Frontiers in Immunology

Unbiased classification of equine dendritic cells (DC) is necessary to address various research questions such as the role of DC subsets in immune-mediated diseases of horses. We applied single-cell RNA sequencing (scRNA-seq) on DC enriched from the blood of two horses. All main DC subsets were detected by key gene expression, including conventional DC type 1 (cDC1; XCR1) and type 2 (cDC2; FCER1A, CD1E) as well as plasmacytoid DC (pDC; TCF4). In addition, we detected a small cluster of hematopoietic progenitors, as well as transitional DC (tDC; FCER1A, TCF4) and putative DC type 3 (DC3; FLT3, CD163). Our data confirms the previously reported phenotype of equine pDC (Flt3+MHC-IIlowCADM1lowCD172aint), cDC1 (Flt3+MHC-IIhighCADM1highCD172alow-int) and cDC2 (Flt3+MHC-IIhighCADM1intCD172ahigh), while also highlighting considerable CD14 expression for cDC2. Two subclusters of equine cDC2 were found to be enriched in FCER1A or CX3CR1 transcripts (cDC2.1 and cDC2.2, respectively), with suggested enhanced extravasation and T-cell stimulatory capacities of the latter. Conservation of DC subsets across species (horse, pig, human, mouse) was illustrated by enrichment analyses with subset-specific gene signatures and by cross-species data integration with publicly available scRNA-seq datasets. Our atlas of equine blood DC is a valuable resource for comparative analyses, and it forms the foundation for understanding the involvement of distinct DC subsets in infections and immune-mediated pathologies.

In chickens and humans, classical class I molecules of the major histocompatibility complex (MHC) can have a hierarchy of correlated properties, including cell surface expression and peptide repertoire. Chicken BF2 alleles that are less well-expressed on the cell surface and bind a very wide range of peptides are expressed by MHC haplotypes that confer protection from a variety of economically-important infectious diseases, while certain human HLA-B alleles that are well-expressed and bind a narrow range of peptides lead to slow progression from HIV infection to AIDS. Understanding the impact of these promiscuous generalists and fastidious specialists is of considerable interest. The promiscuous BF2 molecule from the chicken B21 haplotype, BF2*21:01, binds a wide range of peptides by remodelling the peptide-binding site, allowing co-variation of the anchor residues at peptide positions P2 and Pc-2, and binding of an anchor residue at Pc. By using in vitro refolding assays with peptides and peptide libraries, determining thermostability and crystal structures, and analysing a chicken B21 cell line by immunopeptidomics, we found that BF2*21:01 will accommodate many possible combinations at P2 and Pc-2, as well as several hydrophobic amino acids at Pc. However, marked preferences for particular peptide lengths, particular amino acids at the three anchor residues, combinations of amino acids at P2 and Pc-2, and amino acids at P3 and Pc-3 affecting stability lead to high frequencies of major peptides while still allowing the possibility of presenting a wide peptide repertoire. These simplifying principles may eventually allow predictions of pathogen peptides with stable binding for this iconic promiscuous class I molecule, as well as providing the data for more sophisticated peptide prediction methods.

The high prevalence of Corynebacterium (C.) simulans in lesional and non-lesional psoriatic skin, and its correlation with disease severity, suggest a potential role in psoriasis pathophysiology. Previous exploratory Western blot and peptidome analyses of C. simulans extracts using IgG from psoriasis patients identified B-cell epitopes bound by natural bispecific antibodies (nBsAbs, presumably IgG4). These epitopes were primarily derived from intrinsically disordered proteins, autoantigens, and bacteriophage proteins. Subsequent analyses using pooled psoriasis serum unexpectedly revealed antigenic peptides from numerous Corynebacterium species. Taxonomic filtering identified several thousand Corynebacterium-derived epitopes across 40 species, including C. simulans, C. striatum, C. diphtheriae, common skin commensals, environmental and food-associated strains, the plant pathogen Clavibacter michiganensis, and the zoonotic pathogens C. pseudotuberculosis and C. ulcerans. Additional epitopes originated from related genera (Prescottella, Tsukamurella, Mycobacterium, Gordonia, Nocardia, and Rhodococcus) as well as bacteriophages of the order Caudovirales. Among the identified peptides, 183 epitopes from 46 antigens mapped to 30S and 50S ribosomal proteins. Numerous additional epitopes derived from proteins involved in transcription, translation, aminoacyl-tRNA ligases (covering 17 amino acids), transcriptional regulation, RNA processing and degradation, sigma factors, and ribosome-associated proteins. Notably, 40 epitopes originated from highly conserved FoF1-ATP synthase subunits (, {beta}, {gamma}, {delta}). One peptide containing the catalytic Walker A nucleotide-binding motif showed sequence identity with mitochondrial FoF1-ATP synthase, suggesting potential autoimmune cross-reactivity and implicating this enzyme complex as a psoriasis-associated autoantigen candidate. Thousands of further epitopes were identified from proteins involved in respiratory chain function, stress responses, bacterial immunity, membrane transport, chaperones, cell wall biosynthesis, proteases, and peptidases, particularly ATP-dependent Clp proteases. Antigens from biosynthetic and metabolic pathways represented the most abundant nBsAb targets. In addition, 368 DECOY peptides were assigned to bacteriophage proteins. The detection of epitopes from toxin-producing species such as C. diphtheriae, C. pseudotuberculosis, and C. ulcerans further supports a potential microbial contribution to psoriasis pathogenesis. This exploratory study presents a streamlined strategy for B-cell epitope mapping of Corynebacterium antigens using IDP-enriched antigen-IgG4 complexes. The approach holds promise for the development of B-cell epitope-based vaccines targeting microbial, viral, tumor, and allergen-associated diseases.

Helminths are parasitic worms that secrete a variety of immune-regulating molecules to modulate the hosts inflammatory responses, enabling them to persist within the host over a long period of time, even decades. Their capacity to control host responses has prompted research into helminth-derived molecules as potential therapies for controlling excessive immune and inflammatory activity across a range of diseases. This systematic review with cross-study quantitative analysis aims to synthesize the published data on helminth-derived immunomodulatory peptides/polypeptides/proteins (HDIPs) with a focus on determining the extent of their disease-modifying and anti-inflammatory potential in in vivo animal models of inflammatory disease. In accordance with PRISMA 2020 guidelines, a predefined systematic search of the PubMed, Web of Science and Medline databases identified relevant studies published up to February 2026, and 65 articles were included after screening. We found that, although the HDIPs were assessed in multiple different disease models, most published studies assessed their potential in mouse models of colitis, asthma, arthritis and sepsis. Twenty species from which >65 isolated HDIPs were derived were tested in these models, with the trematode, Fasciola hepatica, and the nematode, Acanthocheilonema viteae, the most explored species. A common property of the HDIPs was the ability to significantly reduce disease severity across the in vivo animal models of inflammatory disease, underpinned by a decrease in pro-inflammatory cytokine levels and an increase in anti-inflammatory cytokine levels. Overall, this systematic review with cross-study quantitative analysis not only synthesizes the existing literature in this field but also highlights the disease-modifying and anti-inflammatory potential of HDIPs for a range of diseases in which immunoregulatory therapeutics may improve disease outcomes. It also encourages accelerated advancement of these helminth-derived molecules into first-in-human clinical trials.

Regulator of G-protein signaling 10 (RGS10) has been shown to regulate multiple inflammatory pathways relevant to disease pathogenesis. Of particular importance is the ability of RGS10 to negatively regulate the NFkB pathway, a prominent pro-inflammatory pathway implicated in multiple inflammatory disease phenotypes. However, the exact mechanism by which RGS10 regulates NFkB is unknown. Considering that RGS10 translocates into the nucleus upon stimulation, we hypothesize that RGS10 may regulate NFKB through transcription. To determine whether RGS10 mediates NFkB transcription, we stimulated RGS10 KO and B6 peritoneal macrophages and collected cell lysate over 24 hours to assess transcript levels of NFkB and related proinflammatory cytokines. Here we found that RGS10 differentially regulates the transcription of N{kappa}KB subunits and NF{kappa}B-dependent cytokines. Further studies are warranted to understand the potential role of RGS10 in transcriptional regulation of inflammatory states.

The T Cell Receptor (TCR) is a highly variable component of the T cell immune response that recognizes unique epitopes presented on MHC molecules (pMHC). Random genetic recombination limits the ability for sequence homology to predict epitope specificity, which is more dependent on the strength of the TCR-pMHC binding interaction. Structures for understanding this interaction only exist for well characterized positive interactors, and there is no information available about the physical interaction of non-specific TCR-pMHCs. In this study, we explore the ability for structural prediction algorithms to generate interacting and non-interacting multimeric TCR-pMHC structures, then, examine features that can predict immune interaction. AlphaFold2 shows more consistent multimeric structure prediction compared to other deep learning structure generators or template based algorithms. Poor structure generation does not correlate with immune interaction, and non-interacting structures show similar structural properties to interacting structures. However, this results in less energetically stable conformations in non-interacting structures. Molecular dynamic simulation supports this finding and reveals a novel structural conformation that contributes mechanistically to proper immune synapse. We show that structural and physical features extracted from generated structures are more predictive of interaction than sequence based features. To support researchers in the prediction of TCR-epitope specificity we have made our structural prediction models available through an accessible notebook based webserver: https://github.com/RobbenLab/TCRSIP.

A definitive correlate of protection (CoP) for SARS-CoV-2 has yet to be formally established. Previously, using data from a series of non-human primate vaccine challenge studies, we reported that neutralising antibodies (NAbs) are the strongest candidate for clinical protection against COVID-19 and that spike binding antibody is the strongest candidate CoP for viral burden post-challenge. In this study, we further characterised the protective binding antibody profile by analysing spike antibody-dependent complement deposition, Fc{gamma}R binding, isotype and antibody glycosylation. Using the machine learning platform SIMON, we demonstrate that antibody-dependent complement deposition (ADCD) and Fc{gamma}R binding are strong candidate co-correlates for each of the post-challenge outcomes; viral load and lung pathology. We found that spike antibody sialylation closely followed by Fc{gamma}R2A, was the spike antibody feature with the strongest negative correlation with histopathology score. Spike antibody ADCD, Fc{gamma}R binding, isotype and glycosylation significantly differed by immunisation regimen and sex, which demonstrates the heterogeneity of immune mechanisms induced by different immunisation platforms. We conclude that spike binding antibody, with the protective functional characteristics described herein, is a candidate CoP that captures both protection from severe clinical disease and protection against a high viral burden. These findings should be taken into consideration for future SARS-CoV-2 vaccine development.

The link between HLA genotype and the presence of pathogenic autoantibodies has previously been established across different autoimmune disorders. However, the functional process linking specific antibodies to specific HLA remains unclear. Additionally, autoantibodies - usually associated with autoimmune disease - are also present in healthy individuals. To this end, we sought to determine the spectrum of self-antigen antibody specificity (the "autoreactome") in healthy individuals, stratified by HLA genotypes. We utilized Phage ImmunoPrecipitation Sequencing (PhIP-Seq), a programmable phage display for interrogation of antibody specificity, which encompasses over 700,000 peptides tiled across the entire human proteome. Serum from 741 donors without diagnosed autoimmune disease were grouped by their five homozygous HLA-DRB1 genotypes and analyzed for differences in autoreactivity profiles. We applied a custom filter to the PhIP-Seq normalized data and obtained a set of enriched peptides for each HLA-DRB1 genotype. We found that the autoreactome in healthy individuals with different HLA-DRB1 genotypes are generally distinct. Binary logistic regression successfully identified whether a sample belongs to a specific HLA-DRB1 genotype (HLA-DRB1*01, HLA-DRB1*03, HLA-DRB1*04, HLA-DRB1*07, and HLA-DRB1*15) with the following accuracies: 96%, 92%, 90%, 94%, and 90%, and multinomial models predicted HLA-DRB1 genotype with up to 90% accuracy. Finally, gene-level analysis suggests that individuals with specific HLA autoimmune risk alleles may harbor potentially pathogenic autoantibodies in the absence of, or prior to the establishment of, overt disease. Our analysis demonstrates that autoreactivity profiles in healthy people vary according to HLA class II genotype, and may provide insight into the pathological processes associated with development of autoimmune and other immune-mediated diseases.

Acquired immunity in mammals depends upon capture and presentation of antigens by specialised macrophage populations in splenic marginal zone and lymph node sinuses and follicular dendritic cells (FDC) within germinal centres. Cells referred to as FDC in chickens express CSF1R, the receptor for macrophage colony-stimulating factor (CSF1) and IL34. We utilised single cell RNA-seq on CSF1R+ cells from chicken spleen to identify monocytes and two distinct populations of macrophages. TIMD4/C1Q/MAFB+ macrophages were enriched for expression of genes involved in iron metabolism. A MARCO/VSIG4+ population expressed SPIC, a transcription factor associated with red pulp macrophages in mammals but also expressed receptors (CR2) and trophic factors (TNFSF13, CXCL13) associated with mammalian FDC. SPIC+ cells were located within follicles in spleen, caecal tonsil and bursa. We generated a CSF1R knockout in the chicken germ line. Mutant birds lack macrophages in the embryo. They were indistinguishable from wild type at hatch and behaved and fed normally but from day 5-6 post hatch they failed to thrive. Loss of CSF1R function in hatchlings led to monocytopenia and granulocytosis and the loss of macrophage subpopulations in lymphoid organs. Consistent with their expression of B cell trophic factors, the loss of follicular macrophages in the bursa was associated with involution and severe B cell deficiency in the circulation and spleen. In summary, lymphoid tissues of chickens contain specialised macrophage populations with distinct expression profiles. The details of regulation by CSF1R, specialised functions and underlying transcriptional regulation are quite different between birds and mammals.

Junctional adhesion molecule-like (JAML) is an adhesion molecule known to promote T cell activation and T cell-mediated tumor rejection. In the current study, we show that JAML expression is enriched on mouse intratumoral NK cells compared with splenic NK cells. JAML+ NK cells were associated with tissue residency and co-expressed the immune checkpoints PD-1 and LAG3. JAML expression could be induced on splenic NK cells by IL-2 and further enhanced by IL-21. JAML levels were inversely correlated with inhibitory signaling, as NK cells expressing self-recognizing Ly49 receptors had reduced JAML expression, suggesting regulation of JAML expression by MHC class I molecules. Interaction with the JAML ligand CXADR also reduced JAML surface expression, indicating that tumor-mediated membrane stripping may represent a mechanism of immunoediting. Although JAML RNA transcripts were detectable in human NK cells, JAML protein was found only intracellularly. Together, these findings identify the JAML-CXADR interaction as a potential regulatory pathway in NK cell-mediated killing of tumors.

Toll-like receptors (TLRs) are vital components of the innate immune system, recognizing both exogenous pathogens signals (PAMPs) and internal stress signals (DAMPs). TLR2 is unique among the human (Homo sapiens) TLR family members, as it contains a large cavity for binding hydrophobic ligands, such as lipoteichoic acid (LTA) and di/triacyl lipopeptides (Pam2/3CSK4). This study analyzed the structural phylogeny of cavity presence in the TLR2 lineage in vertebrates (vTLR) enabled by AI protein structure predictions and explored the potential convergent evolution of similar features in invertebrates (iTLRs). Analysis of AI models of TLR2s shows that this cavity is consistently present in TRL2 orthologs across jawed vertebrates (Gnathostomata). In jawless vertebrates (Cyclostomatha), these cavities were found in lamprey (Petromyzon marinus) TLR2 model, but only in some extant hagfish (Myxini), suggesting an ancestral origin in basal vertebrates followed by lineage-specific losses. TLR2 paralogs were found in several species, with a similar central cavity but potentially different ligand specificities. In silico ligand docking showed Pam2CSK4 binds to this cavity in all TLRs and paralogs consistently, demonstrating the conserved function of the ligand-binding pocket in gram-positive bacteria recognition across TLR2 branches. Changes in the TLR2 cavity size and shape in some vertebrate groups show the evolution of this DAMP recognition mechanism adapted to its respective pathogens. iTLRs form a separate phylogenetic branch with distinct structural features, but in literature some are considered to be TLR2 orthologs. Indeed, TLRs from some species of Helobdella and Ciona, contain a cavity with some similarity to that in the vTLR2 lineage. However, detailed structural comparisons of their location in the LRR domain and the structural details of the models suggest that their cavities have developed independently from that in TLR2s. Smaller cavities are present in other branches of the LRR family, but show different locations, shapes, and features, indicating that the binding of small ligands in the internal cavities within the LRR domains evolved multiple times in the LRR domain family history.

In recent years, immunotherapy of patients with higher-risk non-muscle invasive bladder cancer (NMIBC) in North America has relied on the use of the TICE strain of BCG. However, limitations in the supply chain have warranted investigation of the therapeutic benefit of other strains of BCG, such as BCG-Russia. Trained immunity, a form of innate immune memory, is now widely believed to be an important component of the therapeutic benefit of BCG. Therefore, in the present study we compared the effects of BCG-TICE and BCG-Russia on the acquisition of trained immunity and related secondary immune responses. C57BL/6 mice received a single intravenous injection of BCG-Russia or BCG-TICE. Four weeks later, bone marrow was collected for flow cytometric analysis of hematopoietic stem and progenitor cell (HSPC) populations, generation of bone marrow-derived macrophages, functional assessment of trained immunity, and transcriptomic profiling. Compared with BCG-Russia, BCG-TICE elicited stronger levels of trained immunity, characterized by higher production of several proinflammatory cytokines upon secondary activation. BCG promoted the expansion of HSPCs independent of strain. BCG-TICE was linked to upregulation of key inflammation-related genes and enrichment of functionally relevant pathways. The results of this study reveal strain-dependent differences in the ability of BCG to induce innate immune memory and inflammatory pathways that could ultimately determine efficacy of immunotherapy of patients with NMIBC.

Bovine tuberculosis (bTB), due to Mycobacterium bovis (Mb) infection, is a chronic cattle disease and neglected cause of zoonotic tuberculosis. The role of neutrophils in bTB is overlooked. We recently identified a new neutrophil subset in cattle and mice with a similar morphology to conventional inflammatory neutrophils (Nconv). However, unlike Nconv, these regulatory neutrophils (Nreg) express MHC-II at their surface and can suppress lymphocyte proliferation. In this study, we compared the responses of bovine Nconv and Nreg to infection with a virulent Mb strain circulating in France and the attenuated Mb BCG vaccine. Nreg and Nconv had different transcriptional profiles and were differentially activated by Mb infection. Both Nreg and Nconv efficiently killed Mb, but Nreg had higher levels of phagocytosis activity and ROS production. Nreg had higher levels of mitochondrial activity and an ultrastructural organization different from that of Nconv. Our results provide the first insight into the functional characterization of bovine neutrophil subsets during Mb infection and highlight a new layer of complexity in their functional diversity that must be taken into account to improve our understanding of bTB pathophysiology, which is urgently required to improve the management of this costly disease.

Despite vaccination, cervical tumors remain a health issue and require treatment improvement. In 2023, Pembrolizumab, an anti-PD-1 immune checkpoint blockade (ICB), was introduced in the case of advanced or metastatic cervical tumors. This treatment significantly increased progression free survival from 20% to 50%. However, some patients remain resistant to anti-PD-1 treatment, which calls for new targets. In our study, we highlighted poliovirus receptor (PVR) and Nectin-2 as potential ICB targets. Indeed, PVR and Nectin-2 are TIGIT ligands, an immunomodulatory checkpoint expressed by regulatory T cells or exhausted T cells. The binding of PVR or Nectin-2 to TIGIT maintains the immunosuppressive signal in the immune cells allowing tumor progression. Furthermore, we observed that PVR and Nectin-2 were highly expressed on tumor cells and tumor associated macrophages (TAMs) accross the different histological subsets of cervical tumors. Therefore, we hypothesized that using anti-PVR and anti-Nectin-2 anti-bodies would lift immunosuppression in cervical tumors. To that end, we used CyTOF to asses precise immunophenotyping of the targets ex vivo, high throughput confocal microscopy to assess phagocytosis, monocyte derived macrophages (MDM) coupled with 3D cell culture models to assess the impact of our treatment on MDM and TAM repolarization and tumor growth. We could demonstrate that our treatment repolarized macrophages towards an inflammatory profile and that this was followed by a reactivation of macrophage cytotoxic function such as phagocytosis. We also demonstrated that anti-PVR and Nectin-2 treatment allowed the control of tumor growth in 2D and 3D cell culture models. We could also develop a pre-clinical model of autologous cell culture from cervical cancer patients. Using the MIVO technology, which combine organotypic culture and fluidics, we could assess peripheral blood mononuclear cells recruitment towards tumor cells in the presence or absence of anti-PVR and anti-Nectin-2. In conclusion we could demonstrate that targeting macrophages via the PVR/Nectin-2 couple reactivates cervical tumor growth control and improves immune cell recruitment.

RATIONALEThe host-protective role of alpha-1-antitrypsin (AAT) against mycobacteria may be partly attributed to its binding to the cytoplasmic glucocorticoid receptor (GR) that results in gene regulation in macrophages that favors killing of ingested mycobacteria. The AAT-GR complex was found to be significantly responsible for limiting Mycobacterium avium complex (MAC) burden in macrophages; this host-protective function of AAT-GR is due, in part, to induction of COLONY STIMULATING FACTOR-2 (CSF-2) gene which encodes for granulocyte-monocyte colony stimulating factor (GM-CSF). METHODSTo better understand the role of AAT-GR binding during mycobacterial infection, we performed bulk RNA sequencing (RNA-seq) on four different groups of cells: (i) control THP-1 cells (THP-1control); (ii) THP-1control cells infected with Mycobacterium intracellulare (MAC); (iii) THP-1control cells incubated with MAC + AAT; and (iv) THP-1 cells knocked down for GR (THP-1GR-KD) incubated with MAC + AAT. RESULTSOur analyses revealed that MAC infection significantly upregulated 1,977 genes and significantly downregulated 2,303 genes in THP-1control cells. Additionally, AAT significantly upregulated 1,200 genes and downregulated 890 genes in MAC-infected THP-1control cells. Furthermore, the regulation of 1,624 genes that are regulated by AAT+GR in THP-1control cells was augmented in THP-1GR-KD cells, indicating that the regulation of these genes by AAT+MAC is inhibited by GR. Conversely, the regulation of 1,683 genes by AAT+MAC in THP-1control cells was attenuated in THP-1GR-KD cells, indicating that the regulation of these genes by AAT+MAC is enhanced by GR. MAC also induced both CSF2 (GM-CSF) and CSF1 (encodes for monocyte colony stimulating factor, M-CSF) expression. Whereas AAT inhibited MAC-induced M-CSF mRNA was dependent on GR, this inhibition of M-CSF protein was not dependent on GR. In contrast, AAT did not inhibit MAC-induced CSF2 (GM-CSF) expression. Since either MAC or AAT induced GM-CSF expression in macrophages, further investigation revealed that AAT-inhibition of cell-associated MAC burden was abrogated upon neutralization of endogenous GM-CSF. CONCLUSIONSThe ability of AAT to induce GM-CSF and to inhibit MAC-induced M-CSF may skew macrophages to a phenotype that is better endowed to control mycobacterial infection.

Anemia is one of the most debilitating and frequent complications of inflammatory bowel diseases (IBD) and is often treated with iron supplementation, which has limited efficacy. Damaged intestinal barrier function is a hallmark of IBD and causes the translocation of endotoxins from gut bacteria into the bloodstream. In a previous study in mice, we reported that endotoxin suppresses erythropoiesis by reprogramming erythroblastic island macrophages (EBI M{varphi}). Here, we show that IBD patients and mice with acute colitis developed endotoxemia associated with anemia. Endotoxemia in IBD patients was negatively correlated with blood erythrocyte counts. In line with this, mice with acute colitis caused by drinking water containing dextrin sodium sulphate (DSS) had endotoxemia together with anemia characterized by reduced red blood cell counts, hemoglobin content and hematocrit., and reduced medullary erythropoiesis which was in part compensated by increased extramedullary erythropoiesis. As the endotoxin receptor TLR4 is expressed by CD169+ gut-resident macrophages and erythroid island macrophages in the bone marrow, we tested the hypothesis that TLR4 expressed by these CD169+ macrophages mediate both inflammatory colitis and anemia. Indeed, mice with conditional deletion of the Tlr4 gene specifically in CD169+ tissue-resident macrophages were protected from DSS-induced anemia and colitis. In addition, treatment of DSS mice with the TLR4 inhibitor C34 abated inflammation and anemia. These results suggest that endotoxins leaking from the inflamed gut may play a crucial role in IBD and associated anemia and that drugs targeting TLR4 may protect against IBD-associated anemia. Key pointsO_LIPatients with IBD and mice with acute colitis are anemic with increased endotoxemia and inflammation. C_LIO_LIEndotoxemia is inversely correlated with blood erythrocyte counts in IBD patients. C_LIO_LIConditional deletion of endotoxin receptor gene Tlr4 specifically in CD169+ tissue-resident macrophages or administration of synthetic TLR4 inhibitor significantly reduced colitis-induced anemia in mice. C_LI

Systemic autoimmune rheumatic diseases (SARDs) are a heterogeneous group of autoimmune conditions characterized by immune system dysregulation leading to chronic inflammation and tissue damage. The overlapping clinical manifestations make differential diagnosis challenging, highlighting the need for novel biomarkers to facilitate early diagnosis, stratification, and personalized treatment. Five SARDs including idiopathic inflammatory myopathies (n=210), rheumatoid arthritis (n=84), systemic sclerosis (n=100), Sjogren disease (n=99), and systemic lupus erythematosus (n=99), as well as healthy controls (n=400) and controls with acute infectious diseases (n=218) were selected for plasma protein profiling using Olink Explore 1536. Proteins with known association to SARDs as well as novel associations were identified through differential abundance analysis and machine learning. This explorative cross-sectional study demonstrates the importance of a pan-disease approach to biomarker identification within and between the five SARDs. NPX boxplots from this study are available open-access through the Human Protein Atlas, facilitating further plasma-proteome research on autoimmune diseases.

A delayed-type hypersensitivity (DTH) response induced by the intradermal inoculation of leishmanin antigens is used to detect prior exposure to the protozoan parasite Leishmania. Leishmanin antigen preparations are an important tool in disease surveillance studies in endemic areas. Commercial scale leishmanin antigens are being developed for wider deployment in assessing vaccine efficacy and latent infections in the field. Previous studies with leishmanin induced DTH response were limited to analysis of PBMCs. To investigate the mediators of DTH response, we performed spatial transcriptomic analysis of the DTH skin biopsies obtained from a Leishmania endemic foci. Compared to healthy skin biopsy, macrophages and T cells, and IL-16 and TNF that attract CD4+ T cells, were elevated in Langerhans cells in the DTH biopsies. Both IFN-{gamma} and its receptors were similarly elevated in the DTH biopsies. Chemokines CCL2, CCL5, CCL8 and CCL19, and the corresponding receptors were elevated in DTH biopsies, with CCL19-CCR7 as the most salient interaction in our Cellchat analysis. These data reveal biomarkers of DTH response following leishmanin inoculation and enable appropriate formulation and reintroduction of leishmanin skin test antigens for disease surveillance.

Legionnaires disease (LD), a pneumonia caused by Legionella pneumophila intracellular bacterium, leads to intensive care unit (ICU) admission in 20-40% of cases. While these ICU-LD patients display severe lung injury or septic shock, their functional immune response remains poorly understood. The present study aimed, through a large immune gene expression assessment, to improve the understanding of immune cell functionality after whole blood LPS ex vivo stimulation in ICU-LD patients compared with non-ICU. Both ICU and non-ICU-LD displayed altered gene expression indicating that both patients immune cells are less able to respond to the LPS ex vivo stimulus than a healthy population. ICU-LD patients had 1.6-fold greater number of less-expressed genes (35/93 vs 22/93, p=0.039), and lower Log2(FC) of these genes (median [IQR]: -1.9 [-2.6;-1.5] vs -1.2 [-1.7;-0.9], p=0.0011) than non-ICU-LD. Seven genes were significantly less expressed by ICU-LD patients (IRF7, MX1, NFKBI2, NFKBIA, RELB, SRC, TIM3; p-value range: 0.029-0.0080). Top five gene ontology biological processes, subcellular localisations, and reactome pathways (STRING database) uniquely enriched in ICU-LD-patients and related less-expressed genes were cellular response to LPS (CCL2, NFKBIA, IRAK2, TIM3, SRC, NFKB1), regulation of IFN-{beta} production (IRF7, RIG1, OAS2, RELB), I-{kappa}B/NF-{kappa}B complex (NFKBIA, NFKB1, NFKB2), IFN regulatory factor complex (RIG1, IRF7), and TRAF6-mediated NF-{kappa}B activation pathway (NFKBIA, NFKB1, NFKB2, RIG1). Immune gene expression alterations in LD after LPS stimulation were found herein, with more pronounced alterations in ICU-LD patients. A reduced expression of key genes and pathways involved in controlling Legionella proliferation in ICU-LD patients may contribute to increased disease severity.

The vast diversity of B and T cell receptors generated through the recombination of Variable (V), Diversity (D), and Joining (J) gene segments plays a critical role in adaptive immunity. Profiling immune repertoires at the DNA level provides a robust and stable approach to capture the clonal composition of these receptors. immunoPETE is an assay designed to target recombined human T-cell Receptor Beta (TRB), T-cell Receptor Delta (TRD), and Immunoglobulin Heavy (IGH) chain genes directly from genomic DNA. Simultaneous profiling of B and T cell receptor chains in a single reaction provides internally normalized clone counts and facilitates the study of B-T cell interactions. Full-length amplicon consensus sequences representative of original template DNA molecules are accurately reconstructed using Unique Molecular Identifiers (UMIs). An in-house pipeline compiles VDJ rearrangements from the Complementarity-Determining Region 3 (CDR3) of TRB, TRD and IGH chains into comprehensive readouts at cell-level resolution. In this study, we describe the immunoPETE end-to-end workflow, followed by a comprehensive benchmarking of its performance in adaptive immune profiling. Where applicable, we used both natural and contrived samples and characterized the assays accuracy, linearity, and reproducibility across several metrics: retrieving CDR3 sequences, determining B and T cell ratios, total cell count, yield, fraction of functional rearrangements, clonal diversity, composition of dominant clones, pairwise similarity, and V/J gene usage frequencies. Furthermore, we assessed its quantitative limits concerning the total number of lymphocytes and the detection of rare clones. As an example of its applications, we show that adding immune biomarkers extracted from immunoPETE data to clinical factors improves prediction of progression-free survival in a cohort of non-muscle invasive bladder cancer (NMIBC) patients. Finally, we discuss the broad applications of immunoPETE in the study of aging, cancers, infections, and autoimmune disorders with reference to select published studies.