Biology subjects

Vogl, T.

Publications and source records attributed to Vogl, T..

At least 19 recordsLinked to original sources

bioRxiv2026

Systemic antibody repertoires target specific microbial antigens in patients with colorectal cancer

Colorectal cancer (CRC) represents the third leading cause of cancer related deaths worldwide and is influenced by multiple risk factors. Both exposure to microbiota as well as adaptive immune responses have been implicated in CRC development and suggested as candidate biomarkers. However, the extent to which CRC and adenomas associate with systemic immune signatures against microbes remains unclear. Here, we apply Phage-display ImmunoPrecipitation Sequencing (PhIP-Seq) on 321 individuals of an Austrian CORSA cohort (Colorectal Cancer Study of Austria) including controls, adenomas, and CRC patients. Although antibody repertoires showed global similarity across the different disease status and limited predictive performance, prevalence-based analyses revealed specific signals, such as Helicobacter pylori CagY as candidate marker of CRC and viral antigens as candidate for non-cancer stages. Taken together, this large-scale analysis of antibody reactivity in CRC highlights the potential of serological markers to reflect disease-associated immune signatures.

immunology↗

bioRxiv2026

Pitfalls in understanding PhIP-Seq data: technical variability, replicability, and best practices for interpretation

Phage Display Immunoprecipitation sequencing (PhIP-Seq) is a high throughput method allowing to measure antibody binding against hundreds of thousands of potential antigens. Typically, blood samples of hundreds to thousands of individuals are measured in 96-well plates, necessitating distribution of samples on multiple plates and processing in batches. To correctly interpret PhIP-Seq results, it is crucial to understand its nature and technical limitations. Here, we analyzed 195 technical replicates of controls (anchor samples) from 49 plates measured in 13 immunoprecipitation runs to gauge technical variability and replicability. While there were few false-positive enriched peptides, we observed a substantial fraction of false negatives. The total number of enriched peptides can be affected by batch effects. Additionally, the type of biological material used (serum or plasma) influences enrichment profiles with an antigen library containing bacterial proteins due to the interaction of phages with plasma proteins. Finally, replicating measurements in different labs produces comparable enrichment profiles, but slight differences in a subset of peptides are noticeable. These results suggest best practices for PhIP-Seq experiments. Most importantly, due to batch effects, samples of cases and controls should be evenly distributed between 96-well plates to avoid confounding with biological effects. Also, for highly complex libraries, the total number of enriched peptides can be a technical artifact and potentially not a feature useful in comparisons.

bioinformatics↗

bioRxiv2026

S100A9-Dependent CXCR2hi Neutrophils Mediate Systemic Immune Suppression and Checkpoint Resistance in Metastatic TNBC

Most high-dimensional studies of tumor-immune interactions focus on metastatic models, limiting insight into how immune remodeling in primary tumors shapes metastatic competence. Here, integrating single-cell RNA sequencing, CyTOF, and functional studies across metastatic (4T1) and non-invasive (EMT6) triple-negative breast cancer (TNBC) murine models, we define tumor state-specific immune programs that distinguish metastatic competence. Tumors with metastatic capacity uniquely drive early bone marrow expansion of CXCR2 neutrophils, which infiltrate primary tumors acquiring a CXCL2-producing phenotype that promotes EMT-associated cancer stem cell (CSC) plasticity. This program depends on TGF-{beta}/CEBPD-mediated induction of S100A9. Elevated CXCL2, together with G-CSF, establishes a feed-forward circuit that drives systemic neutrophil mobilization and recruitment to distant organs, where neutrophil-derived S100A8/A9 (calprotectin) promotes MET-driven CSC outgrowth and metastatic colonization. Clinically, gene signatures associated with CXCR2 neutrophils predict poor survival in TNBC patients, whereas monocyte/macrophage (CX3CR1) and T cell activation signatures correlate with improved outcomes. S100A9 ablation disrupts this cascade and enhances immunotherapy responsiveness, defining a TGF-{beta}/S100A9/CXCR2 axis linking immune remodeling, CSC plasticity and metastasis. HighlightsO_LIMetastatic TNBC engages a TGF-{beta}/C/EBP{delta}/S100A9 axis that expands CXCR2 neutrophils C_LIO_LINon-invasive EMT6 tumors retain a CX3CR1 monocyte/macrophage and T-cell landscape C_LIO_LICXCR2+ neutrophils in pre-metastatic niches suppress T cell response while promoting tumor cell proliferation C_LIO_LIS100A9 loss redirects myelopoiesis and potentiates anti-PD-L1 in TNBC models C_LI In BriefAlkan et al. dissect how tumor state programs the myeloid compartment in TNBC. Metastatic 4T1 tumors uniquely engage a TGF-{beta}/C/EBP{delta}/S100A9 axis driving CXCR2 neutrophil expansion and CXCL2/G-CSF-dependent systemic mobilization, coupling immune remodeling to EMT/MET cancer-stem-cell plasticity, while S100A9 loss restores CX3CR1 myeloid identity and unlocks checkpoint-inhibitor responsiveness.

cancer biology↗

bioRxiv2026

Epigenetic control of S100A8/A9-driven monocytic inflammation licenses anti-leukemic functionality of immature NK cells during hematopoietic stem cell differentiation.

Inflammation is a key driver of hematopoietic dysfunction in myeloid malignancies, but its role in the context of hypomethylating therapy remains incompletely understood. Although 5-Azacytidine is used posttransplant in high-risk myelodysplastic syndrome (MDS), only 50% of patients show a clinical response. We provide evidence that inherent inflammatory properties of healthy donor CD34+ stem cells exist that are likely to contribute to the "response" seen in MDS patients. These are linked to epigenetic priming of the myeloid niche, resulting in S100A8/A9-driven inflammatory program that promotes functionality of immature NK cells. Using in vitro differentiation systems, multi-omic profiling, and a S100A9-/- mouse model, we find that 5-AzaC modulates inflammatory transcriptional programs through epigenetic rewiring of upstream regulatory elements. Loss of S100A9 disrupts myeloid differentiation, impairs NK cell maturation, and alters key developmental regulators including CEBPB, JUN, and NFIL3. In vivo, 5-AzaC restores these defects and primes NK cells in a time- and context-dependent manner. Re-analysis of the published Australian MDS/CMML cohort shows that "responders" display increased S100A8/A9 expression together with enhanced IFN-{gamma}, IL6-JAK-STAT3, and TNF signaling. These findings suggest that inflammatory myeloid programs may serve as predictive biomarkers and therapeutic targets to enhance NK cell-mediated graft-versus-leukemia activity posttransplant. SummaryO_LIWe provide compelling evidence that inherent properties of healthy donor CD34+ hematopoietic stem cells (SCs) exist that are likely to contribute to the "response" seen upon pre-emptive posttransplant 5-AzaC therapy of patients with high-risk myelodysplastic syndrome (MDS). C_LIO_LIThese properties are linked to a distinct form of epigenetic plasticity at upstream-located transcription factor (TF) binding sites. This may indirectly contribute to acute S100A8/A9-driven inflammation, which is demonstrable in distinct monocyte subsets and, importantly, also in NK cells thereby determining the characteristics of inflammatory monocyte-NK cell crosstalk. C_LIO_LIMice with a targeted deletion of S100A9 fail to upregulate CEBPB / JUN and NFIL3 which results in impaired myeloid priming and dysfunctional NK cell maturation, respectively. C_LIO_LIRe-analysis of the Australian MDS/CMML cohort confirms that MDS patients that "respond" to 5-AzaC exhibit activated IFN-{gamma}, IL6-JAK-STAT3, and TNF-signaling pathways in the context of upregulated S100A8/A9 after six months of treatment. C_LIO_LIOur study indicates that screening of healthy donors SCs for specific inflammatory markers in early developing monocytes could be used as a marker to predict which donor will have the potential of generating a S100A8/A9-driven inflammatory response. This may help identify patients with MDS as well as AML who are likely to benefit from low-dose, short-term 5-AzaC therapy as early as day 7 after transplantation, potentially resulting in increased graft-versus-leukemia (GvL) activity. C_LI

immunology↗

bioRxiv2026

Preimplantation factor (PIF) is an endogenous inhibitor of potassium channel KV1.3 regulating neutrophil function during pregnancy

Pregnancy is a unique period regarding immune cell regulation. Within the placenta, maternal immune cells play a central role in immune surveillance and tissue remodeling. However, regulatory mechanisms of systemic immunity during pregnancy are less clear. Here, we show that neutrophil function is altered in pregnant mice (E13.5), indicated by increased slow rolling velocity and reduced adhesion. Mechanistically, PreImplantation factor (PIF), a 15 amino acid peptide which is produced by human and murine trophoblast cells of the placenta, is continuously secreted into the maternal circulation and plays a key role in modulating neutrophil function via blocking the voltage-gated potassium channel KV1.3. This resulted in impaired intracellular Ca2+ signaling and subsequently disturbance of neutrophil post-arrest modifications and a higher susceptibility to physiological shear forces in vivo and in vitro. Furthermore, PIF-mediated KV1.3 blockade impaired E-selectin-mediated release of S100A8/A9 and phagocytosis. Taken together, we have identified PIF as an important modulator of neutrophil function during pregnancy suggesting a critical role in regulating innate immune responses throughout gestation.

immunology↗

bioRxiv2025

The nuclear receptor NR4A1 serves as a neutrophil-intrinsic regulator mitigating stroke severity

Ischemic stroke is accompanied by recruitment and activation of immune cells which play an important role in the progression of the brain damage. The nuclear receptor NR4A1 emerged as a key regulator within the inflammatory response of several immune diseases by regulating immune cell activation. In this study, we investigated the role of NR4A1 in the activation and recruitment of brain resident and peripheral immune cells after cerebral ischemia. Here, we show that NR4A1 mediates an anti-inflammatory and damage-limiting effect after stroke. This effect is largely mediated by neutrophil recruitment and importantly, NR4A1 activation with its ligand Cytosporone B improves functional outcome and reduces brain damage. Modulation of NR4A1 is therefore a promising therapeutic target for the treatment of the nuclear receptor NR4A1 in the activation and recruitment of peripheral and brain resident immune cells after cerebral ischemia and its consequences for stroke outcome. We demonstrate that NR4A1 ablation augments neutrophil activation and CNS recruitment within days after stroke thereby increasing infarct size, CNS inflammation, neuronal damage and deteriorating functional outcome. This effect is mediated via modulation of cell-intrinsic neutrophil function and maturation as illustrated by neutrophil-specific NR4A1 ablation and mixed bone-marrow chimera experiments. Notably, the NR4A1 agonist Cytosporone B reduced CNS neutrophil infiltration, infarct size and functional outcome after stroke in a bicentric preclinical stroke trial, demonstrating that NR4A1-mediated control of neutrophil reactivity is amenable to pharmacological modulation. In humans, NR4A1 expressing neutrophils are present in the peripheral blood of stroke patients and neutrophil NR4A1 expression correlates with improved long-term outcome after 3 months. Furthermore, NR4A1 expression in brain parenchyma neutrophils is negatively correlated with neuronal cell loss, illustrating a role of NR4A1 in regulating neutrophil mediated neuronal cell death in human stroke. Together our data reveal the nuclear factor NR4A1 as a brake of intrinsic neutrophil activity controlling neutrophil-mediated brain inflammation and neurotoxicity in stroke which may serve as a novel therapeutic target to limit inflammation-associated augmentation of ischemic damage after stroke.

neuroscience↗

bioRxiv2025

Phage-display immunoprecipitation sequencing reveals distinct antibody repertoire patterns across a rural-urban gradient

Environmental microbial exposures are hypothesized to drive immune profile differences across rural-urban gradients, yet direct evidence linking exposures to immune phenotypes remains limited. Here, we employed phage-displayed immunoprecipitation sequencing (PhIP-seq) to profile antibody repertoires against 357,192 epitopes from >700 organisms in 62 age-matched healthy adults from rural Senegal (n=29), urban Senegal (n=20), and urban Netherlands (n=13). PhIP-Seq analysis identified two major patterns of antibody repertoire variation: geographically restricted signatures distinguishing Senegal from the Netherlands, and a trajectory associated with rural-urban gradients spanning from rural Senegal to urban Netherlands. Integration of PhIP-seq data with high-dimensional immunological profiling revealed immune signatures correlated with the rural-urban antibody repertoire trajectory. Our findings demonstrate that antibody repertoire profiling captures distinct microbial exposure histories across both geographic regions and rural-urban gradients and correlates with variation in immune signatures. This work establishes PhIP-seq as a powerful tool for linking environmental exposure histories to population-level immune landscapes and provides insights into immune adaptation across diverse environments.

immunology↗

bioRxiv2025

The SAFE Labs Handbook: community-driven commitments for group leaders to improve lab culture

Creating positive and equitable lab environments has become a growing priority for the scientific community and funders of scientific research. Research institutions typically respond to this need by providing mandatory or optional training opportunities for their staff. However, there is no established resource for group leaders to improve their lab culture with concrete action points for implementation. Here, we introduce the SAFE Labs Handbook: a collection of thirty "commitments" which can be verifiably actioned without requiring institutional support. These commitments were collaboratively developed by thirteen group leaders in life sciences, from institutions across eight countries, instigated through the 2024 SAFE Labs workshop. The importance of each commitment has been scored by more than 200 researchers, at various career stages, from more than twenty countries. Even though all commitments were rated as significantly important by scientists from all career stages, implementation rates were notably low (< 25%). Lab members reported higher importance scores than group leaders, with large divergences indicating where group leaders may underestimate the potential impact on lab culture. Indeed, the overall implementation rate was correlated with importance score for group leaders, but not lab members. Strikingly, more than 95% of group leaders said they would consider implementing the handbook commitments. Given the high importance-scores and low-implementation rates, the SAFE Labs Handbook represents a unique, community-driven tool with significant potential to improve lab culture on a global scale.

scientific communication and education↗

bioRxiv2025

Mapping adaptive immune responses toward fungal antigens in inflammatory bowel disease using T cell repertoire sequencing and phage-immunoprecipitation sequencing

Inflammatory bowel disease (IBD) is an idiopathic, immune-mediated chronic inflammatory disease of the gut with two primary clinical forms, Crohns disease (CD) and ulcerative colitis (UC). Several genetic susceptibility variants have been associated with IBD, such as ATG16L, NOD2, and several human leukocyte antigen (HLA) alleles, nonetheless, the actual disease causes remain unknown. Whereas previous findings have shown elevated responses toward fungal antigens in individuals with IBD, e.g., elevated anti-Saccharomyces cerevisiae antibody (ASCA) levels, an exhaustive mapping of immune responses toward fungal antigens remains incomplete. Thus, we analyzed the fungal mycobiome profiled using internal transcribed spacer 2 (ITS2)-sequencing simultaneously with the T cell repertoire of 637 individuals with IBD from the SPARC IBD cohort, which enabled us to identify 31 T cell clonotypes targeting several prevalent members of the gut mycobiome. Subsequently, we developed a novel phage-immunoprecipitation sequencing (PhIP-Seq) library covering 12,000 potential antigens from the proteome of S. cerevisiae and screened for antibody responses in 100 individuals with CD and 60 healthy controls with known ASCA status, enabling us to identify public and private antibody responses against several S. cerevisiae proteins. In conclusion, we corroborated previous findings showing elevated T cell responses against fungal antigens in individuals with IBD and identified multiple antigenic proteins from the proteome of S. cerevisiae that are targeted by the immune system of individuals with and without CD.

immunology↗

bioRxiv2025

Disease Severity Across Psychiatric Disorders Is Linked to Pro-Inflammatory Cytokines

ImportanceNumerous studies indicate that the traditional categorical classification of severe mental disorders (SMD), such as schizophrenia, bipolar disorders, and major depressive disorders, does not align with the underlying biology of those disorders as they frequently overlap in terms of symptoms and risk factors. ObjectiveThis study aimed to identify transdiagnostic patient clusters based on disease severity and explore the underlying biological mechanisms independently of the traditional categorical classification. DesignWe utilized data from 443 participants diagnosed with SMD of the PsyCourse Study, a longitudinal study with deep phenotyping across up to four visits. We performed longitudinal clustering to group patients based on symptom trajectories and cognitive performance. The resulting clusters were compared on cross-sectional variables, including independent measures of severity as well as polygenic risk scores, serum protein quantification, miRNA expression, and DNA methylation. ResultsWe identified two distinct clusters of patients that exhibited marked differences in illness severity but did not differ significantly in age, sex, or diagnostic proportions. We found 19 serum proteins significantly dysregulated between the two clusters. Functional enrichment pointed to a convergence of immune system dysregulation and neurodevelopmental processes. ConclusionThe observed differences in serum protein expression suggest that disease severity is associated with the convergence of immune system dysregulation and neurodevelopmental alterations, particularly involving pathways related to inflammation and brain plasticity. The identification of pro-inflammatory proteins among the differentially expressed markers underscores the potential role of systemic inflammation in the pathophysiology of SMD. These results highlight the importance of considering illness severity as a core dimension in psychiatric research and clinical practice and suggest that targeting immune-related mechanisms may offer promising new therapeutic avenues for patients with SMD. Key points QuestionCan analyzing symptom trajectories and cognitive profiles across diagnostic categories reveal clinically relevant subgroups in severe mental disorders? FindingsIn this longitudinal study of 443 individuals with severe mental disorders, two distinct clusters emerged, differing significantly in illness severity, with the more severe group displaying elevated pro-inflammatory serum proteins, suggesting an association between disease severity and inflammation. MeaningThese findings suggest that transdiagnostic clustering clarifies shared mechanisms, underscores the importance of inflammation in severe mental disorders, and highlights a promising avenue for novel therapeutic approaches.

immunology↗

bioRxiv2024

Derivation of aerial insect concentration with a 94 GHz FMCW cloud radar

Aerial insects are vital for nature and society. Though methods to observe flying insects have consistently improved in the last decades, insects remain difficult to monitor systematically and consistently over large spatial and temporal scales. Remote sensing with radars has proved to be one of the more effective tools for observation. However, as radars are most sensitive to targets that are of similar size to the radar wavelength, the detectable sub-group of aerial insects of a certain size range depends on the employed radar. Here, we present a novel method based on spectral data of zenith-pointing Doppler cloud radars to estimate insect concentration in a vertical profile. Multiple meteorological state-of-the-art algorithms are combined to extract insect signals from the radar data and quantify their abundance from 150 m to 3000 m above the ground. For evaluation, this method is applied to triple frequency data from X-band ({lambda} = 3.2 cm), Ka-band ({lambda} = 0.85 cm) and W-band ({lambda} = 0.32 cm) Doppler cloud radars from a three months summertime observation period in Germany. Observations of a case study of two elevated aerial insect layers are presented. Furthermore, differences in diel cycles of aerial insect concentration (aic) obtained from the three radar instruments are compared. With its superior sensitivity to very small insects like aphids, W-band shows the highest aerial insect concentrations during day-time in the lower altitudes. Generally, the higher wavelength radars show higher aerial insect concentrations in higher altitudes (Ka-band) and during the night (X-band).

ecology↗

bioRxiv2024

Cytosolic S100A8/A9 promotes Ca2+ supply at LFA-1 adhesion clusters during neutrophil recruitment

S100A8/A9 is an endogenous alarmin secreted by myeloid cells during many acute and chronic inflammatory disorders. Despite increasing evidence of the proinflammatory effects of extracellular S100A8/A9, little is known about its intracellular function. Here, we show that cytosolic S100A8/A9 is indispensable for neutrophil post-arrest modifications during outside-in signaling under flow conditions in vitro and neutrophil recruitment in vivo, independent of its extracellular functions. Mechanistically, genetic deletion of S100A9 in mice (Mrp14-/-, functional S100a8/a9-/-) caused dysregulated Ca2+ signatures in activated neutrophils resulting in reduced Ca2+ availability at the formed LFA-1/F-actin clusters with defective {beta}2 integrin outside-in signaling during post-arrest modifications. Consequently, we observed impaired cytoskeletal rearrangement, cell polarization and spreading, as well as cell protrusion formation in Mrp14-/- compared to WT neutrophils, making Mrp14-/- cells more susceptible to detach under flow, thereby preventing efficient neutrophil recruitment and extravasation into inflamed tissue. One-sentence summaryintracellular S100A8/A9 is indispensable for firm leukocyte adhesion under flow

physiology↗

bioRxiv2024

Physiological bias governs neutrophil inflammatory threat perception

Background and PurposeThe functional G protein-coupled receptor (GPCR) signalling unit consists of an agonist acting on a receptor that is coupled to a G protein that transduces the signals to effectors within a complex cellular environment. While much attention is given to GPCR-agonist or GPCR-transducer relationships, the contribution of the cellular environment remains significantly unexplored. Experimental ApproachHere, we juxtaposed the signalling responses triggered by the activation of two GPCR pattern recognition receptors, Formyl peptide receptor 1 and Formyl peptide receptor 2, in a recombinant cell system against their signalling dynamics in the native neutrophilic environment. Key resultsWe observed that agonist activation leads to cell context-dependent substantial differences in the receptor signalling texture. While the impact of receptor activation on de novo cAMP formation varied depending on the cell type, MAPK activation was similar in both systems. This physiological bias was conserved across species. Expression analysis unveiled the absence of the Gi-sensitive adenylyl cyclases ADCY5 and ADCY6 in neutrophils, implying that cAMP de novo synthesis cannot be inhibited by Gi-coupled receptors. The signalling behaviour of the Gi-coupled LTB4 high-affinity receptor BLT1 in neutrophils corroborated our findings. Conclusion and ImplicationsOur data underscore the profound impact of the specific cellular environment on GPCR signalling, causing physiological bias in GPCR signalling, thereby affecting drug efficacy and therapeutic targeting.

systems biology↗

bioRxiv2022

Gαq modulates the energy metabolism of osteoclasts

The bacterial protein toxin Pasteurella multocida toxin (PMT) mediates RANKL-independent osteoclast differentiation. Although these osteoclasts are small, their resorptive activity is high and destroys the nasal turbinate bones of pigs. Analysis of the proteome of classical and toxin-derived osteoclasts showed that PMT induces the upregulation of metabolic pathways. This includes strong glycolytic activity, increased expression of GLUT1 and upregulation of the mTOR pathway. As OxPhos components are also expressed more efficiently, cells display increased mitochondrial respiration. We found that the heterotrimeric G protein Gq plays a central role in this hypermetabolic cell activation. Gq triggers mitochondrial relocalisation of pSerSTAT3 and an increase in OPA1 expression. Overexpression of Gq in Hoxb8 cells mimicked this hypermetabolic phenotype and resulted in higher glycolytic and mitochondrial activity as well as increased bone resorptive activity. Rheumatoid arthritis patients show an increase in Gnaq expression especially in the synovial fluid, suggesting that Gq is a target of pathophysiological relevance.

immunology↗

bioRxiv2022

The nuclear receptor NR4A1 restrains neutrophil granulocyte mediated brain damage in cerebral ischemia

Immigration and activation of immune cells play a significant role in damage progression after ischemic stroke. It has been shown that the nuclear receptor NR4A1 exerts a crucial role within the inflammatory response of various immune diseases via regulating immune cell activation. In this study, we investigated the role of NR4A1 on the activation and recruitment of brain resident and peripheral immune cells after cerebral ischemia. Here, we show that NR4A1 mediates an anti-inflammatory and damage limiting effect after ischemic stroke through immigrating neutrophil granulocytes. Importantly, NR4A1-activation with its ligand Cytosporone-B improves functional outcome and diminishes brain damage. Therefore, modulation of NR4A1 is a promising therapeutic target in the treatment of stroke.

neuroscience↗

bioRxiv2021

C/EBPδ-induced epigenetic changes control the dynamic gene transcription of S100A8 and S100A9

The proinflammatory alarmins S100A8 and S100A9 are among the most abundant proteins in neutrophils and monocytes but completely silenced after differentiation to macrophages. The molecular mechanisms of the extraordinarily dynamic transcriptional regulation of s100a8 and s100a9 genes, however, are only barely understood. Using an unbiased genome-wide CRISPR/Cas9 knockout based screening approach in immortalized murine monocytes we identified the transcription factor C/EBP{delta} as a central regulator of S100A8 and S100A9 expression. S100a8 and S100a9 expression was further controlled by the C/EBP{delta}-antagonists ATF3 and FBXW7. We confirmed the clinical relevance of this regulatory network in subpopulations of human monocytes in a clinical cohort of cardiovascular patients. Moreover, we identified specific C/EBP{delta}-binding sites within s100a8 and s100a9 promoter regions, and demonstrated that C/EBP{delta}-dependent JMJD3-mediated demethylation of H3K27me3 is indispensable for their expression. Overall, our work uncovered C/EBP{delta} as a novel regulator of S100A8 and S100A9 expression. Therefore, C/EBP{delta} represents a promising target for modulation of inflammatory conditions that are characterised by S100A8 and S100A9 overexpression.

cell biology↗

bioRxiv2021

In-depth characterization of the serum antibody epitope repertoire in inflammatory bowel disease using phage-displayed immunoprecipitation sequencing

Inflammatory bowel diseases (IBD), e.g. Crohns disease (CD) and ulcerative colitis (UC), are chronic immune-mediated inflammatory diseases. A comprehensive overview of an IBD-specific antibody epitope repertoire is, however, lacking. We leveraged a high-throughput phage-displayed immunoprecipitation sequencing (PhIP-seq) workflow to identify antibodies against 344,000 antimicrobial, immune and food antigens in 497 IBD patients as compared to 1,326 controls. IBD was characterized by 373 differentially abundant antibodies (202 overrepresented and 171 underrepresented), with 17% shared by both IBDs, 55% unique to CD and 28% unique to UC. Antibodies against bacterial flagellins dominated in CD and were associated with ileal involvement, fibrostenotic disease and anti-Saccharomyces cerevisiae antibody positivity, but not with fecal microbiome composition. Antibody epitope repertoires accurately discriminated CD from controls (AUC=0.89), and similar discrimination was achieved when using only ten antibodies (AUC=0.87). IBD patients thus show a distinct antibody repertoire against selected peptides, allowing patient stratification and discovery of immunological targets.

immunology↗

bioRxiv2021

Genetic, environmental and intrinsic determinants of the human antibody epitope repertoire

Phage-displayed immunoprecipitation sequencing (PhIP-Seq) has successfully enabled high-throughput profiling of human antibody profiles. However, a comprehensive overview of environmental and genetic determinants shaping human adaptive immunity is currently lacking. In this study, we aimed to investigate the effects of genetic, environmental and intrinsic factors on the variation in human antibody repertoires. We characterized serological antibody repertoires against 344,000 peptides using PhIP-Seq libraries from a wide range of microbial and environmental antigens in 1,443 participants from a population cohort. We demonstrate individual-specificity, temporal consistency and co-housing similarities in antibody repertoire. Genetic analyses showed involvement of the HLA, IGHV and FUT2 regions. Furthermore, we uncovered associations between 48 phenotypic factors and 544 antibody-bound peptides, including age, cell counts, sex, smoking behavior and allergies, among others. Overall, our results indicate that human antibody epitope repertoires are shaped by both host genetics and environmental exposures and highlight unique signatures of distinct phenotypes and genotypes.

immunology↗