Biology subjects

Jongejan, A.

Publications and source records attributed to Jongejan, A..

15 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↗

bioRxiv2025

Systematic evaluation of robustness to cell type mismatch of deconvolution methods for spatial transcriptomics data

Sequencing-based spatial transcriptomics (ST) approaches preserve spatial information but with limited cellular resolution, whereas single-cell RNA-sequencing (scRNA-seq) techniques provide single-cell resolution but lose spatial context during tissue dissociation. Given these complementary strengths, computational tools have been developed to combine scRNA-seq and ST data. These methods use deconvolution techniques to identify cell types and estimate their proportions at each spatial location in ST data, using scRNA-seq reference data. However, these methods are sensitive to missing cell types in the scRNA-seq reference, a problem known as cell type mismatch. Using two reference datasets, we performed extensive simulations to systematically evaluate the robustness to cell type mismatch of six deconvolution methods (CARD, cell2location, RCTD, Seurat, SPOTlight, Stereoscope) tailored for ST data, and two designed for bulk RNA-seq data (MuSiC, SCDC). At baseline, that is, with no cell types missing from the reference datasets, cell2location showed the strongest performance, while Seurat performed the worst. By simulating different cell type mismatch scenarios, we found that the performance of deconvolution methods decreases proportionally to the number of cell types missing from the reference. Moreover, compared to baseline, for most methods the relative decrease in performance is similar. Additionally, methods that perform well at baseline tend to assign the proportions of a missing cell type to the transcriptionally most similar cell types present in the reference data. Our results highlight the adverse effects of cell type mismatch on the performance of deconvolution methods for ST data and stress the need for more robust approaches to this issue.

bioinformatics↗

bioRxiv2025

Pure CD32+ CD4+ Cells Are Cytotoxic Memory CD4+ T Lymphocytes Highly Enriched for HIV-1 DNA

The elusive viral reservoir is the major obstacle to an HIV-1 cure. Cell surface protein CD32 has been proposed to pinpoint cells with a very high proviral enrichment, potentially providing a tool for selective therapeutic targeting of the reservoir. However, this finding has been challenged by subsequent reports. In order to clarify the nature of CD32 expression on CD4+ T cells, here we designed a purification strategy allowing single-cell analysis using state-of-the-art technologies. The established multilevel sorting strategy allowed to characterize a rare (median 0.06% of CD4+ T cells) but bona fide CD32+ CD4+ T-cell population. In vitro cell stimulation could not lead to CD32 upregulation. Detailed phenotyping revealed that CD32+ T cells reside mostly in the memory T-cell compartment with heightened levels of acute and chronic activation markers. Single-cell RNA sequencing identified that CD32+ CD4+ T cells are mostly highly cytotoxic CD4+ cells. Importantly. in HIV-1 infected donors under suppressive antiretroviral therapy, we found that these cells are highly enriched for HIV-1 provirus, harbor a clear cytotoxic memory T-cell transcriptome, as well as TCR clonal enrichment. These findings indicate that CD32 remains a promising candidate marker of the HIV-1 reservoir and underline the importance of further investigation of this marker during latent infection.

immunology↗

bioRxiv2024

Infiltrative classical monocyte-derived and SPP1 lipid-associated macrophages mediate inflammation and fibrosis in ANCA-associated glomerulonephritis

BackgroundKidney macrophage infiltration is a histological hallmark of vasculitic lesions and is strongly linked to disease activity in anti-neutrophil cytoplasmic antibodies (ANCA)-associated glomerulonephritis (AGN). The precise mechanisms by which kidney macrophages influence local inflammation and long-term damage remain largely unknown. MethodsHere, we investigate kidney macrophage diversity using single-cell transcriptome analysis of 25,485 freshly retrieved unfrozen, high-quality kidney CD45+ immune cells from five AGN patients, a lupus nephritis and nephrectomy control. Detailed subclustering of myeloid cells was performed to identify disease-specific macrophage subtypes. Next, transcriptome differences between macrophage subsets and disease serotypes were assessed. Findings were validated by immunostainings of an extended cohort of kidney biopsies and flow cytometric analysis of peripheral blood monocytes. ResultsFour main macrophage subsets were identified, including a classical monocyte-derived macrophage (MDM) subset expressing a chemotactic (CXCL2, CXCL3, CXCL8, CCL3) and pro-inflammatory (IL1{beta}, TNF) set of markers and a osteopontin/SPP1+ lipid-associated macrophage (SPP1 LAMs) subtype exhibiting distinctive upregulation of fibrotic genesets. AGN samples revealed a markedly increased proportion of CD163+ macrophages, predominantly composed of classical MDMs, accompanied by resident-like C1Q macrophages, and SPP1 LAMs. An analogous trend was observed in the expansion of peripheral blood classical monocytes during active disease. The proteinase 3 (PR3)-AGN subtype exhibited heightened classical MDM infiltration and markers of acute inflammation, while interferon signaling and markers of chronicity were reduced compared to myeloperoxidase (MPO)-AGN. ConclusionsOur findings highlight the expression of inflammatory and fibrotic genes by kidney macrophage subsets in AGN. Classical monocyte dysregulation might contribute to inflammation in the pathogenesis of AGN. Targeting these specific monocyte/macrophage subsets may potentially control the inflammatory cascade and attenuate resulting fibrosis in AGN and kidney disease in general. Key points- Classical monocyte-derived macrophages are predominant in ANCA-associated glomerulonephritis and exhibit chemotactic and pro-inflammatory markers - Osteopontin/SPP1+ lipid-associated macrophages (SPP1 LAMs) show distinctive upregulation of fibrotic genesets - Understanding of the macrophage immune response supports exploration of macrophage-directed therapies for the treatment of autoimmune kidney diseases

immunology↗

bioRxiv2024

Cardiovascular risk in ANCA-associated vasculitis: monocyte phenotyping reveals distinctive signatures between serological subsets

ObjectivesAnti-neutrophil cytoplasmic antibodies (ANCA)-associated vasculitides (AAV) is associated with an increased cardiovascular risk, particularly the myeloperoxidase AAV serotype (MPO-AAV). Distinct alterations in monocyte phenotypes may cause accelerated atherosclerotic disease in AAV. MethodsA cohort including 43 AAV patients and 19 healthy controls were included for downstream analyses. Extensive phenotyping of monocytes and monocyte-derived macrophages was performed using bulk RNA-sequencing and flow cytometry. An in vitro transendothelial migration assay reflecting intrinsic adhesive and migratory capacities of monocytes was employed. Subsequent sub-analyses were performed to investigate differences between serological subtypes. ResultsMonocyte subset analysis showed increased classical monocytes during active disease, whereas non-classical monocytes were decreased. RNA-sequencing revealed upregulation of distinct inflammatory pathways and lipid metabolism-related markers in monocytes of active AAV patients. No differences were detected in the intrinsic monocyte adhesion and migration capacity. Monocytes of MPO-AAV patients in remission expressed genes related to inflammation, coagulation, platelet-binding and interferon signalling, whereas the expression of chemokine receptors indicative of acute inflammation and monocyte extravasation (i.e., CCR2 and CCR5) was increased in monocytes of proteinase-3(PR3)-AAV patients. During active disease, PR3-AAV was linked with elevated serum CRP and increased platelet counts compared to MPO-AAV. ConclusionThese findings highlight changes in monocyte subset composition and activation, but not in the intrinsic migration capacity of AAV monocytes. MPO-AAV monocytes are associated with sustained upregulation of inflammatory genes, whereas PR3-AAV monocytes exhibit chemokine receptor upregulation. These molecular changes may play a role in elevating cardiovascular risk as well as in the underlying pathophysiology of AAV. Key messages- Monocytes are activated during active ANCA-associated vasculitis (AAV) and upregulate lipid metabolism-related markers - AAV monocytes have a normal intrinsic adhesion and migration capacity, although overall monocyte migration likely rises by other mechanisms - The two serological subsets MPO-AAV and PR3-AAV exhibit differences in monocyte activation and chemokine receptor expression

immunology↗

bioRxiv2023

Treatment with a selective histone deacetylase (HDAC) 1 and 2 inhibitor in aged mice rejuvenates multiple organ systems

The process of aging increases the risk of developing age-related diseases, which come at great societal healthcare costs and suffering to individuals. Meanwhile, targeting the basic mechanisms of aging can reduce the risk of developing age-related diseases during aging, essentially resulting in a healthy aging process. Multiple aging pathways exist, which over past decades have systematically been confirmed through gene knockout or overexpression studies in mammals and the ability to increase healthy lifespan. In this work, we perform transcriptome-based drug screening to identify small molecules that mimic the transcriptional profiles of long-lived genetic interventions in mammals. We identify one small molecule whose transcriptional effects mimic diverse known genetic longevity interventions: compound 60 (Cmpd60), which is a selective inhibitor of histone deacetylase 1 (HDAC1) and 2 (HDAC2). In line with this, in a battery of molecular, phenotypic, and bioinformatic analyses, in multiple disease cell and animal models, we find that Cmpd60 treatment rejuvenates multiple organ systems. These included the kidney, brain, and heart. In renal aging, Cmpd60 reduced partial epithelial-mesenchymal transition (EMT) in vitro and decreased fibrosis in vivo. For the aging brain, Cmpd60 reduced dementia-related gene expression in vivo, effects that were recapitulated when treating the APPSWE-1349 Alzheimer mouse. In cardiac aging, Cmpd60 treatment activated favorable developmental gene expression in vivo and in line with this, improved ventricular cardiomyocyte contraction and relaxation in a cell model of cardiac hypertrophy. Our work establishes that a systemic, two-week treatment with an HDAC1/2 inhibitor serves as a multi-tissue, healthy aging intervention in mammals. This holds potential for translation towards therapeutics that promote healthy aging in humans.

pathology↗

bioRxiv2023

Identification and mapping of human lymph node stromal cell subsets by combining single-cell RNA sequencing with spatial transcriptomics.

Lymph node stromal cells (LNSCs) have a crucial immunomodulatory function, but their heterogeneity in human is incompletely understood. Here, we report the single cell RNA sequencing (scRNA-seq) of 12000 LNSCs isolated from a human lymph node (LN). This study comprehensively defines the gene signatures of 10 fibroblast subtypes: CCL21+SC, CCL19+SC, CD34+CXCL14+SC, pericytes, DES+SC, LAMP5+SC, NR4A1+BCAM+ SC, HLA-DR+SC, SEPT4+SC and GLDN+SC. To explore the heterogeneous stromal compartment within the complex LN tissue architecture, we integrated the scRNA-seq profiles of the identified LNSC subsets with a publicly available human spatial transcriptomic LN dataset and predicted their location within the complex LN tissue architecture. Each LNSC subtype was spatially restricted to specific LN regions, indicating different LNSC-lymphocyte interactions which was further investigated using NicheNet. The positioning of distinct LNSC subtypes in different LN regions sets the stage for future research on the relationship between LNSC-specific niches and immunomodulatory function during health and disease.

cell biology↗

bioRxiv2023

Profiling of microglia nodules in multiple sclerosis reveals propensity for lesion formation

Clusters of ramified HLA-DR+ cells, known as microglia nodules, are associated with brain pathology. Here we investigated if microglia nodules in the normal-appearing white matter (NAWM) of multiple sclerosis (MS) are different from microglia nodules in white matter (WM) in stroke and whether they may relate to the start of demyelinating MS lesions. We studied the relation between microglia nodules and pathological severity in an MS autopsy cohort (n=167), and we compared frequency, size, and gene expression of microglia nodules in MS (n=7) and stroke (n=7). MS donors with microglia nodules (64%) had a higher lesion load and a higher proportion of active lesions compared to donors without microglia nodules (36%). We found altered expression of genes in microglia nodules in MS compared to stroke, including genes previously shown to be upregulated in MS lesions. Genes associated with lipid metabolism, presence and proliferation of T and B cells, production of and response to immunoglobulins and cytokines (specifically TNF and IFN), activation of the complement cascade, and metabolic stress were upregulated. Using immunohistochemistry, we confirmed that in MS, more than in stroke, microglia nodules are associated with membrane attack complexes, have phagocytosed oxidized phospholipids, and have a tubular mitochondrial network reflecting increased metabolic activity. Furthermore, in MS, some nodules encapsulated partially demyelinated axons. Taken together, we propose that activation of some microglia nodules in MS by pro-inflammatory cytokines and immunoglobulins in combination with phagocytosis of oxidized phospholipids may lead to a volatile phenotype prone to form MS lesions.

neuroscience↗

bioRxiv2021

A public antibody class recognizes a novel S2 epitope exposed on open conformations of SARS-CoV-2 spike

Delineating the origins and properties of antibodies elicited by SARS-CoV-2 infection and vaccination is critical for understanding their benefits and potential shortcomings. Therefore, we investigated the SARS-CoV-2 spike (S)-reactive B cell repertoire in unexposed individuals by flow cytometry and single-cell sequencing. We found that [~]82% of SARS-CoV-2 S-reactive B cells show a naive phenotype, which represents an unusually high fraction of total human naive B cells ([~]0.1%). Approximately 10% of these naive S-reactive B cells shared an IGHV1-69/IGKV3-11 B cell receptor pairing, an enrichment of 18-fold compared to the complete naive repertoire. A proportion of memory B cells, comprising switched ([~]0.05%) and unswitched B cells ([~]0.04%), was also reactive with S and some of these cells were reactive with ADAMTS13, which is associated with thrombotic thrombocytopenia. Following SARS-CoV-2 infection, we report an average 37-fold enrichment of IGHV1-69/IGKV3-11 B cell receptor pairing in the S-reactive memory B cells compared to the unselected memory repertoire. This class of B cells targets a previously undefined non-neutralizing epitope on the S2 subunit that becomes exposed on S proteins used in approved vaccines when they transition away from the native pre-fusion state because of instability. These findings can help guide the improvement of SARS-CoV-2 vaccines.

immunology↗

bioRxiv2020

Core Circadian Clock Genes Per1 and Per2 regulate the Rhythm in Photoreceptor Outer Segment Phagocytosis

Retinal photoreceptors undergo daily renewal of their distal outer segments, a process indispensable for maintaining retinal health. Photoreceptor Outer Segment (POS) phagocytosis occurs as a daily peak, roughly about one hour after light onset. However, the underlying cellular and molecular mechanisms which initiate this process are still unknown. Here we show that, under constant darkness, mice deficient for core circadian clock genes (Per1 and Per2), lack a daily peak in POS phagocytosis. By qPCR analysis we found that core clock genes were rhythmic over 24h in both WT and Per1, Per2 double mutant whole retinas. More precise transcriptomics analysis of laser capture microdissected WT photoreceptors revealed no differentially, expressed genes between time-points preceding and during the peak of POS phagocytosis. By contrast, we found that microdissected WT retinal pigment epithelium (RPE) had a number of genes that were differentially expressed at the peak phagocytic time-point compared to adjacent ones. We also found a number of differentially expressed genes in Per1, Per2 double mutant RPE compared to WT ones at the peak phagocytic time-point. Finally, based on STRING analysis we found a group of interacting genes which potentially drive POS phagocytosis in the RPE. This potential pathway consists of genes such as: Pacsin1, Syp, Camk2b and Camk2d among others. Our findings indicate that Per1 and Per2 are necessary clock components for driving POS phagocytosis and suggest that this process is transcriptionally driven by the RPE. DeclarationsO_ST_ABSFundingC_ST_ABSThis project has been funded with support from the NeuroTime Erasmus+ grant (European Union), Rotterdamse Stichting Blindenbelangen (Netherlands), Nelly Reef fund (Netherlands), Stichting voor Ooglijders (Netherlands), Stichting tot Verbetering van het Lot der Blinden (Netherlands) and Retina France (France). Conflicts of interest/Competing interestsThe authors declare no competing interests. Availability of data and materialData supporting the conclusions of this article are included within the article and are available from the corresponding authors on reasonable request. Code availabilityThe R code for analysis is available from the corresponding authors on reasonable request. Ethics approvalAll experimental procedures were performed in accordance with the Association for Research in Vision and Ophthalmology Statement on Use of Animals in Ophthalmic and Vision Research, as well as with the European Union Directive (2010/63/EU). Consent to participateNot applicable Consent for publicationAll authors read and approve of the contents of this manuscript. Author contributionsN.M. performed experiments, analysis, prepared figures, wrote the manuscript and obtained funding. O.A.-H.H. performed experiments, data analysis, prepared figures and obtained funding. P.D.M. and A.J. performed bioinformatics analysis and edited the manuscript. U.B., J.B.t.B. and C.S. provided technical assistance, performed experiments, prepared figures and edited the manuscript. D.H., A.A.B. and M.-P.F.-S. conceptualized and directed the project, obtained funding, provided resources, performed analysis and edited the manuscript.

neuroscience↗

bioRxiv2020

Reduced ech-6 Expression Attenuates Fat-induced Premature Aging in C. elegans

Deregulated energy homeostasis represents a hallmark of aging and results from complex gene-by-environment interactions. Here, we discovered that reducing the expression of the gene ech-6 encoding enoyl-CoA hydratase remitted fat diet-induced deleterious effects on lifespan in Caenorhabditis elegans, while a basal expression of ech-6 was important for survival under normal dietary conditions. Lipidomics revealed that supplementation of fat in ech-6-silenced worms had marginal effects on lipid profiles, suggesting an alternative fat utilization for energy production. Transcriptomics further suggest a causal relation between the lysosomal pathway, energy production, and the longevity effect conferred by the interaction between ech-6 and high-fat diets. Indeed, enhancing energy production from endogenous fat by overexpressing lysosomal lipase lipl-4 recapitulated the lifespan effects of high-fat diets on ech-6-silenced worms. Collectively, these results reveal that the gene ech-6 modulates metabolic flexibility and may be a target for promoting metabolic health and longevity.

cell biology↗

bioRxiv2020

Inhibition of the neuromuscular acetylcholine receptor with atracurium activates FOXO/DAF-16-induced longevity

Transcriptome-based drug screening is emerging as a powerful tool to identify geroprotective compounds to intervene in age-related disease. We hypothesized that, by mimicking the transcriptional signature of the highly conserved longevity intervention of FOXO3 (daf-16 in worms) overexpression, we could identify and repurpose compounds with similar downstream effects to increase longevity. Our in silico screen, utilizing the LINCS transcriptome database of genetic and compound interventions, identified several FDA-approved compounds that activate FOXO downstream targets in mammalian cells. These included the neuromuscular blocker atracurium, which also robustly extends both lifespan and healthspan in C. elegans. This longevity is dependent on both daf-16 signaling and inhibition of the neuromuscular acetylcholine receptor. Other neuromuscular blockers tubocurarine and pancuronium caused similar healthspan benefits. We demonstrate nuclear localization of DAF-16 upon atracurium treatment, and, using RNAseq transcriptomics, identify activation of DAF-16 downstream effectors. Together, these data demonstrate the capacity to mimic genetic lifespan interventions with drugs, and in doing so, reveal that the neuromuscular acetylcholine receptor regulates the highly conserved FOXO/DAF-16 longevity pathway.

molecular biology↗

bioRxiv2020

Framing the potential of public frameshift peptides as immunotherapy targets in colon cancer

Approximately 15% of Colon Cancers are Microsatellite Instable (MSI). Frameshift Peptides (FPs) formed in MSI Colon Cancer are potential targets for immunotherapeutic strategies. Here we comprehensively characterize the mutational landscape of 71 MSI Colon Cancer patients from the cancer genome atlas (TCGA-COAD). We confirm that the mutations in MSI Colon Cancers are frequently frameshift deletions (23% in MSI; 1% in microsatellite stable), We find that these mutations cluster at specific locations in the genome which are mutated in up to 41% of the patients. We filter these for an adequate variant allele frequency, a sufficient mean mRNA level and the formation of a Super Neo Open Reading Frame (SNORF). Finally, we check the influence of Nonsense Mediated Decay by comparing RNA and DNA sequencing results. Thereby we identify a set of 20 NMD-escaping Public FPs (PFPs) that cover over 90% of MSI Colon Cancer patients and 3 out of 4 Lynch patients in the TCGA-COAD. This underlines the potential for PFP directed immunotherapy, both in a therapeutic and a prophylactic setting.

cancer biology↗

bioRxiv2018

Glycine promotes longevity in Caenorhabditis elegans in a methionine cycle-dependent fashion

The deregulation of metabolism is a hallmark of aging. As such, changes in the expression of metabolic genes and the profiles of amino acid levels are features associated with aging animals. We previously reported that the levels of most amino acids decline with age in Caenorhabditis elegans (C. elegans). Glycine, in contrast, substantially accumulates in aging C. elegans. In this study we show that this is coupled to a decrease in gene expression of enzymes important for glycine catabolism. We further show that supplementation of glycine significantly prolongs C. elegans lifespan and ameliorates specific transcriptional changes that are associated with aging. Glycine feeds into the methionine cycle. We find that mutations in components of this cycle, methionine synthase (metr-1) and S-adenosylmethionine synthetase (sams-1), completely abrogate glycine-induced lifespan extension. Strikingly, the beneficial effects of glycine supplementation are conserved when we supplement with serine, also driving the methionine cycle. RNA sequencing of serine- and glycine-supplemented worms reveals similar transcriptional profiles including widespread gene suppression. Taken together, these data uncover a novel role of glycine in the deceleration of aging through its function in the methionine cycle.\n\nAuthor summaryThere are a growing number of studies showing that amino acids function as signal metabolites that influence aging and health. Although contemporary -OMICs studies have uncovered various associations between metabolite levels and aging, in many cases the directionality of the relationships is unclear. In a recent metabolomics study, we found that glycine accumulates in aged C. elegans while other amino acids decrease. The present study shows that glycine supplementation prolongs longevity and drives a genome-wide inhibition effect on C. elegans gene expression. Glycine as a one-carbon donor fuels the methyl pool of one-carbon metabolism composed of folates and methionine cycle. We find that glycine-mediated longevity effect is fully dependent on methionine cycle, and that all of these observations are conserved with supplementation of the other one-carbon amino acid, serine. These results provide a novel role for glycine as a promoter of longevity and bring new insight into the role of one-carbon amino acids in the regulation of aging that may ultimately be beneficial for humans.

systems biology↗

bioRxiv2017

Distinct prophase arrest mechanisms in human male meiosis

To prevent chromosomal aberrations to be transmitted to the offspring, strict meiotic checkpoints are in place to remove aberrant spermatocytes. However, in about 1% of all males these checkpoints cause complete meiotic arrest leading to azoospermia and subsequent infertility. We here unravel two clearly distinct meiotic arrest mechanisms that act during the prophase of human male meiosis. Type I arrested spermatocytes display severe asynapsis of the homologous chromosomes, disturbed XY-body formation and increased expression of the Y-chromosome encoded gene ZFY and seem to activate a DNA damage pathway leading to induction of p63 mediated spermatocyte elimination. Type II arrested spermatocytes display normal chromosome synapsis, normal XY-body morphology and meiotic crossover formation but have a lowered expression of several cell cycle regulating genes and fail to properly silence the X-chromosome encoded gene ZFX. Discovery and understanding of these meiotic arrest mechanisms increases our knowledge on how genomic stability is guarded during human germ cell development.

cell biology↗