Biology subjects

Lundin, K. E. A.

Publications and source records attributed to Lundin, K. E. A..

11 recordsLinked to original sources

bioRxiv2025

A predisposing effect of HLA class II genes in celiac disease by skewing the naive CD4+ T-cell receptor repertoire

Polymorphisms of human leukocyte antigen (HLA) genes confer risks for many human diseases. For predisposing effects relating to T-cell receptor (TCR) recognition of peptide-HLA, the effect can be both selection of the TCR repertoire and preferential presentation of disease-driving epitopes. In celiac disease (CeD) HLA-DQ2.5 predisposes by presenting deamidated 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 {beta} 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 HLA and TRA and TRB polymorphisms. Individuals carrying the HLA-DQ2.5 allotype exhibited increased frequencies of TCR genes involved in stereotyped recognition of gluten epitopes thus demonstrating a disease-predisposing effect of HLA by selection of a disease-relevant TCR repertoire.

immunology↗

bioRxiv2025

Distinct systemic and gut IgA responses to bacteria of the human upper gastrointestinal tract

The mucosa lining the gastrointestinal tract harbors the bodys largest population of plasma cells, most of which produce dimeric IgA destined for release into the lumen. In addition, there is systemic production of monomeric IgA circulating in the blood. Little is known about the connection between systemic and mucosal IgA. To address this relationship and to explore antibody responses against the microbiota, we isolated bacteria from duodenal biopsies and assessed antibody reactivity. Systemic IgA showed reactivity to bacteria of the upper gastrointestinal tract with a preference for binding Neisseria species, while duodenal IgA showed broader reactivity. We found limited clonal overlap between gut and bone marrow plasma cells of individual donors, yet a few shared clones specific to bacterial antigens were identified. Despite showing clonal overlap, gut and bone marrow plasma cells have distinct IgA subclass distributions, and they likely depend on B-cell activation at discrete anatomical sites.

immunology↗

bioRxiv2024

Gene expression and eQTL analysis reflect the heterogeneity in the inflammatory status of the duodenal epithelial lining in coeliac disease

In coeliac disease (CeD), the epithelial lining (EL) of the small intestine is severely damaged through a complex auto-inflammatory response that results in intraepithelial lymphocytes (IELs) attacking epithelial cells (ECs). To better understand the changes occurring in the EL in CeD, including after initiation of a gluten-free diet, and the regulatory mechanisms that affect mucosal homeostasis, we investigated ECs and IELs in the CeD duodenal EL using RNA-seq and eQTL analysis on predicted cell types. The study included 82 duodenal biopsies from volunteers, grouped into controls (CTRL), gluten-free diet treated CeD (TCD) and untreated CeD (UCD). We identified 2,868 differential expressed genes, which clustered into four sets with specific functions related to CeD. Two sets, one upregulated for cell cycle function and one downregulated for digestion, transmembrane transport, and laminin pathways, defined three groups of samples based on inflammation status: non-inflamed, mild inflammation or severe inflammation. These inflammation states correlated with but were not specific to disease state. The remaining two sets of genes were enriched for immune, extracellular matrix, and barrier functions. These latter two sets allowed the classification of samples into their disease conditions: CTRL, TCD, and UCD. Finally, deconvoluting eQTL effects from ECs and immune cells in the EL identified 7 and 9 cell-type-mediated eQTL genes, respectively. In sum, we identified genes expressed in the duodenal EL whose expression might be used as biomarkers to assess CeD condition and its mucosal and immune status. HighlightsO_LIGene expression in epithelial lining in CeD patients reflects inflammation status C_LIO_LIThe transcriptome can classify epithelium as no, mild, or severe inflammation C_LIO_LICell cycle, absorption, and basal lamina genes are indicators of mucosal damage C_LIO_LIImmune and extracellular matrix genes distinguish untreated from treated cases C_LIO_LIPredicted-cell-type eQTLs pinpoint effects in immune and epithelial cells C_LI

immunology↗

bioRxiv2023

Generation of circulating autoreactive pre-plasma cells fueled by naive B cells in celiac disease

Autoantibodies against the enzyme transglutaminase 2 (TG2) are characteristic of celiac disease (CeD), and TG2-specific IgA plasma cells are abundant in gut biopsies of patients. We here describe the corresponding population of autoreactive B cells in blood. Circulating TG2-specific IgA cells were found in untreated patients on a gluten-containing diet but not in controls. They were clonally related to TG2-specific small intestinal plasma cells, and they expressed gut-homing molecules, indicating that they are plasma cell precursors. Unlike other IgA-switched cells, the TG2-specific cells were negative for CD27, placing them in the double negative (IgD-CD27-) category. They had a plasmablast or activated memory B-cell phenotype, and they harbored fewer variable region mutations than other IgA cells. Based on their similarity to naive B cells, we propose that autoreactive IgA cells in CeD are generated mainly through chronic recruitment of naive B cells via an extrafollicular response involving gluten-specific CD4+ T cells.

immunology↗

bioRxiv2023

Separate Gut Plasma Cell Populations Produce Autoantibodies Against Transglutaminase 2 and Transglutaminase 3 in Dermatitis Herpetiformis

Dermatitis herpetiformis (DH) is an inflammatory skin disorder often considered as an extraintestinal manifestation of celiac disease (CeD). Hallmarks of CeD and DH are autoantibodies to transglutaminase 2 (TG2) and transglutaminase 3 (TG3), respectively. DH patients have autoantibodies reactive with both transglutaminase enzymes. We here report that in DH both gut plasma cells and serum autoantibodies are specific for either TG2 or TG3 with no TG2-TG3 cross-reactivity. By generating monoclonal antibodies from TG3-specific duodenal plasma cells of DH patients, we define three conformational epitope groups. Both TG2-specific and TG3-specific gut plasma cells have few immunoglobulin mutations, and the two transglutaminase-reactive populations show distinct selection of certain heavy and light chain V-genes. Mass spectrometry analysis of TG3-specific serum IgA corroborates preferential usage of IGHV2-5 in combination with IGKV4-1. Collectively, our results demonstrate parallel induction of anti-TG2 and anti-TG3 autoantibody responses involving separate B-cell populations in DH patients.

immunology↗

bioRxiv2022

Multiplexed measurement of binding- and neutralizing antibodies to SARS-CoV-2 variants in 12.000 post-vaccine sera

Diagnostic assays currently used to monitor the efficacy of COVID-19 vaccines measure levels of antibodies to the receptor-binding domain of ancestral SARS-CoV-2 (RBDwt). However, the predictive value for protection against new variants of concern (VOCs) has not been firmly established. Here, we used bead-based arrays and flow cytometry to measure binding of antibodies to spike proteins and receptor-binding domains (RBDs) from VOCs in 12,000 sera. Effects of sera on RBD-ACE2 interactions were measured as a proxy for neutralizing antibodies. The samples were obtained from healthy individuals or patients on immunosuppressive therapy who had received two to four doses of COVID-19 vaccines and from COVID-19 convalescents. The results show that anti-RBDwt titers correlate with the levels of binding- and neutralizing antibodies against the Alpha, Beta, Gamma, Delta, Epsilon and Omicron variants. The benefit of multiplexed analysis lies in the ability to measure a wide range of anti-RBD titers using a single dilution of serum for each assay. The reactivity patterns also yield an internal reference for neutralizing activity and binding antibody units per milliliter (BAU/ml). Results obtained with sera from vaccinated healthy individuals and patients confirmed and extended results from previous studies on time-dependent waning of antibody levels and effects of immunosuppressive agents. We conclude that anti-RBDwt titers correlate with levels of neutralizing antibodies against VOCs and propose that our method may be implemented to enhance the precision and throughput of immunomonitoring.

immunology↗

bioRxiv2022

Antibodies to native gluten arise from cross-reactive B cells with implications for epitope spreading in celiac disease

Antibodies to deamidated gluten peptides are accurate diagnostic markers of celiac disease (CeD). However, antibody binding to all possible gluten epitopes has not previously been investigated. To map antibody reactivity in detail and to understand the connection between disease-relevant B-cell and T-cell epitopes, we took advantage of a high-density peptide array for assessment of serum antibody specificity in CeD across the wheat gluten proteome. We confirm the importance of peptide deamidation for antibody binding, and we show that the response is remarkably focused on the known epitope QPEQPFP (where E results from deamidation of Q). In addition, we describe a new epitope in native (non-deamidated) gluten, QQPEQII (where E is gene encoded), which was associated with both B-cell and T-cell reactivity. By generating monoclonal antibodies from peptide-binding gut plasma cells of CeD patients, we show that antibodies to this native gluten epitope are cross-reactive with the major deamidated epitope due to recognition of the shared PEQ motif. Hence, antibodies to native gluten appear to arise from cross-reactive B cells that are generated as a side effect of the immune response to deamidated gluten. Since cross-reactive B cells could present peptides to different gluten-specific T cells, we suspect that such B cells can play a role in epitope spreading by engaging T cells with multiple specificities.

immunology↗

bioRxiv2020

Machine learning analysis of naïve B-cell receptor repertoires stratifies celiac disease patients and controls

Celiac disease (CeD) is a common autoimmune disorder caused by an abnormal immune response to dietary gluten proteins. The disease has high heritability. HLA is the major susceptibility factor, and the HLA effect is mediated via presentation of deamidated gluten peptides by disease-associated HLA-DQ variants to CD4+ T cells. In addition to gluten-specific CD4+ T cells the patients have antibodies to transglutaminase 2 (autoantigen) and deamidated gluten peptides. These disease-specific antibodies recognize defined epitopes and they display common usage of specific heavy and light chains across patients. Interactions between T cells and B cells are likely central in the pathogenesis, but how the repertoires of naive T and B cells relate to the pathogenic effector cells is unexplored. To this end, we applied machine learning classification models to naive B cell receptor (BCR) repertoires from CeD patients and healthy controls. Strikingly, we obtained a promising classification performance with an F1 score of 85%. Clusters of heavy and light chain sequences were inferred and used as features for the model, and signatures associated with the disease were then characterized. These signatures included amino acid (AA) 3-mers with distinct bio-physiochemical characteristics and enriched V and J genes. We found that CeD-associated clusters can be identified and that common motifs can be characterized from naive BCR repertoires. The results may indicate a genetic influence by BCR encoding genes in CeD. Analysis of naive BCRs as presented here may become an important part of assessing the risk of individuals to develop CeD. Our model demonstrates the potential of using BCR repertoires and in particular, naive BCR repertoires, as disease susceptibility markers.

immunology↗

bioRxiv2020

The human small intestine comprises two subsets of regulatory Foxp3+ CD4 T cells with very different life span and functional properties.

BackgroundRegulatory CD4 T cells (Tregs) in the mice gut are mainly specific for intestinal antigens and play an important role in the suppression of immune responses against harmless dietary antigens and members of the microbiota. However, information about the phenotype and function of Tregs in the human gut is limited. ObjectiveHere, we performed a detailed characterization of Foxp3+ CD4 Tregs in the human small intestine. MethodsTregs and conventional CD4 T cells derived from normal intestine as well as from transplanted duodenum and celiac disease lesions were subjected to extensive immunophenotyping and their suppressive activity and ability to produce cytokines were assessed. ResultsSmall intestinal Foxp3+ CD4 T cells were CD45RA- CD127- CTLA4+ and suppressed proliferation of autologous T cells. Approximately 60% of the Tregs expressed the transcription factor Helios. When stimulated, Helios- Tregs produced IL-17, IFN-{gamma} and IL-10, whereas Helios+ Tregs produced very low levels of these cytokines. By sampling mucosal tissue from transplanted human duodenum we demonstrated that donor Helios+ Tregs have a short life span whereas Helios- Tregs persisted for at least 1 year post-transplantation. In normal small intestine, Foxp3+ Tregs constituted only 2% of all CD4 T cells, while in active celiac disease both subsets expanded 5-10-fold. ConclusionThe small intestine contains two subsets of Tregs with different functional capacities and very different life span. Both subsets are scarce in the normal situation but increase dramatically in a chronic inflammatory setting.

immunology↗

bioRxiv2019

Affinity-engineered human antibodies detect celiac disease gluten pMHC complexes and inhibit T-cell activation

Antibodies specific for antigenic peptides bound to major histocompatibility complex (MHC) molecules are valuable tools for studies of antigen presentation. Such T-cell receptor (TCR)-like antibodies may also have therapeutic potential in human disease due to their ability to target disease-associated antigens with high specificity. We previously generated celiac disease (CeD) relevant TCR-like antibodies that recognize the prevalent gluten epitope DQ2.5-glia-1a in complex with HLA-DQ2.5. Here, we report on second-generation high-affinity antibodies towards this epitope as well as a panel of novel TCR-like antibodies to another immunodominant gliadin epitope, DQ2.5-glia-2. The strategy for affinity engineering was based on Rosetta modeling combined with pIX phage display and is applicable to similar protein engineering efforts. We isolated picomolar affinity binders and validated them in Fab and IgG format. Flow cytometry experiments with CeD biopsy material confirm the unique disease specificity of these TCR-like antibodies and reinforce the notion that B cells and plasma cells have a dominant role in gluten antigen presentation in the inflamed CeD gut. Further, the lead candidate 3.C11 potently inhibited CD4+ T-cell activation and proliferation in vitro in an HLA and epitope specific manner, pointing to a potential for targeted disease interception without compromising systemic immunity. Significance StatementConsumption of gluten-containing food drives celiac disease in genetically predisposed individuals. The underlying disease mechanism is not fully understood, but it is strictly dependent on activation of pathogenic T cells. We have engineered high-affinity human antibodies recognizing the T-cell target HLA-DQ2.5 in complex with gluten epitopes and studied cell-specific antigen presentation in patients, which shows that plasma cells and not dendritic cells dominate the inflamed tissue. The only available treatment is lifelong adherence to a gluten-free diet, which is difficult and not effective in all cases. We show that at least one of our antibodies can specifically inhibit activation of pathogenic T-cells in vitro and therefore shows promise for therapy.

immunology↗

bioRxiv2018

Mosaic deletion patterns of the human antibody heavy chain gene locus

Analysis of antibody repertoires by high-throughput sequencing is of major importance in understanding adaptive immune responses. Our knowledge of variations in the genomic loci encoding antibody genes is incomplete, mostly due to technical difficulties in aligning short reads to these highly repetitive loci. The partial knowledge results in conflicting V-D-J gene assignments between different algorithms, and biased genotype and haplotype inference. Previous studies have shown that haplotypes can be inferred by taking advantage of IGHJ6 heterozygosity, observed in approximately one third of the population. Here, we propose a robust novel method for determining V-D-J haplotypes by adapting a Bayesian framework. Our method extends haplotype inference to IGHD- and IGHV-based analysis, thereby enabling inference of complex genetic events like deletions and copy number variations in the entire population. We generated the largest multi individual data set, to date, of naive B-cell repertoires, and tested our method on it. We present evidence for allele usage bias, as well as a mosaic, tiled pattern of deleted and present IGHD and IGHV nearby genes, across the population. The inferred haplotypes and deletion patterns may have clinical implications for genetic predispositions to diseases. Our findings greatly expand the knowledge that can be extracted from antibody repertoire sequencing data.

genomics↗