Biology subjects

van der Maarel, S. M.

Publications and source records attributed to van der Maarel, S. M..

12 recordsLinked to original sources

bioRxiv2026

Distinct transcriptional programs define human IgG4+ memory B cells

Human immunoglobulin G4 (IgG4) shapes both protective and pathogenic immunity, influencing conditions ranging from allergy and autoimmunity to cancer. However, subclass-specific targeting of memory B cells remains challenging due to limited knowledge of their phenotypic and functional heterogeneity. Here, we show that IgG4+ memory B cells are overrepresented in a niche of FCER2+BAFFR+ memory B cells, can be classified in several subtypes, have a distinct transcription factor profile and are the only memory B cell subset to express sterile IGHE transcripts. While IgG4+ B cells display a unique transcriptional profile, only BAFFR, IL5Rb and the B cell receptor were upregulated on protein level on IgG4+ cells. IgG4+ B cells have normal repertoire diversity, but a distinct germline V-gene usage, suggesting IgG4 responses are driven by specific antigens. By labeling autoreactive B cells, we confirmed that MuSK myasthenia gravis (an archetypal IgG4-mediatedautoimmune disease) patients have a normal memory B cell profile and that autoreactive IgG4+ memory B cells are extremely rare. These results highlight the unique features of IgG4+ B cells, provide insight on potential subclass-specific therapeutic targets and point towards an antigen-driven IgG4 response within a largely non-autoreactive memory B cell pool.

immunology↗

bioRxiv2026

Resolution of the D4Z4 repeat responsible for facioscapulohumeral muscular dystrophy with HiFi sequencing

The D4Z4 macrosatellite repeat encompasses some of the most difficult-to-resolve disease-related variations in the human genome. D4Z4 has a repeat unit of 3.3 kb (encoding the DUX4 gene) that is present in up to 100 copies on two chromosomes (4 and 10), while DUX4 can only be expressed in somatic cells from the permissive A haplotype that usually occurs on chromosome 4. Facioscapulohumeral muscular dystrophy (FSHD) is caused by chromatin relaxation and ectopic expression of DUX4 in skeletal muscle, mediated by contraction of D4Z4 to 1-10 copies (FSHD1, 95% of FSHD cases) or mutations in chromatin factor genes such as SMCHD1 (FSHD2, 5% of FSHD cases). Due to its large size, disease specific haplotypes and sequence homology between chromosomes, D4Z4 is challenging to resolve by current sequencing technologies. We report a computational tool, Kivvi, to genotype D4Z4 using PacBio whole-genome long-read sequence data. Kivvi detects all D4Z4 alleles in a sample, reporting the repeat size, chromosome (4 vs. 10), distal haplotype (A vs. non-permissive haplotypes) and the methylation level of each allele. We validated Kivvi against gold standard assays for FSHD diagnostics, detecting 100% of contracted alleles and correctly classifying 90% of noncontracted alleles. We showed differential methylation signals between FSHD1 and candidate FSHD2 samples. We profiled D4Z4 across 601 individuals from five ancestral populations, revealing extensive genetic diversity. We identified common haplotypes of D4Z4 alleles and characterized hybrid repeat units, hybrid repeat arrays, and translocation alleles. Combined with HiFi long reads, Kivvi enables the consolidation of multiple FSHD assays into a single workflow and facilitates the discovery of novel genetic modifiers of FSHD through population-scale studies.

genetics↗

bioRxiv2026

MuSK antibodies differently affect the MuSK signaling cascade depending on valency and epitope specificity

Muscle-specific kinase (MuSK) is a pivotal player in forming and maintaining healthy neuromuscular junctions (NMJ). In MuSK myasthenia gravis (MG), autoantibodies targeting MuSK disrupt its function, impairing neuromuscular transmission and causing fatigable skeletal muscle weakness. MuSK autoantibodies predominantly belong to the IgG4 subclass, which bind in a monovalent fashion due to Fab-arm exchange, although autoantibodies of other subclasses also exist. Polyclonal autoreactive IgG from patients may therefore harbor a variety of monovalent and bivalent MuSK antibodies with potentially distinct effects on MuSK signaling. To further unravel the pathomechanisms underlying MuSK MG, we have investigated how MuSK antibody-binding affects MuSK functioning with a diverse panel of (patient-derived) monoclonal MuSK antibodies. Our findings reveal that the valency of antibody-binding influences binding kinetics to MuSK, inhibition of agrin-induced MuSK activation, Dok7 binding to MuSK and NMJ gene expression. Monovalent binding to the frizzled domain of MuSK did not inhibit agrin-induced MuSK activation, while monovalent binding to the Ig-like domain 1 does. Moreover, the kinetics of Dok7 degradation induced by bivalent MuSK antibodies appear to depend on binding-epitope of MuSK. Surprisingly, none of the clones tested (both bivalent and monovalent) increased MuSK internalization. Taken together, the cumulative pathogenic effect of polyclonal MuSK antibodies in individual MuSK MG patients thus likely depends on autoantibody titer, affinity and the unique composition of MuSK autoantibodies varying in epitope and valency. This research enriches our understanding of the intricate interactions between antibodies and MuSK in MuSK MG and offers potential insights into novel therapeutic strategies using MuSK antibodies.

immunology↗

bioRxiv2025

A discrete region of the D4Z4 is sufficient to initiate epigenetic silencing

The DUX4 transcription factor is briefly expressed in the early embryo and is epigenetically repressed in somatic tissues. Loss of epigenetic repression can result in the aberrant expression of DUX4 in skeletal muscle and can cause facioscapulohumeral dystrophy (FSHD). Multiple factors have been identified as necessary to maintain epigenetic silencing of DUX4 in skeletal muscle, but whether specific sequences at the DUX4 locus are sufficient for epigenetic silencing has been unknown. We cloned fragments of the D4Z4 macrosatellite repeat, the DNA region that encompasses the DUX4 retrogene, adjacent to a reporter driven by a constitutive promoter and identified a single fragment sufficient to epigenetically repress reporter gene expression. Previously identified suppressors of DUX4 expression--SETDB1, ATF7IP, SIN3A/B, and LRIF1--were necessary for silencing activity and p38 inhibitors enhanced suppression. These findings identify a key regulatory sequence for D4Z4 epigenetic repression and establish a model system for mechanistic and discovery studies.

molecular biology↗

bioRxiv2024

Lrif1 modulates Trim28-mediated repression of the Dux locus in mouse embryonic stem cells

Germline mutations in SMCHD1, DNMT3B and LRIF1 can cause facioscapulohumeral muscular dystrophy type 2 (FSHD2). FSHD is an epigenetic skeletal muscle disorder in which partial failure in heterochromatinization of the D4Z4 macrosatellite repeat causes spurious expression of the repeat-embedded DUX4 gene in skeletal muscle, ultimately leading to muscle weakness and wasting. All three proteins play a role in chromatin organization and gene silencing; however, their functional relationship has not been fully elucidated. Here, we show that knockdown of Lrif1, but not of the other two FSHD2 genes, in mouse embryonic stem cells leads to modest upregulation of the 2-cell cleavage stage transcriptional program driven by the transcription factor Dux, which is the mouse functional homologue of human DUX4. Furthermore, we show that Lrif1 interacts with Trim28, a known Dux repressor and that this interaction is independent of Cbx proteins and Smchd1. We uncover that modest Dux upregulation in Lrif1 knockdown mESCs coincides with decreased Trim28 occupancy at the Dux locus. Together, our results provide evidence for a conserved function of Lrif1 in repressing an early zygotic genome activator in mice and humans.

molecular biology↗

bioRxiv2024

SUMOylation differentially regulates SMCHD1 complex formation and function in a genomic context-specific manner

Structural Maintenance of Chromosomes Hinge Domain Containing 1 (SMCHD1) is a chromatin repressor regulating gene expression and chromatin architecture of distinct autosomal and X-chromosomal loci. SMCHD1 mutations cause derepression of the D4Z4 macrosatellite repeat-embedded DUX4 gene in skeletal muscle of facioscapulohumeral muscular dystrophy (FSHD) patients Little is known about the regulation and post-translational modification of SMCHD1. Here we report the SUMOylation dynamics of SMCHD1 and its impact on autosomal single copy and repetitive loci, and the inactive X chromosome (Xi). We identify that SMCHD1 is SUMOylated primarily at lysine 1374, uncover factors regulating SMCHD1 SUMOylation, and demonstrate that SMCHD1 interacts with chromatin repressors TRIM28, HNRNPK and SETDB1 in a SUMO-dependent manner. We find that SUMOylation impacts Xi engagement of SMCHD1, maintenance of a repressive D4Z4 chromatin structure preventing DUX4 expression, and regulation of LRIF1 promoter activity. The rapid, SUMO-dependent upregulation of DUX4 could explain the bursts of DUX4 expression typical for FSHD muscle.

molecular biology↗

bioRxiv2024

Patient-specific therapeutic benefit of MuSK agonist antibody ARGX-119 in MuSK myasthenia gravis passive transfer models

Muscle-specific kinase (MuSK) orchestrates establishment and maintenance of neuromuscular synapses, which enable muscle contraction. Autoantibodies targeting MuSK cause myasthenia gravis (MG), a disease characterized by fatigable skeletal muscle weakness which requires chronic immunosuppressive treatment and ventilatory support at some point in [~]30% of patients. MuSK autoantibodies are predominantly IgG4 and are bispecific, functionally monovalent antibodies due to Fab-arm exchange. Through monovalent binding, MuSK IgG4 autoantibodies act as antagonists on the MuSK signalling pathway, impairing neuromuscular synaptic function. In contrast, bivalent MuSK antibodies act as agonists of the MuSK signalling pathway. Since symptoms in MuSK MG are largely caused by antagonistic monovalent MuSK antibodies, we hypothesized that a bivalent MuSK agonist could rescue MuSK MG, bypassing the need for generalized immunosuppression. In this study, we investigated whether an agonist antibody targeting the Frizzled-like domain of MuSK, ARGX-119, can ameliorate disease in MuSK MG models induced by passive transfer of polyclonal IgG4 from unrelated patients. For each patient material we first established the minimal dose for a progressive MG phenotype based on muscle function tests. ARGX-119 significantly improved survival and muscle weakness in a mouse model induced by one patient material, but not by three others. Mechanistically, this patient-specific efficacy could not be explained by autoantibody epitope specificity, titer or competition for ARGX-119 binding, but rather correlated to the presence of MuSK activating antibodies in some patients. We further provide evidence that an in vitro assay may predict which patients potentially benefit from ARGX-119 and that this treatment, when effective in MuSK MG mice, follows a bell-shaped dose-effect curve. These results provide first proof of concept of a MuSK agonist in a clinically relevant model for MuSK MG. We anticipate this to be a starting point for investigating the therapeutic benefit of ARGX-119 in MuSK MG and other neuromuscular diseases hallmarked by neuromuscular synaptic dysfunction. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=151 SRC="FIGDIR/small/606156v1_figu1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@15c08faorg.highwire.dtl.DTLVardef@1517281org.highwire.dtl.DTLVardef@3498c2org.highwire.dtl.DTLVardef@118e9af_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIMuSK agonist ARGX-119 can rescue MuSK MG in a patient-specific manner C_LIO_LIMuSK agonism follows a bell-shaped efficacy curve in this MuSK MG mouse model C_LIO_LIVariation in ARGX-119 efficacy between patient models is not explained by competition for binding on MuSK, but rather appears related to an agonistic fraction of patient antibodies C_LIO_LIAn in vitro assay is potentially predictive for treatment efficacy of the MuSK agonist C_LI

neuroscience↗

bioRxiv2023

Autoantibody subclass predominance is not driven by aberrant class switching or impaired B cell development

A subset of autoimmune diseases is characterized by predominant pathogenic IgG4 autoantibodies (IgG4-AIDs). Why IgG4 predominates in these disorders is unknown. We hypothesized that dysregulated B cell maturation or aberrant class switching causes overrepresentation of IgG4+ B cells and plasma cells. Therefore, we compared the B cell compartment of patients with muscle-specific kinase (MuSK) myasthenia gravis (MG), pemphigus, leucine-rich glioma inactivated (LGI1) encephalitis and contactin-associated protein-like 2 (CASPR2) encephalitis (four IgG4-AIDs) to patients with acetylcholine receptor (AChR) MG, Lambert-Eaton myasthenic syndrome (LEMS) (two IgG1-3-AIDs) and age-matched healthy donors, using flow cytometry. B cell subset relative abundance at all maturation stages was normal, except for a, possibly treatment-related, reduction in immature and naive CD5+ cells in IgG4-AIDs. IgG4+ B cell and plasma cell fractions were normal in IgG4-AID patients, however they had an (sub)class-independent 8-fold increase in circulating mature CD20-CD138+ plasma cells. No autoreactivity was found in this subset after sorting. In conclusion, patients with IgG4-AID do not show increased numbers of IgG4-expressing cells. These results argue against aberrant B cell development in these patients and rather suggest the autoantibody subclass predominance to be antigen-driven. The similarities between B cell subset numbers among these patients suggest that these IgG4-AIDs, despite displaying variable clinical phenotypes, share a similar underlying immune profile. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=119 SRC="FIGDIR/small/546522v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@1444429org.highwire.dtl.DTLVardef@d70867org.highwire.dtl.DTLVardef@168a7c0org.highwire.dtl.DTLVardef@1dd4483_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2023

Validation of the association between MRI and gene signatures in facioscapulohumeral dystrophy muscle: implications for clinical trial design

Identifying the aberrant expression of DUX4 in skeletal muscle as the cause of facioscapulohumeral dystrophy (FSHD) has led to rational therapeutic development and clinical trials. Several studies support the use of MRI characteristics and the expression of DUX4-regulated genes in muscle biopsies as biomarkers of FSHD disease activity and progression, but reproducibility across studies needs further validation. We performed lower-extremity MRI and muscle biopsies in the mid-portion of the tibialis anterior (TA) muscles bilaterally in FSHD subjects and validated our prior reports of the strong association between MRI characteristics and expression of genes regulated by DUX4 and other gene categories associated with FSHD disease activity. We further show that measurements of normalized fat content in the entire TA muscle strongly predict molecular signatures in the mid-portion of the TA. Together with moderate-to-strong correlations of gene signatures and MRI characteristics between the TA muscles bilaterally, these results suggest a whole muscle model of disease progression and provide a strong basis for inclusion of MRI and molecular biomarkers in clinical trial design.

molecular biology↗

bioRxiv2021

SMCHD1 has separable roles in chromatin architecture and gene silencing that could be targeted in disease

The interplay between 3D chromatin architecture and gene silencing is incompletely understood. Here, we report a novel point mutation in the non-canonical SMC protein SMCHD1 that enhances its silencing capacity at endogenous developmental targets and at the facioscapulohumeral muscular dystrophy associated macro-array, D4Z4. Heightened SMCHD1 silencing perturbs developmental Hox gene activation, causing a homeotic transformation in mice. Paradoxically, the mutant SMCHD1 appears to enhance insulation against another epigenetic regulator complex, PRC2, while depleting long range chromatin interactions akin to what is observed in the absence of SMCHD1. These data suggest that SMCHD1s role in long range chromatin interactions is not directly linked to gene silencing or insulating the chromatin, refining the model for how the different levels of SMCHD1-mediated chromatin regulation interact to bring about gene silencing in normal development and disease.

molecular biology↗

bioRxiv2020

Functional monovalency amplifies the pathogenicity of anti-MuSK IgG4 in myasthenia gravis

Human IgG4 usually displays anti-inflammatory activity, and observations of IgG4 autoantibodies causing severe autoimmune disorders are therefore poorly understood. In blood, IgG4 antibodies naturally engage in a stochastic process termed Fab-arm exchange in which unrelated IgG4s exchange half-molecules continuously. The resulting IgG4 antibodies are composed of two different binding sites, thereby acquiring monovalent binding and inability to cross-link for each antigen recognized. Here, we demonstrate this process amplifies autoantibody pathogenicity in a classic IgG4-mediated autoimmune disease: muscle-specific kinase (MuSK) myasthenia gravis (MG). In mice, monovalent anti-MuSK IgG4s caused rapid and severe myasthenic muscle weakness, whereas the same antibodies in their parental bivalent form were less potent or did not induce a phenotype. Mechanistically this could be explained by opposing effects on MuSK signaling. Isotype switching to IgG4 in an autoimmune response thereby may be a critical step in the development of disease. Our study establishes functional monovalency as a novel pathogenic mechanism in IgG4-mediated autoimmune disease and potentially other disorders. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=146 HEIGHT=200 SRC="FIGDIR/small/296293v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@45c221org.highwire.dtl.DTLVardef@1cc31cdorg.highwire.dtl.DTLVardef@d9b09borg.highwire.dtl.DTLVardef@1d9b681_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2019

DUX4-induced bidirectional HSATII satellite repeat transcripts form intranuclear double stranded RNA foci in human cell models of FSHD

The DUX4 transcription factor is normally expressed in the cleavage stage embryo and regulates genes involved in embryonic genome activation. Mis-expression of DUX4 in skeletal muscle, however, is toxic and causes facioscapulohumeral muscular dystrophy (FSHD). We recently showed DUX4-induced toxicity is due, in part, to the activation of the double-stranded RNA (dsRNA) response pathway and the accumulation of intranuclear dsRNA foci. Here, we determined the composition of DUX4-induced dsRNAs. We found that a subset of DUX4-induced dsRNAs originate from inverted Alu repeats embedded within the introns of DUX4-induced transcripts and from DUX4-induced dsRNA-forming intergenic transcripts enriched for endogenous retroviruses, Alu and LINE-1 elements. However, these repeat classes were also represented in dsRNAs from cells not expressing DUX4. In contrast, pericentric human satellite II (HSATII) repeats formed a class of dsRNA specific to the DUX4 expressing cells. Further investigation revealed that DUX4 can initiate the bidirectional transcription of normally heterochromatin-silenced HSATII repeats. DUX4 induced HSATII RNAs co-localized with DUX4-induced nuclear dsRNA foci and with intranuclear aggregation of EIF4A3 and ADAR1. Finally, gapmer-mediated knockdown of HSATII transcripts depleted DUX4-induced intranuclear ribonucleoprotein aggregates and decreased DUX4-induced cell death, suggesting that HSATII formed dsRNAs contribute to DUX4 toxicity.

molecular biology↗