Biology subjects

Guikema, J. E.

Publications and source records attributed to Guikema, J. E..

5 recordsLinked to original sources

bioRxiv2026

AbSolution: interactive exploration of sequence-derived features in AIRR-seq repertoires

High-throughput sequencing of B-cell and T-cell immune receptor repertoires provides unprecedented insight into adaptive immune responses. The data produced are structured by clonal relationships and somatic mutation signatures, and yield extremely rich information in sequence-derived features, including physicochemical properties and compositional patterns. However, integrated analysis across datasets, conditions, and time points remains challenging. Current analytical tools typically focus only on certain features within individual repertoires, without enabling integrated, multivariable comparisons across datasets, conditions, and time points to address their diversity and variability. Here we present AbSolution, a user-friendly and flexible interactive application for comprehensive exploration of immune repertoires and their sequence-based properties. AbSolution enables multiscale analysis of thousands of sequence-derived features across receptor regions, while accounting for V(D)J usage, clonal composition and experimental groupings. We demonstrate its utility by identifying distinct sequence-based profiles associated with dominant (highly abundant) and non-dominant B-cell clones in peripheral blood BCR repertoires from patients with idiopathic inflammatory myopathies, and with antigen-responsive T-cell populations over time in a longitudinal in vitro antigen-stimulation dataset. Through interactive, interlinked visualizations, statistical feature selection and multi-sample comparisons, AbSolution facilitates integrated feature profiling that supports the interpretation of immune selection processes and enables systematic analysis of complex repertoire datasets.

bioinformatics↗

bioRxiv2023

Levamisole suppresses activation and proliferation of human T cells by the induction of a p53-dependent DNA damage response

Levamisole (LMS) is a small molecule used in the treatment of idiopathic nephrotic syndrome (INS). The pathogenesis of INS remains unknown, but most evidence points towards an immunological basis of the disease. Recently, LMS has been shown to increase the relapse-free survival in INS patients treated in combination with corticosteroids with relatively few side effects. While LMS has been hypothesized to exert an immunomodulatory effect, its mechanism of action remains unknown. To provide insight into the working mechanism of LMS, we studied its immunomodulatory activity on in vitro activated human T cells. We show here that treatment with LMS decreased activation and proliferation of human CD4+ and CD8+ T cells. In addition, production of T cell activation-associated cytokines such as IL-2, TNF- and IFN-{gamma} were reduced upon LMS treatment, whereas IL-4 and IL-13 production was increased. Gene expression profiling confirmed the suppressive effects of LMS on proliferation as numerous genes involved in cell cycle progression were downregulated. Furthermore, genes associated with p53 activation and cell cycle arrest were upregulated by LMS. In agreement, LMS treatment resulted in p53 phosphorylation and increased expression of the p53 target gene FAS. Accordingly, LMS sensitized activated T cells for Fas-mediated apoptosis. Cell cycle analysis showed that LMS induced a mid-S phase arrest indicating the activation of a replication stress-associated checkpoint. In support, LMS treatment resulted in {gamma}H2AX-foci formation and phosphorylation of CHK1. Our findings indicate that LMS acts as an immunosuppressive drug that directly affects the activation and proliferation of human T cells by induction of DNA damage and the activation of a p53-dependent DNA damage response.

immunology↗

bioRxiv2022

Germinal Centers Convergent Evolution and B cell Recirculation in Human Lymph Nodes

Germinal centers (GCs) are specialized compartments within the secondary lymphoid organs where B cells proliferate, differentiate, and mutate their antibody genes in response to the presence of foreign antigens. They play a central role in generating an effective immune response against infectious pathogens, and failures in their regulating mechanisms can lead to the development of autoimmune diseases and cancer. While previous works study experimental systems of the immune response with mouse models that are immunized with specific antigens, our study focuses on a real life situation, with an ongoing GC response in a human lymph node (LN) involving multiple asynchronized GCs reacting simultaneously to unknown antigens. We combined laser capture microdissection (LCM) of individual GCs from human LN with next-generation repertoire sequencing (Rep-seq) to characterize individual GCs as distinct evolutionary spaces. In line with well-characterized GC responses in mice, elicited by immunization with model antigens such as NP-CGG, we observe a relatively low sequence similarity, as well as heterogeneous clonal diversity across individual GCs from the same human LN. Still, we identify shared clones in several individual GCs, and phylogenetic tree analysis combined with paratope modeling suggest the re-engagement and rediversification of B-cell clones across GCs as well as expanded clones exhibiting shared antigen responses across distinct GCs, indicating convergent evolution of the GCs. Finally, our study allows for the characterization of non-functional clones, where frequencies of V(D)J or SHM induced stop codons are quantified.

evolutionary biology↗

bioRxiv2020

DNA polymerase β prevents AID-instigated mutagenic non-canonical mismatch DNA repair

In B cells, the error-prone repair of activation-induced cytidine deaminase (AID)-induced lesions in immunoglobulin variable genes cause somatic hypermutation (SHM) of antibody genes. Due to clonal selection in the germinal centers (GC) this active mutation process provides the molecular basis for antibody affinity maturation. AID deaminates cytosine (C) to create uracil (U) in DNA. Typically, the short patch base excision repair (spBER) effectively restores genomic U lesions. We here demonstrate that GC B cells actively degrade DNA polymerase {beta} (Pol{beta}), resulting in the inactivation of the gap-filling step of spBER. Consequently, lesions instigated by AID, and likely other base damages, are channeled towards mutagenic non-canonical mismatch repair (mncMMR), responsible for the vast majority of mutations at adenine and thymine (A:T) bases. Apparently, GC B cells prohibit faithful spBER, thereby favoring A:T mutagenesis during SHM. Lastly, our data suggest that the loss of Pol{beta} relates to hypoxia that characterizes the GC microenvironment.

immunology↗

bioRxiv2019

Targeting AKT elicits tumor suppressive functions of FOXO transcription factors and GSK3 kinase in Multiple Myeloma

The phosphatidylinositide-3 kinases (PI3K) and the downstream mediator AKT drive survival and proliferation of multiple myeloma (MM) cells and several AKT inhibitors are currently being tested in clinical trials for MM patients. AKT inhibition has pleiotropic effects, and the key aspects that determine therapeutic efficacy are not fully clear. Therefore, we investigated the antimyeloma mechanism(s) of AKT inhibition. Among the various downstream AKT targets are Forkhead box O (FOXO) transcription factors, and we demonstrate that they are crucial for changes in gene expression upon AKT inhibition. Based on gene expression profiling we defined an AKT-induced FOXO-dependent gene set that has prognostic significance in a large cohort of MM patients, where low FOXO activity correlates with inferior survival. We show that cell cycle exit and cell death of MM cells after AKT inhibition required FOXO. In addition, glycogen synthase kinase 3 (GSK3), a negatively regulated AKT substrate, proved to be pivotal to induce cell death and to inhibit cell cycle progression after AKT inhibition. Finally, we demonstrate that FOXO and GSK3 induced cell death by increasing the turnover of the myeloid cell leukemia 1 (MCL1) protein. In concordance, the AKT inhibitor MK2206 greatly sensitized MM cells for the MCL1 inhibitor S63845. Thus, our results indicate that FOXO and GSK3 are crucial mediators of the antimyeloma effects of AKT inhibition, and suggest combination therapies that may have therapeutic potential in MM.\n\nKEYPOINTSO_LIFOXO transcription factors and the GSK3 kinase are pivotal tumor suppressors downstream of AKT inhibition in MM cells.\nC_LIO_LIFOXO and GSK3 activation after AKT inhibition leads to a decrease in MCL1 levels in MM cells resulting in cell death.\nC_LI

cancer biology↗