Biology subjects

Hoivik, M. L.

Publications and source records attributed to Hoivik, M. L..

7 recordsLinked to original sources

bioRxiv2026

JAK and TYK2 inhibitors differentially modulate interferon/TNF-driven inflammation, stemness and proliferation in the colonic epithelium of ulcerative colitis

BackgroundJanus kinase (JAK)-Signal Transducer and Activator of Transcription (STAT) pathway is a key regulator of inflammatory signaling in ulcerative colitis (UC). While most studies have focused on JAK/tyrosine kinase 2 (TYK2) inhibitors effects on immune cell-mediated responses, their direct epithelial impact remains less known. We investigated epithelial-specific transcriptional responses to JAK/TYK2 inhibitors using patient-derived intestinal epithelial organoids (IEOs) under UC-relevant conditions. MethodsColonic IEOs from UC patients were pretreated with various concentrations of tofacitinib, upadacitinib, filgotinib, brepocitinib, and deucravacitinib for 1 hour prior to stimulation with IFN{beta}, IFN{gamma}, or IFN{lambda}1 for Western blot analysis of STAT1/3 and TYK2 phosphorylation. For transcriptomic profiling, IEOs were pretreated with upadacitinib or deucravacitinib for 16 hours, followed by 8-hour stimulation with IFN{gamma}, IFN{lambda}1, TNF, or IFN{gamma} + TNF. Bulk RNA sequencing assessed differential gene expression, and multiplex assays quantified chemokine secretion. Ki67 immunohistochemistry on colonic biopsies from healthy controls, and UC patients with and without JAK inhibitors-treatment were assessed for epithelial proliferation. ResultsIFNs induced distinct STAT1/3 and TYK2 activation, with IFN{beta}/{gamma} eliciting stronger phosphorylation than IFN{lambda}1. All JAK/TYK2 inhibitors regulated pSTAT1/3 and pTYK2, with upadacitinib most strongly inhibiting pSTAT1/3 and deucravacitinib selectively targeting pTYK2. Transcriptomic analysis revealed extensive cytokine-driven gene regulation, with IFN{gamma} + TNF eliciting the strongest response. Enrichment analysis highlighted upregulation of IFN signaling, antigen presentation, and innate immune pathways, alongside downregulation of cell-cycle processes. Drug-response profiling showed minimal transcriptional changes with upadacitinib and deucravacitinib alone. Upadacitinib broadly modulated IFNs and IFN{gamma} + TNF-regulated genes, attenuating JAK-STAT, NF{kappa}B, antiviral, and cell death pathways, while restoring genes linked to mucosal healing. Upadacitinib also reduced IFNs and IFN{gamma} + TNF-driven chemokine genes and protein secretion. In contrast, deucravacitinib showed selective, potent inhibition of inflammatory genes under IFN{lambda}1-stimulation. Both inhibitors minimally impacted TNF-driven pathways. Ki67 immunohistochemistry confirmed enhanced epithelial proliferation in JAK inhibitor-treated UC patients regardless of mucosal inflammation status. ConclusionsOur findings provide novel evidence that JAK/TYK2 inhibitors influence epithelial transcriptional programs associated with inflammation and mucosal healing. Upadacitinib demonstrated broader modulation of cytokine-driven gene networks compared to TYK2-selective inhibition. These findings provide insight into epithelial-specific drug actions and support precision approaches for UC therapy.

molecular biology↗

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↗

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↗

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↗