoded by these germline genes contribute to plague resistance through receptor-like molecular mimicry. Consistent with this hypothesis, we show that these genes are under strong purifying selection in mustelids, are actively expressed in antibody repertoires, and monoclonal antibodies encoded by them reduced intracellular Y. pestis survival in macrophages. In contrast, all analyzed black-footed ferrets carried a frameshifting deletion resulting in loss of gene expression. These findings identify a naturally disrupted germline antibody gene as a candidate determinant of plague susceptibility in black-footed ferrets, demonstrating that variation in germline immunoglobulin genes can influence susceptibility to a lethal infectious disease. Ultimately, these findings lay the groundwork for genetically informed conservation management and the development of new antibody-based anti-plague strategies.

Polymorphisms of human leukocyte antigen (HLA) genes confer risks for human diseases. Predisposing effects related to T cell receptor (TCR) recognition of peptide–HLA can be selection of TCR repertoire and/or preferential presentation of disease-driving epitopes. In celiac disease (CeD), HLA-DQ2.5 predisposes by presenting gluten peptides to CD4 ⁺ T cells that typically employ stereotyped TCRs. Here, we analyzed whether genetic variants within the HLA and TR loci shape the naive TCR repertoire. We sequenced the αβ TCR repertoires of naive CD4 ⁺ T cells of 103 CeD subjects and 103 controls and performed gene usage quantitative trait loci analyses. The naive CD4 ⁺ TCR repertoire was significantly affected by TRA, TRB, and in particular HLA polymorphisms. The presence of HLA-DQ2.5 influenced the TCR repertoire, resulting in significant enrichment of TCR genes being involved in recognition of gluten epitopes in the repertoires of CeD subjects versus controls. HLA thus affects disease risk by selection of a disease-relevant TCR repertoire.

Human immunoglobulin (IG) loci are highly polymorphic, yet existing germline resources remain noisy and incomplete, limiting our ability to link inherited variation to antibody repertoires. Here, we integrate high-fidelity long-read genomic sequencing with matched adaptive immune receptor repertoire sequencing (AIRR-seq) to construct HUSA, a population-scale, evidence-resolved germline resource. Using a conservative allele inference framework, HUSA expands current references more than three-fold, identifying over 1300 alleles while preserving allele-level evidence provenance across genomic and repertoire data. By linking genotype and expressed repertoires within individuals, we show that coding-region similarity predicts the structure of adjacent recombination signal sequences and leader regions, revealing that IG alleles are organized as linked cis-regulatory units associated with differences in recombination context and allele usage. These results define key germline constraints shaping repertoire formation and establish a robust, genotype-aware foundation for the analysis of immune receptor repertoires.

Genetic variation in the loci encoding immunoglobulin genes (IGH, IGK and IGL) affects the repertoire of B-cell receptors (BCRs). Such effects were previously demonstrated for total peripheral blood B cells, but so far have not been investigated at scale for isolated naïve B cells. As B cells are implicated in the pathogenesis of autoimmune diseases, genetically encoded features of the naïve BCR repertoire may affect disease risk, for instance in celiac disease (CeD) which is hallmarked by stereotyped disease-specific antibodies that recognize antigen in their germline configuration. Here we have characterized the BCR repertoire of naïve B cells in 102 individuals with CeD and 102 control subjects by undertaking gene usage quantitative trait loci analyses based on repertoire sequencing and single nucleotide polymorphism genotyping. Variants within each of the loci had significant effects on the naïve BCR repertoires, with the usage of 80% of IGH genes, 54% of IGK genes and 84% of IGL genes being significantly affected by gene polymorphisms. Effects of genetic polymorphisms on BCR usage were observed for genes implicated in stereotypic responses previously associated with CeD, yet no strong evidence for CeD predisposing effects of polymorphisms within the IGH, IGK and IGL loci was uncovered.

Introduction: Non-small cell lung cancer is the leading cause of cancer-related mortality worldwide, with lung adenocarcinoma (LUAD) as the most common subtype. Although early-stage disease is often treated surgically, advanced LUAD typically requires chemotherapy, radiation, and/or immunotherapy, largely focused on T cell–mediated responses. Therapeutic efficacy, however, is also shaped by tumor-infiltrating (TI) B cells, whose roles in LUAD remain incompletely understood. Methods: We performed cytometry by time of flight (CyTOF) using 44 markers on matched tumor, adjacent lung, and peripheral blood samples from 48 LUAD patients to define TI immune landscapes. 66 immune cell subsets were identified, and patients were stratified into four groups based on TI cell composition. Adaptive immune receptor repertoire sequencing (AIRR-seq) of IgM and IgG was conducted on matched samples from 29 patients to assess clonal expansion and affinity maturation. Subisotype-resolved AIRR-seq was additionally performed on tumor samples from 18 patients. Results: CyTOF analysis revealed four patient groups with distinct TI immune profiles. AIRR-seq demonstrated increased clonal expansion and affinity maturation in tumors compared to adjacent lung and blood. Tumor-specific IGHV enrichment patterns were observed but were not associated with patient group assignment. Instead, clonal expansion was greatest in tumors with higher lymphocyte proportions. Subisotype-resolved analysis showed enrichment of IGHG2 and IGHG3 in tumors from patients with low TI B cell abundance, whereas IGHG4 was enriched in patients with high TI B cell infiltration and correlated with four CyTOF-defined immune subsets. Discussion: These findings reveal substantial inter-individual variation in TI immune landscapes and highlight distinct B cell repertoire and subisotype features within LUAD tumors. Together, these data suggest that B cell composition and antibody subisotype usage may contribute to immune contexture and could inform the development of more tailored immunotherapeutic strategies in LUAD.

Variation in antibody (Ab) responses contributes to variable disease outcomes and therapeutic responsiveness, the determinants of which are incompletely understood. This study demonstrates that polymorphisms in immunoglobulin (IG) light chain loci dictate the composition of the Ab repertoire, establishing fundamental baseline differences that influence functional Ab-mediated responses. Using long-read genomic sequencing of the IG kappa (IGK) and IG lambda (IGL) loci, we resolve genetic variation, including structural variants, single nucleotide variants, and gene alleles. By integrating these genetic data with Ab repertoire profiling, we find that all forms of IG germline variation contribute to inter-individual gene usage differences for >70% of light chain genes in the repertoire, directly impacting the amino acids of expressed light chain transcripts. The genomic locations of usage-associated variants in both intergenic and coding regions indicate that IG polymorphisms modulate gene usage via diverse mechanisms, likely including the modulation of V(D)J recombination, heavy and light chain pairing biases, and transcription/translation. Finally, relative to IGL, IGK is characterized by more extensive linkage disequilibrium and genetic co-regulation of gene usage. These results firmly establish the critical contribution of IG light chain polymorphism in Ab repertoire diversity, with important implications for investigating Ab responses in health and disease.

Accurate characterization of adaptive immune receptor repertoires through high-throughput sequencing is critical for understanding immune responses, disease biomarkers, vaccine design, and antibody engineering. However, progress depends on precise knowledge of germline reference sequences, which are challenging to define due to extensive allelic variation and structural complexity in immunoglobulin and T cell receptor loci. To address these challenges, we present major updates to two complementary community resources: the Open Germline Receptor Database (https://ogrdb.airr-community.org) and VDJbase (https://www.vdjbase.org). These resources enable reproducible, evidence-based analysis of immune receptor diversity across populations and species, supporting both fundamental immunology research and precision medicine applications.