Search Results (262)

Background: Adoptive cell therapy using genetically engineered recombinant T cell receptors (rTCRs) expressed in T cells (TCR-T cell therapy) provides precision targeting of cancer cells expressing tumor-associated or tumor-specific antigens recognized by the rTCRs. Standardized analytical tools are lacking to easily quantify receptor expression. Methods: To overcome this hindrance, a universal tagging system (UniTope & TraCR) was designed consisting of a minimal peptide epitope (UniTope) inserted into the constant region of the rTCR α or β chain and a high-affinity monoclonal antibody (TraCR) specific to this tag. Detailed biophysical, biochemical, and functional assays were performed to evaluate rTCR expression, folding, pairing, and antigen recognition, as well as antibody performance, using the UniTope & TraCR System. Results: Tagged rTCRs were stably expressed in human T cells with surface densities comparable to untagged rTCRs. The TraCR antibody bound UniTope with nanomolar affinity and no detectable cross-reactivity was observed for endogenous proteins expressed by human cells of diverse origin, importantly, including T cells of the natural T cell repertoires of multiple human donors. Functional assays confirmed that UniTope-tagged rTCRs preserved their antigen-specific cytokine secretion and cytolytic activity upon antigen-specific stimulation. The UniTope & TraCR System enabled robust detection of rTCR-expressing T cells by flow cytometry, and rTCR protein expression by Western blot or immunoprecipitation, supporting the quantitative assessment of receptor copy number and structural integrity. Conclusions: The UniTope & TraCR System provides a modular, construct-agnostic platform for monitoring engineered rTCRs, integrated into TCR-T cell therapies currently in development. Full article

The thymus, as the primary lymphoid organ for T cell development, orchestrates a complex continuum of processes encompassing precursor migration, lymphocyte lineage commitment, and antigen-guided selection to generate a self-tolerant and immunocompetent T cell repertoire. The thymus is anatomically divided into the cortex, which facilitates the positive selection of thymocytes through interactions between T cell receptors and self-peptide–MHC complexes on cortical epithelial cells, and the medulla, which mediates negative selection by medullary epithelial cells in concert with dendritic cells via the presentation of self-antigens. Key regulatory elements controlling thymocyte development include the transcription factors ThPOK/Runx3 and Sox13/PLZF, chemokine-driven migration mediated by CXCR4 and CCR7, and cytokine signaling. These components collectively exert a profound influence on the final outcome: the establishment of TCR affinity thresholds for tissue-specific antigens in mature T cells. In summary, the integration of multidimensional methodologies highlights the pivotal role of the thymus in immune tolerance, with translational implications for autoimmunity, cancer immunotherapy, and regenerative medicine, as reviewed herein. Full article

Background: Tumor immunogenicity is a concept for modeling the susceptibility of tumors to immune checkpoint inhibitors (ICIs) and other immunotherapies. Single biomarkers, such as tumor mutation burden (TMB) or PDL1 expression, have been shown to correlate with ICI outcomes but are poor predictors of overall and progression-free survival (OS, PFS). Complex machine learning models that integrate multiple biomarkers have shown improved predictions but often lack clear a priori interpretability. In this study, we developed a coherent Multi-Omics Tumor Immunogenicity score (MOTIscore) that combines immunogenicity biomarkers derived from genomic and transcriptomic data and demonstrated its generalizability across multiple cancer types. Methods: Several immunogenicity biomarkers, including TMB, neoantigen burden, T-cell receptor repertoire, PDL1 expression, B2M expression, and variants in pathways of ICI response and resistance, were integrated using a weighted sum scoring scheme. The weights were determined using statistical tests in a large melanoma ICI cohort. We compared the MOTIscore with a machine learning (ML) model trained using the same biomarkers and evaluated the model using melanoma, gastric cancer, and pan-cancer datasets. Results: MOTIscore achieved results similar to those of the ML model in predicting ICI in melanoma and gastric cancer, with both outperforming TMB. Gastric cancer and melanoma patients with high MOTIscores had a significantly extended overall and progression-free survival. Gene set enrichment analysis revealed the enrichment of immune-related pathways in patients with high MOTIscores. Differential expression analysis between patients with high and low immunogenicity identified highly expressed C-X-C motif chemokine ligands as important characteristics associated with successful ICI therapy and significantly improved PFS. MOTIscores varied widely across cancers treated in the molecular tumor board at our hospital and showed distinct distributions between non-immunogenic and immunogenic cancer types. Conclusions: MOTIscore demonstrated improved ICI outcome predictions compared to single-omics biomarkers. Patients with higher tumor immunogenicity also show significantly improved OS and PFS in melanoma and gastric cancer. The results demonstrate the potential use of the MOTIscore to prioritize ICI in personalized cancer treatment. However, ICI outcomes and survival should be investigated in prospective studies, and additional cancer types and larger patient cohorts are needed. Full article

Multiple myeloma (MM) is a clonal malignancy of plasma cells that remains largely incurable despite major advances in proteasome inhibitors, immunomodulatory drugs, and monoclonal antibodies. Chimeric antigen receptor (CAR)-engineered immune cells have transformed the therapeutic landscape, but CAR-T cell therapy faces challenges such as severe cytokine release syndrome (CRS), neurotoxicity, limited persistence, and logistical complexity. In recent years, natural killer (NK) cells have emerged as a promising platform for next-generation cellular immunotherapy, offering innate antitumor activity, a reduced risk of graft-versus-host disease (GvHD), and the feasibility of “off-the-shelf” allogeneic production. This review summarizes current advances in CAR-NK cell therapy for MM, focusing on two major aspects: the diversity of cell sources—including NK-92, peripheral (PB) and cord blood (CB), and induced pluripotent stem cell (iPSC)-derived NK cells—and the expanding repertoire of target antigens such as BCMA (B-cell maturation antigen), NKG2D, CD38, CD70, SLAMF7, CD138, and GPRC5D. We highlight preclinical and early clinical studies demonstrating potent cytotoxicity, favorable safety profiles, and innovative multi-targeting strategies designed to overcome antigen escape and enhance persistence. Emerging clinical data suggest that CAR-NK cell therapy may combine the specificity of CAR recognition with the inherent safety and versatility of NK biology, offering a potential paradigm shift in the treatment of relapsed or refractory MM. Further clinical validation will determine whether CAR-NK cell therapy can achieve durable remission and complement or surpass current CAR-T modalities. Full article

Background: The origin of natural anti-galactose-α-1,3-galactose (anti-Gal) antibodies in humans is only partially understood. The gut microbiome has been proposed as an important source of galactose-α-1,3-galactose (αGal) epitopes that drive the maturation of anti-Gal–reactive B cells. Certain bacteria expressing αGal epitopes, notably Escherichia coli O86:B7, have been shown to elicit anti-Gal antibody responses in α1,3-galactosyltransferase knockout (α3GalT1 KO) mice. In this study, we investigated the interaction between currently widely used bacteria polysaccharide vaccine, the 23-valent pneumococcal polysaccharide vaccine (PPV23), which contains capsular polysaccharides (CPS) from multiple Streptococcus pneumoniae serotypes, and host anti-Gal antibodies. Methods: We conducted a genomic analysis to identify α1,3-galactosyltransferase (α3GalT1) genes in S. pneumoniae strains. Binding of PPV23 to anti-Gal monoclonal antibodies was evaluated by ELISA, and αGal epitope content in PPV23 was estimated using a four-parameter logistic (4PL) model fitted to the ELISA calibration data. To assess in vivo immunogenicity, we immunized α3GalT1 KO mice with PPV23 and measured serum anti-Gal IgG and IgM titers before and after vaccination. Results: Genomic analysis revealed the presence of α3GalT1 genes in S. pneumoniae strains. PPV23 showed specific binding to anti-Gal monoclonal antibodies as detected by ELISA. Quantitative modeling indicated that αGal epitopes are present at low abundance within PPV23, consistent with limited expression of αGal among a minority of included serotypes. Immunization of α3GalT1 KO mice with PPV23 induced a significant rise in anti-Gal IgG titers (mean value from 124 to 384), whereas anti-Gal IgM titers remained relatively unchanged (mean value at the range of 6500–7500). High baseline anti-Gal IgM levels observed in α3GalT1 KO mice are consistent with age-dependent induction by the gut microbiota. Conclusions: These results provide genetic and immunological evidence that αGal epitopes derived from S. pneumoniae are present in PPV23 and can engage pre-existing anti-Gal antibodies. Our findings underscore a complex interplay among bacterial glycosyltransferase genes, vaccine polysaccharide composition, and host anti-Gal antibody repertoires, which may influence vaccine immunogenicity. Consideration of host natural antibody profiles may therefore be important for interpreting responses to carbohydrate-based vaccines and for guiding vaccine design. Full article

Human T-lymphotropic virus type 1 (HTLV-1) infection is associated with a spectrum of clinical outcomes, ranging from lifelong asymptomatic carriage to severe conditions such as HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) and adult T-cell leukemia/lymphoma (ATLL). Although antibody responses are known to shape immune regulation, the functional relevance of IgG idiotype repertoires in HTLV-1 pathogenesis remains poorly understood. This study investigated the immunomodulatory effects of IgG from individuals with distinct HTLV-1 clinical outcomes. IgG was purified from pooled serum samples of asymptomatic carriers (ACs), HAM/TSP, and ATLL patients and used to stimulate peripheral blood mononuclear cells (PBMCs) from healthy donors. Cytokine production in CD4⁺, CD8⁺, and γδ T cells was assessed by flow cytometry. Additionally, proteome-wide IgG reactivity was evaluated using a human protein microarray encompassing over 21,000 proteins, and bioinformatic analyses were conducted to identify protein–protein interaction networks and tissue-specific autoreactivity. HAM/TSP-derived IgG selectively enhanced IFN-γ production in all T-cell subsets and suppressed IL-4 in CD4⁺ T cells. ATLL-derived IgG induced IL-9 and IL-13 production in CD4⁺ T cells, and both HAM/TSP and ATLL IgG elevated IL-13 levels in CD8⁺ T cells. Microarray data revealed distinct autoreactive IgG profiles across clinical groups, targeting immune-related proteins, apoptotic regulators, and proteins expressed in T cells, monocytes, and non-immune tissues such as brain and testis. Notably, no functional or structural clustering was observed in protein–protein interaction networks, suggesting these reactivities reflect complex, idiotype-specific immune alterations rather than compensatory responses. The present findings suggest that HTLV-1 infection may be associated with the development of distinct IgG repertoires that potentially modulate cytokine responses and exhibit broad reactivity toward human proteins. Such patterns could contribute to immune dysregulation and may partially explain the divergent clinical trajectories observed in HAM/TSP and ATLL. Further investigations are warranted to validate these observations at the individual level and to clarify their mechanistic relevance in disease progression. Full article

There exists an urgent need to improve colorectal cancer (CRC) diagnosis due to limitations in current diagnostic approaches. Systematic characterization of the human T cell receptor (TCR) repertoire, coupled with advanced computational methods, provides a promising opportunity to develop more accurate and less invasive diagnostic strategies for this major malignancy. The main objective of this work is to establish a TCR repertoire-based diagnostic model for CRC using machine learning algorithms and to identify the most significant features contributing to accurate diagnosis. Through comprehensive comparative analysis of several machine learning algorithms, our results demonstrated that the Transformer model exhibited superior performance capabilities. The trained model achieved an area under the receiver operating characteristic curve (AUC) of 0.973 in predicting disease status in the internal test set. Furthermore, TCR repertoire analysis from the independent test set demonstrated robust predictions with an AUC of 0.814. Notably, we identified a panel of 50 TCR repertoire features that showed a diagnostic AUC of 0.869 using these 50 TCR CDR3 sequences. Together, this TCR repertoire-based disease model demonstrates significant potential for clinical applications in CRC diagnosis and treatment response monitoring. Furthermore, similar diagnostic models could be established for other immune-related diseases based on disease-specific TCR repertoire data. Full article

Background: Understanding the immune mechanisms that differentiate protective from pathogenic responses during dengue virus (DENV) infection is critical for effective vaccine development. Objective: To investigate how CD4⁺ T cell depletion alters viral control and the humoral immune response during primary DENV2 infection in a non-human primate (NHP) model. Methods: Rhesus macaques were depleted of CD4⁺ T cells prior to DENV2 infection. Viral kinetics, B cell activation, antibody specificity, and functional outcomes were evaluated longitudinally, including cross-reactivity and antibody-dependent enhancement (ADE) potential. Results: CD4⁺ T cells were essential for early viral clearance and the generation of robust, type-specific neutralizing antibodies. In their absence, animals exhibited early non-specific polyclonal B cell activation, delayed isotype switching, and an expanded repertoire of cross-reactive antibodies to DENV and Zika virus (ZIKV), with diminished neutralizing capacity. CD4-depleted macaques also showed increased ADE potential, particularly against ZIKV, and elevated anti-NS1 IgG titers that persisted one-year post-infection. Conclusion: CD4⁺ T cells play a critical role in orchestrating effective, durable, and type-specific antibody responses during primary DENV infection. Their absence leads to delayed antibody maturation, greater cross-reactivity, and higher ADE potential. These findings emphasize the need for DENV and ZIKV vaccines to include CD4⁺ T cell epitopes that promote high-quality, type-specific antibody responses and minimize ADE risk. Full article

Ammonia is a key factor in the water, impacting the physiological functions of aquatic organisms. To explore the effect of ammonia stress on mature eggs, female A. baerii at the end of the fourth stage of ovarian development were subjected to varying ammonia concentrations (0 mg/L (control, C), 10 mg/L (low concentration, T1), and 50 mg/L (high concentration, T2)) for 96 h. After 96 h of stress, histological analysis revealed that the follicular membranes of group T1 remained intact and clear compared to group C, although the vacuole fusion had begun. In contrast, the T2 group exhibited ruptured follicular membranes and adhered yolk granules compared to the C group, indicating structural damage. Transcriptome analysis generated 97.89 Gb of clean data, with each sample yielding over 6.09 Gb. A total of 5576, 3719, and 9446 differentially expressed genes (DEG_S) were screened from T1 vs. C, T2 vs. C, and T2 vs. T1 comparisons, respectively. Gene Ontology analysis (GO) functional enrichment analysis showed that DEG_S were significantly enriched in multicellular organism processes (T1 vs. C), cell surface receptor signaling pathways (T2 vs. C), and immune system processes (T2 vs. T1) during biological processes. It indicates that ammonia exposure may enrich cellular components in the extracellular space, potentially disrupting the function of the extracellular matrix. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment indicated significant impacts on amino acid metabolism, particularly glutamate and arginine pathways, as well as key pathways involved in steroid biosynthesis and antioxidation. Weighted gene co-expression network analysis (WGCNA) revealed that a total of 26,369 DEGs were divided into 29 distinct modules, displaying obvious associations with their traits. In the T2 vs. C group, antioxidation-related genes such as GST and GCLM were significantly downregulated, and the expressions of key enzymes for steroid synthesis, such as CYP11A1, CYP17, and CYP19A1 were suppressed, indicating that high ammonia nitrogen concentrations impair oocyte function by inducing oxidative stress and disrupting hormone synthesis. This study provides a comprehensive repertoire of candidate genes associated with ammonia stress in the mature egg of A. baerii, which will be useful for development of sturgeon breeding and reproduction. Full article

The γδ T cells belong to a subgroup of T cells known as non-conventional T cells due to their limited T cell receptor (TCR) repertoire and ability to recognize non-peptide antigens. They play a crucial role in combating infections and tumors. Vγ9Vδ2 T cells are typically activated by molecules containing diphosphate groups, collectively known as phosphoantigens (pAgs), through a non-canonical mechanism which involves the intracellular domain of butyrofilin (BTN)3A1 protein. However, no FDA-approved drugs have yet been shown to activate them, and the underlying cellular mechanisms remain unknown. In this study, we combined high-throughput virtual screening of an FDA-approved drug database with in vitro cellular assays to identify potential γδ T cells activators. Our findings demonstrate that Nitazoxanide (NTZ) and Tinidazole induce moderate elicited a statistically significant increase in interferon (IFN)-γ production of Vγ9Vδ2 T cells by their probably interaction with the pAg binding site of BTN3A1. Additionally, NTZ induces expression of CD107a, but only at the highest concentrations tested and promotes the upregulation of HLA-DR in total PBMCs and CD14⁺ monocytes. Blocking BTN3A with a specific antibody led to a marked reduction in all NTZ-induced activations. This work identifies NTZ as a previously unrecognized activator of γδ T cells, highlighting its immunomodulatory potential beyond its known clinical uses. These findings broaden our understanding of γδ T cells pharmacology and suggest new opportunities for drug repurposing and the design of novel chemical scaffolds. Further mechanistic studies will be essential to fully define how NTZ engages the BTN3A–γδ T cells axis. Full article

Human T-cell leukemia virus type 1 (HTLV-1) is the causative agent of adult T-cell leukemia/lymphoma (ATL). The trans-activator protein Tax of HTLV-1 is thought to play a crucial role in the early-stage transformation of the virus-infected cells. Tax is a multi-functional protein and modulates cellular signaling pathways that promote proliferation and survival of HTLV-1-infected cells, primarily through the trans-activation of cellular target genes. Tax interacts with a variety of host cell factors including signal transducers and transcription factors, leading to the activation of transcription factors such as CREB, NF-κB, and SRF and activates both its own promoter and those of a variety of host cellular genes. Tax activates its own promoter mainly through CREB and host cellular genes through NF-κB, SRF, and CREB. Accumulating evidence indicates that the Tax-mediated trans-activation of target genes through NF-κB plays an essential role in the transformation of HTLV-1 infected cells. However, the repertoire of Tax target genes, especially those crucial for leukemogenesis, are not known in detail. In this review, we summarize transcriptional activation mechanisms and target genes of Tax, especially focusing on transformation, to facilitate understanding of the underlying mechanisms of leukemogenesis induced by HTLV-1 infection. Full article

Unlike conventional T cells, which express a highly diverse repertoire of dimeric αβ T-cell receptors (TCRs) restricted by classical, polymorphic MHC class I molecules (MHC-Ia), a distinct group of T cells—collectively termed “innate-like T (iT) cells”—exhibits limited TCR diversity and depends instead on nonclassical, nonpolymorphic MHC class I molecules (MHC-Ib) for their development and function. While mounting evidence supports the role of iT cells as pivotal regulators and effectors in both innate and adaptive immune responses, many aspects of their biology remain incompletely understood. In humans, iT cells represent a significant fraction of the total T cell population, and evolutionarily conserved subsets have also been identified in other mammals and amphibians. Moreover, the expanding catalog of nonpolymorphic MHC-Ib genes and lineages—distinct from polymorphic MHC-Ia genes—across jawed vertebrate genomes suggests a broader and potentially more integral role for MHC-Ib molecules in T cell function and immune surveillance. In this review, we explore the immunological significance of MHC-Ib molecules and iT cells through an evolutionary lens, highlighting recent advances that shed light on their contributions to immune homeostasis and defense. Full article

Background: Most immunologically “cold” tumors do not respond durably to checkpoint blockade because tumor antigen (TA) release and presentation are insufficient to prime effective T-cell immunity. While prior work demonstrated synergy between cisplatin and a TLR7/8/9 agonist (CR108) in 4T1 tumors, the underlying mechanism—particularly whether chemotherapy functions as a broad antigen-releasing agent enabling TLR-driven immune amplification—remained undefined. Methods: Using murine models of breast (4T1), melanoma (B16-F10), and colorectal cancer (CT26), we tested multiple chemotherapeutic classes combined with CR108. We quantified intratumoral and systemic soluble TAs, antigen presentation and cross-priming by antigen-presenting cells, tumor-infiltrating lymphocytes, and cytokine production by flow cytometry/ICS. T-cell receptor β (TCRβ) repertoire dynamics in tumor-draining lymph nodes were profiled to assess amplitude and breadth. Tumor microenvironment remodeling was analyzed, and public datasets (e.g., TCGA basal-like breast cancer) were interrogated for expression of genes linked to TA generation/processing and peptide loading. Results: Using cisplatin + CR108 in 4T1 as a benchmark, we demonstrate that diverse chemotherapies—especially platinum agents—broadly increase the repertoire of soluble tumor antigens available for immune recognition. Across regimens, chemotherapy combined with CR108 increased T-cell recognition of candidate TAs and enhanced IFN-γ⁺ CD8⁺ responses, with platinum agents producing the largest expansions in soluble TAs. TCRβ sequencing revealed increased clonal amplitude without loss of repertoire breadth, indicating focused yet diverse antitumor T-cell expansion. Notably, therapeutic efficacy was not predicted by canonical damage-associated molecular pattern (DAMP) signatures but instead correlated with antigen availability and processing capacity. In human basal-like breast cancer, higher expression of genes involved in TA generation and antigen processing/presentation correlated with improved survival. Conclusions: Our findings establish an antigen-centric mechanism underlying chemo–TLR agonist synergy: chemotherapy liberates a broadened repertoire of tumor antigens, which CR108 then leverages via innate immune activation to drive potent, T-cell-mediated antitumor immunity. This framework for rational selection of chemotherapy partners for TLR7/8/9 agonism and support clinical evaluation to convert “cold” tumors into immunologically responsive disease. Full article

T cell receptor (TCR) profiling using next-generation sequencing (NGS) enables high-throughput, in-depth analysis of repertoire diversity, offering numerous clinical applications. We developed a DNA-based strategy to analyse the TCRβ-chain using NGS and established reference values for T cell repertoire characteristics in 74 healthy donors, including 44 adults, 20 paediatrics, and 10 cord blood units (CBUs). Additionally, four paediatric patients with combined immunodeficiency (CID) or severe CID (SCID) due to deleterious mutations in recombination activating genes (RAG) were analysed. The developed strategy demonstrated high specificity, reproducibility, and sensitivity, and all functional variable and joining genes were detected with minimal PCR bias. All donors had a Gaussian-like distribution of complementary-determining region 3 length, with lower presence of non-templated nucleotides and higher proportion of non-functional clonotypes in CBUs. Both CBUs and paediatrics showed greater convergence and TCRβ diversity was significantly lower in adults and donors with cytomegalovirus-positive serostatus. Finally, an analysis of paediatric patients with RAG-SCID/CID showed significantly shorter CDR3 region length and lower repertoire diversity compared to healthy paediatrics. In summary, we developed a reliable and feasible TCRβ sequencing strategy for application in the clinical setting, and established reference values that could assist in the diagnosis and monitoring of pathological conditions affecting the T cell repertoire. Full article

Celiac disease (CD) is a chronic autoimmune disorder triggered by gluten in genetically susceptible individuals. While gluten-free diet (GFD) remains the primary treatment, the molecular mechanisms underlying immune reconstitution remain poorly understood in pediatric populations. This study aimed to characterize T cell receptor (TCR) repertoire remodeling in pediatric CD patients following short-term GFD. We conducted a longitudinal observational study analyzing peripheral blood circulating T cells from five pediatric CD patients at two time points: pre-GFD (at diagnosis) and post-GFD (after 9–10 months of strict dietary adherence). Single-cell TCR sequencing was performed to analyze clonotype diversity, gene usage patterns and TRAV-TRBV pairing combinations. Analysis of 9661 T cells revealed significant TCR repertoire remodeling post-GFD. Expanded clones, predominantly cytotoxic CD8+ T cells, contracted post-GFD (p = 0.02), while increasing clonotype diversity. Notably, specific αβ chain pairings underwent clear reorganization in the complete T cell compartment. Pathogenic combinations were depleted post-GFD, especially in CD4+ T cells, while beneficial pairings became enriched. GFD induced comprehensive TCR repertoire remodeling, revealing that changes occur at the level of specific TCR pairings rather than individual gene usage. Our findings highlight the precision of single-cell approaches in capturing functionally relevant immune changes for monitoring treatment response in pediatric CD. Full article