Biology subjects

ElAbd, H.

Publications and source records attributed to ElAbd, H..

12 recordsLinked to original sources

bioRxiv2025

The dynamic role of HLA proteins on compositional alterations of T-cell repertoires in inflammatory bowel disease

BackgroundInflammatory bowel disease (IBD), which is characterised by genetic predispositions and dysregulated immune responses, is rapidly emerging as a global health challenge. Genetic variations in the human leukocyte antigen (HLA) region are strongly associated with IBD; nonetheless, the functional consequences of this variation on the composition of T-cell receptors remain poorly understood. MethodsWe conducted comprehensive CDR3-QTL mapping using T-cell receptor beta (TRB) repertoires paired with HLA allotypes from 1,973 individuals, including 1,201 individuals with IBD and 772 healthy controls (HCs), to explore the role of the HLA allelic variants on TRB composition. Using network analyses, we defined key CDR3 motifs of public clones that were linked to risk HLA alleles for chronic inflammatory diseases. ResultsWe identified novel sites within both HLA class I and class II proteins that were strongly linked to TRB amino acid composition - cdr3QTLs, in both HCs and individuals with IBD. Those sites in HLA-DRB1 and HLA-DQ had stronger effects on CDR3 composition than did the disease in the IBD cohort. In HCs, but not in UC or CD, the strongest HLA signals that affected expanded clones, overlapped with primary CD risk loci from GWAS, e.g., DRB1 site 70 and DQA1 site 25. The strongest CD-specific effects on TRB composition were found in HLA-B, especially at sites that modulate viral responses (e.g., HLA-B sites 9, 67). Finally, the main risk HLA alleles for chronic inflammatory diseases clustered together based on the physicochemical properties of residues mapped to cdr3QTLs, suggesting that risk alleles might exert similar effects on the TRB repertoire. ConclusionStructurally, the main cdr3QTLs in both HLA class I/II are located in peptide-binding sites or sites contacting TCRs, highlighting their direct and antigen-mediated influences on TRB repertoires. Our findings suggest that cdr3QTLs in HLA class I exert IBD-specific effects on the TRB composition, influencing the dysregulated T cell responses implicated in IBD pathogenesis, possibly on the earlier stages of T cell development. While HLA class II cdr3QTLs show universal effects and strong associations with T-cell receptors, irrespective of disease.

immunology↗

bioRxiv2025

High throughput profiling of the B cell repertoire identifies systematic changes in the repertoire of individuals with Crohn's disease

The B cell repertoire contains the recombined DNA sequences that encodes the entire antibody repertoire of an individual. The repertoire is made from three antigenic binding chains, namely the immunoglobulin heavy chain (IGH) and two immunoglobulin light chains, {kappa} (IGK) and {lambda} (IGL). Compared to the T cell repertoire, the B cell repertoire is understudied in inflammatory bowel diseases (IBD) even though different antibodies such as ASCA and ANCA have been shown to be elevated in individuals with IBD. Furthermore, most IBD B cell repertoire studies have profiled the repertoire of treated individuals, thus capturing the combined effect of treatment and disease on the repertoire. To address this limitation, we profiled the repertoire of 24 treatment-naive individuals with CD with matching 24 symptomatic controls. The repertoire of individuals with CD showed a significant reduction in diversity and an increase in clonality, suggesting an antigen-driven expansion of clonotypes that might be driving the disease. Furthermore, we observed a significant reduction in the expansion of IgM and IgD and an expansion of IgA2 and IgG2 clonotypes in individuals with CD relative to controls. Lastly, we observed a reduction in the somatic hypermutation rate in the IGH J gene, particularly in IgM and IgA1 clonotypes, among individuals with CD relative to controls. Thus, despite the small sample size, we identified multiple alterations in the B cell repertoire of individuals with CD, highlighting the potential of the B cell repertoire in identifying antigenic exposures implicated in the diseases, demanding now larger international studies ideally including also treatment-naive and pre-clinical cases.

immunology↗

bioRxiv2025

Quantifying The Impact of Bulk TCR-Seq Methodological Choices on The Profiled T Cell Repertoire

Bulk T cell repertoire profiling using sequencing (TCR-Seq) is a powerful method to investigate T cell responses to natural infections, vaccines, cancers, and autoimmune diseases. This assay can be conducted using various techniques, such as multiplex PCR or 5-RACE. However, each methods introduces systematic biases that can result in different pictures of the underlying T cell repertoire. Furthermore, the impact of technical variables on the accuracy of these methods remains understudied. Thus, in this study, we systematically characterized different multiplex PCR-based protocols, focusing on the quality and quantity of the utilized RNA/DNA, extraction methods, amplification programs, variations between production batches, and technical handling of samples. Our findings highlight the important role of RNA/DNA quality in shaping the profiling results of T cell repertoires. Whereas low RNA/DNA quantities can be partially compensated for by increasing the number of PCR cycles, this is partially not possible with lower quality. In conclusion, our results highlight the influence of different technical choices on the biological conclusions drawn from TCR-Seq data and provide practical guidelines to finetune these variables to ensure consistent and reliable results under diverse experimental constraints.

immunology↗

bioRxiv2025

Analyzing the T cell receptor repertoire of 2,804 individuals with inflammatory bowel disease identifies public T cell responses involved in the pathogenesis

Whereas altered immune processes have been identified in individuals with inflammatory bowel disease (IBD), potentially causative antigens remain to be identified. By interrogating the immune repertoire of individuals with IBD, an identification of common antigenic exposures associated with the disease can be obtained. We analyzed the T cell receptor beta (TRB) chain repertoire of 1,890 individuals with Crohns disease (CD) and 914 individuals with ulcerative colitis (UC), enabling the identification of 327 TRB clonotypes associated with CD and 130 with UC. We validated the expansion of these clonotypes in a cohort of treatment-naive individuals with either CD, UC or symptomatic control (n=855). These disease-associated clonotypes were restricted to disease-associated risk HLA alleles and their expansion correlated with disease-severity but not with surgery or treatment trajectory. In conclusion, we identified and validated TRB clonotypes that are associated with either CD or UC, these clonotypes are a novel therapeutic target in IBD.

immunology↗

bioRxiv2025

Multi-centered T cell repertoire profiling identifies novel alterations in the immune repertoire of individuals with inflammatory bowel disease and validates previous findings

IntroductionIBD is an incurable immune-mediated inflammatory disease (IMID), affecting the gut with a high rate of primary- and secondary-loss-of-response to therapy. By investigating the T cell receptor repertoire of individuals with IBD, novel therapeutic and preventive strategies can be identified, and a better understanding of IBD can be obtained. MethodsWhereas most studies have so far focused on the more diverse T cell receptor beta (TRB) repertoire, we here profiled the alpha (TRA) repertoire of three cohorts containing treatment-naive and treated individuals in addition to individuals living with the disease for >20 years, resulting in an exhaustive dataset containing the TRA repertoire of 2,151 individuals. ResultsUsing the generated datasets, we were able to replicate previous findings describing the expansion of Crohns-associated invariant T (CAIT) cells in individuals with Crohns disease (CD) in the three cohorts. Using a hypothesis-free statistical testing framework, we identified clonotypes that were associated with the disease at its different stages, e.g., at the time of diagnosis and decades post-diagnosis. By conducting a meta-analysis across the three cohorts, we were able to identify a set of clonotypes that were associated with the disease regardless of its stage. We validated our findings in a previously published independent test dataset from a German cohort, showing the robustness of the identified sets of clonotypes. ConclusionThe identified clonotypes are potential novel therapeutic targets to treat IBD, e.g., through targeted depletion. These clonotypes are also of major interest as they can be investigated in a targeted fashion to identify culprit antigen(s) in IBD.

immunology↗

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

Decoding the restriction of T cell receptors to human leukocyte antigen alleles using statistical learning

Conventional T cells recognize peptides presented by the human leukocyte antigen (HLA) proteins through their T cell receptors (TCRs). Given that thousands of HLA proteins have been discovered, each presenting thousands of different peptide antigens, decoding the cognate HLA protein of a TCR experimentally is a challenging task. To address this problem, we combined statistical learning methods with a unique dataset of paired T cell repertoires and HLA allele information for 6,794 individuals. This enabled us to discover 53,870 T cell receptor alpha (TRA) and 1,095,576 beta (TRB) clonotypes that were associated with 437 unique HLA alleles. The identified clonotypes were targeting prevalent infections, e.g. influenza, cytomegalovirus and Epstein-Barr virus. Utilizing these clonotypes, we developed statistical models that impute the carriership of common HLA alleles from the TRA- or TRB-repertoire. In conclusion, the identified allele-associated clonotypes encode the HLA fingerprints and the immune exposure history of individuals and populations.

immunology↗

bioRxiv2024

Simultaneous Profiling of the Blood and Gut T and B Cell Repertoires in Crohn's Disease and Symptomatic Controls Illustrates Tissue-specific Alterations in the Immune Repertoire of Crohn's Disease Patients

Crohns disease (CD) is a clinical subset of inflammatory bowel disease that is characterized by patchy transmural inflammation across the gastrointestinal tract. Although the exact etiology remains unknown, recent findings suggest that it is a complex multifactorial disease with contributions from the host genetics and environmental factors such as the microbiome. We have shown that the T cell repertoire of CD patients harbors a group of highly expanded T cells which hints toward an antigen-mediated pathology. To profile the immunological signature of CD at a high-resolution we simultaneously profiled the {beta} and {gamma}{delta} T cell repertoire in addition to the B cell repertoire of both the blood and the colonic mucosa for 27 treatment-naive CD patients and 27 age-matched symptomatic controls. Regardless of disease, we observed multiple physiological differences between the immune repertoire of blood and colonic mucosa. Additionally, by comparing the repertoire of CD patients relative to controls, we observed different alterations that were only detected in the blood or colonic mucosa. These include a depletion of mucosal-associated invariant T (MAIT) cells in the blood repertoire, an expansion of TRAV29/DV5-TRAJ5+ clonotypes and a significant depletion of multiple IGHV3-33-IGHJ4+and IGHV3-33-IGHJ6+ clonotypes in the blood and gut IGH repertoire of CD patients. In conclusion, our findings highlight the importance of studying the immune repertoire in a tissue-specific manner and the need to profile the T and B cell immune repertoire of gut tissues.

immunology↗

bioRxiv2024

Antigen-driven expansion of public clonal T cell populations in inflammatory bowel diseases

BackgroundInflammatory Bowel Diseases (IBDs), including Crohns disease (CD) and ulcerative colitis (UC), are known to involve shifts in the T-cell repertoires of affected individuals. These include a reduction in regulatory T cells in both diseases, increase in TNF production in CD, expansion of an unconventional T-cell population in CD, and clonal expansion of abundant T-cell populations in CD mucosal tissue. There are also differential HLA risk and protective alleles between CD and UC, implying CD- and UC-specific repertoire changes that have not yet been identified. MethodsWe performed ImmunoSequencing on blood samples from 3,853 CD cases, 1,803 UC cases, and 5,596 healthy controls. For each sample we imputed HLA type and cytomegalovirus (CMV) infection status based on public T-cell receptor {beta} (TCRB) usage and identified public TCRBs enriched in CD or UC cases. FindingsWe determine that there is more expansion across clonotypes in CD, but not UC, compared with healthy controls. We also identify novel interactive effects of HLA-DQ heterodimers with CD and UC risk. Strikingly, from blood we identify public TCRBs specifically expanded in CD or UC. These sequences are more abundant in intestinal mucosal samples, form groups of similar CDR3 sequences, and can be associated to specific HLA alleles. Although the prevalence of these sequences is higher in ileal and ileocolonic CD than colonic CD or UC, the TCRB sequences themselves are shared across CD and not between CD and UC. InterpretationThere are peptide antigens that commonly evoke immune reactions in IBD cases and rarely in non-IBD controls. These antigens differ between CD and UC. CD, particularly ileal CD, also seems to involve more substantial changes in clonal population structure than UC, compared to healthy controls.

immunology↗

bioRxiv2024

Seq2MAIT: A Novel Deep Learning Framework for Identifying Mucosal Associated Invariant T (MAIT) Cells

Mucosal-associated invariant T (MAIT) cells are a group of unconventional T cells that mainly recognize bacterial vitamin B metabolites presented on MHC-related protein 1 (MR1). MAIT cells have been shown to play an important role in controlling bacterial infection and in responding to viral infections. Furthermore, MAIT cells have been implicated in different chronic inflammatory diseases such as inflammatory bowel disease and multiple sclerosis. Despite their involvement in different physiological and pathological processes, a deeper understanding of MAIT cells is still lacking. Arguably, this can be attributed to the difficulty of quantifying and measuring MAIT cells in different biological samples which is commonly done using flow cytometry-based methods and single-cell-based RNA sequencing techniques. These methods mostly require fresh samples which are difficult to obtain, especially from tissues, have low to medium throughput, and are costly and labor-intensive. To address these limitations, we developed sequence-to-MAIT (Seq2MAIT) which is a transformer-based deep neural network capable of identifying MAIT cells in bulk TCR-sequencing datasets, enabling the quantification of MAIT cells from any biological materials where human DNA is available. Benchmarking Seq2MAIT across different test datasets showed an average area-under-the-receiver-operator-curve (AU[ROC]) >0.80. In conclusion, Seq2MAIT is a novel, economical, and scalable method for identifying and quantifying MAIT cells in virtually any biological sample.

bioinformatics↗

bioRxiv2022

Predicting Peptide HLA-II Presentation Using Immunopeptidomics, Transcriptomics and Deep Multimodal Learning

The human leukocyte antigen (HLA) class II proteins present peptides to CD4+ T cells through an interaction with T cell receptors (TCRs). Thus, HLA proteins are key players in shaping immunogenicity and immunodominance. Nevertheless, factors governing peptide presentation by HLA-II proteins are still poorly understood. To address this problem, we profiled the blood transcriptome and immunopeptidome of 20 healthy individuals and integrated the profiles with publicly available immunopeptidomics datasets. In depth multi-omics analysis identified expression levels and subcellular locations as import sequence-independent features governing presentation. Levering this knowledge, we developed the Peptide Immune Annotator Multimodal (PIA-M) tool, as a novel pan multimodal transformer-based framework that utilises sequence-dependent along with sequence-independent features to model presentation by HLA-II proteins. PIA-M illustrated a consistently superior performance relative to existing tools across two independent test datasets (area under the curve: 0.93 vs. 0.84 and 0.95 vs. 0.86), respectively. Besides achieving a higher predictive accuracy, PIA-M with its Rust-based pre-processing engine, had significantly shorter runtimes. PIA-M is freely available with a permissive licence as a standalone pipeline and as a webserver (https://hybridcomputing.ikmb.uni-kiel.de/pia). In conclusion, PIA-M enables a new state-of-the-art accuracy in predicting peptide presentation by HLA-II proteins in vivo.

bioinformatics↗

bioRxiv2022

VCF2Prot: An Efficient and Parallel Tool for Generating Personalized Proteomes from VCF Files

MotivationThe ability to generate sample-specific protein sequences is a crucial step in neo-antigen discovery, cancer vaccine development, and proteogenomics. The revolutionary increase in the throughput of sequencers has fueled large-scale genomic and transcriptomic studies, holding great promises for the emerging field of personalized medicine. However, most sequencing projects store their sequencing data in an abbreviated variant calling format (VCF) that is not immediately amenable to subsequent proteomic and peptidomic analyses. Furthermore, data processing of such increasingly massive genome-scale datasets calls for parallel and concurrent programming, and consequently refactoring of existing algorithms and/or the development of new parallel algorithms. ResultsHere, we introduce sequence intermediate representation (SIR), a novel and generic algorithm for generating personalized or sample-specific protein sequences from a consequence-called VCF file and the corresponding reference proteome. An implementation of SIR, named VCF2Prot, was developed to aid personalized medicine and proteogenomics by generating personalized proteomes in FASTA format from a collection of consequence-called genomic alterations stored in a VCF file. Benchmarking VCF2Prot against the recently published PrecisionProDB showed an ~1000-fold improvement in runtime (depending on the input size). Furthermore, in a scale-up study VCF2Prot processed a VCF file containing 99,254 variants observed across 8,192 patients in ~ 11 minutes, demonstrating the massive improvement in the execution speed and the utility of SIR and VCF2prot in bridging large-scale genomic and proteomic studies. Availability and ImplementationVCF2Prot comes with a permissive MIT-license, enabling the commercial and non-commercial utilization of the tool. The source code along with precompiled versions for Linux/Mac OS are available at https://github.com/ikmb/vcf2prot. The modular units used for building VCF2Prot are available as a Rust crate at https://crates.io/crates/ppgg with documentations and examples at https://docs.rs/ppgg/0.1.4/ppgg/ under the same MIT-license.

genomics↗