Biology subjects

Smit, A.

Publications and source records attributed to Smit, A..

10 recordsLinked to original sources

bioRxiv2026

The TREM-receptor family interactome in the human brain

The Triggering Receptors Expressed on Myeloid cells (TREMs) are a family of cell-surface receptors instrumental in the activation of different myeloid cells. TREM2, its most studied member, is genetically linked to Alzheimer disease (AD), and its interactions with BAmyloid; and APOE have placed it at the forefront of microglia dysfunction in the brain. However, the ligands and binding partners of the other TREM members (TREM1, TREML1, TREML2 and TREML4) are less well defined. Here, we used human AD and non-AD brain lysate to profile the interactome of the ligand binding domains of the different TREM receptors. Besides identifying known ligands for TREM1 (PGLYRP1), TREM2 (C1QL3, LGALSL) and TREML1 (Fibrinogens), we identified complement components and the apolipoproteins APOA1 and APOA4 as novel interactors of TREML1, and heparan sulfate modified proteins as binding partners for TREML2. Furthermore, similar to TREM2, all the TREMLs interacted with the apolipoproteins APOE and Clusterin. Using in vitro pulldowns with heparin, we confirmed that specifically TREML2 interacted with heparan sulfates, in a manner unaffected by the AD-linked S144G mutation. Together, our proteomics approach identified novel interactors for TREML1 and TREML2, cementing the role of the different TREM-proteins in lipid trafficking and immunity.

neuroscience↗

bioRxiv2026

Spatial Logic and Evolutionary Innovation in Human Placentation

Human pregnancy unfolds in a unique mosaic tissue context. Embryonic/fetal placental and maternal uterine cells (decidua basalis) coalesce, forming the basal plate where immune tolerance is coordinated and the utero-placental circulation is initiated. The remaining approximately 70% of the maternal-fetal interface is comprised of the chorionic membranes, an epithelial-like layer of placental cells that lies adjacent to but does not coalesce with the overlying decidua capsularis and parietalis. It is unknown how these two regions of the maternal-fetal interface, which are comprised of seemingly similar cell types, diverge anatomically and functionally. Likewise, it is unknown whether the molecular characteristics of the maternal-fetal interface vary across human populations, potentially contributing to population disparities in pregnancy complications. Here, we generated large-scale paired single-nucleus RNA-seq and chromatin-accessibility profiles of the basal plate and chorionic membranes-associated decidual compartments from diverse-ancestry pregnancies, integrated with spatial transcriptomics and multiplexed protein imaging. We show that the two interfaces share a conserved cytotrophoblast differentiation hierarchy, which is deployed differently resulting in the observed distinct architectures. In the chorionic membranes, progenitor, early, and mature extravillous cytotrophoblast (EVT) states form an epithelial-like laminar shell. In the basal plate, this hierarchy is elaborated upon to enable deep placentation: EVTs that arise early in pregnancy invade the farthest into the uterus, while mature EVTs accumulate superficially to sculpt the local maternal immune microenvironment. Comparative analysis identified DSC4, a decidual stromal cell subtype, as an anti-invasive barrier that is densely enriched adjacent to the chorionic membranes but substantially reduced at the basal plate. Population-resolved analysis further identified the DSC4 marker NID2, which encodes the basement-membrane glycoprotein nidogen-2, as an ancestry-associated rheostat of EVT invasion. A specific NID2 promoter haplotype arose on the modern-human lineage, is absent from available archaic-human genomes, and shows evidence of positive selection in Eurasian populations. This haplotype is associated with reduced local chromatin accessibility and lower NID2 expression in DSC4 cells. Consistent with this genetic association, extracellular NID2 directly suppressed the invasion of primary human cytotrophoblasts in vitro. Together, these findings reveal how a shared developmental program is spatially reconfigured across distinct regions of the maternal-fetal interface and identify a recent modern-human regulatory innovation that modulates maternal decidual restraint of fetal trophoblast invasion across populations.

genomics↗

bioRxiv2026

Sharing power: effects of rider ability and position on tandem performance

ObjectiveTandem cycling requires a coordinated effort between the pilot and the stoker. Previous research suggests that randomly paired tandem cyclists produce lower power output than when cycling solo. This study examined how a cyclists individual ability and their position on the tandem (pilot or stoker) affects pair performance, when partners are either closely matched or differ substantially in solo cycling capacity, as this might be relevant for training and selection. MethodsTwenty-three trained cyclists completed three 10-minute time trials: solo, equal-capacity tandem ([≤]25 W difference in solo performance), and unequal-capacity tandem ([≥]40 W difference). Mean power output, heart rate, cadence, and rating of perceived exertion (RPE) were recorded. Positions (pilot or stoker) were counterbalanced. Linear mixed-effects models assessed effects of capacity and position. ResultsRelative to solo cycling, equal-capacity tandem pairs revealed lower power output (-3.9%), lower heart rate (-2.3%), and lower RPE (-11.5%). Unequal-capacity tandems differed from solo only in heart rate (-2.7%). Stokers produced lower power relative to solo (-5.3%) and relative to pilots (-3.7%) and reported lower RPE relative to solo (-13.9%), while pilots matched their solo power at a lower heart rate (-2.9%). Cadence did not differ across conditions. Total tandem power averaged 95.6% of combined solo power, and differences in partner capacity did not significantly affect combined power output. ConclusionThis study provides the first known experimental data on how partner matching affects individual and combined power output in tandem cycling. Equal- and unequal-capacity tandem pairs showed similar performance. Lower power and RPE among stokers suggest reduced engagement or a redistribution of effort between riders. These findings highlight that effective tandem performance depends on physiological capacity and rider position on the tandem, but not on the difference in capacity between partners.

physiology↗

bioRxiv2026

Deletion of astrocyte intermediate filaments GFAP and Vimentin enhances protein synthesis and prevents early synaptic and cognitive dysfunction in a mouse model of Alzheimer's disease

In Alzheimers disease (AD) astrocytes become reactive, displaying hypertrophic morphology, increased expression of intermediate filament proteins GFAP and Vimentin and impaired homeostatic support to neurons. However, the contribution of reactive astrocytes to AD progression, particularly the role of cytoskeletal hypertrophy, remains unclear. Here, we investigate whether astrocyte intermediate filaments actively contribute to early AD progression. We show that astrogliosis appears as early as at 3 months in APP/PS1 mice, preceding amyloid-{beta} plaque deposition, and is characterized by a strong upregulation of GFAP and Vimentin. Genetic ablation of GFAP and Vimentin attenuated astrogliosis, as evidenced by the absence of hypertrophy of astrocyte processes and restored expression of glutamine synthetase and other proteins altered in reactive astrocytes in AD. Importantly, GFAP and Vimentin deletion prevented cognitive decline in 4-month old male and female mice, independently of amyloid plaque pathology or microglial reactivity. Mass-spectrometry based proteomics of the dorsal hippocampus revealed a downregulation of synaptic proteins and dysregulation of ribosomal and RNA-binding proteins in APP/PS1 mice, both of which were rescued by GFAP and Vimentin deletion. Using astrocyte-specific CRISPR-Cas9-mediated knockout of GFAP and Vimentin, we further demonstrate translation impairments in AD astrocytes, and that GFAP and Vimentin deletion restores this impaired astrocytic translation. Together, our findings identify intermediate filament proteins GFAP and Vimentin as active regulators of astrocyte protein synthesis, and reveal a previously unrecognized mechanism by which reactive astrocytes contribute to early cognitive dysfunction in AD. This highlights these astrocyte intermediate filaments as promising therapeutic targets to counteract reactive astrocyte-driven cognitive decline in the early stages of Alzheimers disease.

neuroscience↗

bioRxiv2023

Offline RL for generative design of protein binders

Offline Reinforcement Learning (RL) offers a compelling avenue for solving RL problems without the need for interactions with an environment, which may be expensive or unsafe. While online RL methods have found success in various domains, such as de novo Structure-Based Drug Discovery (SBDD), they struggle when it comes to optimizing essential properties derived from protein-ligand docking. The high computational cost associated with the docking process makes it impractical for online RL, which typically requires hundreds of thousands of interactions during learning. In this study, we propose the application of offline RL to address the bottleneck posed by the docking process, leveraging RLs capability to optimize non-differentiable properties. Our preliminary investigation focuses on using offline RL to conditionally generate drugs with improved docking and chemical properties.

bioinformatics↗

bioRxiv2023

Early-life stress exposure impacts the hippocampal synaptic proteome in a mouse model of Alzheimer's disease: age- and pathology-dependent effects on mitochondrial proteins

Epidemiological evidence indicates that early life stress (ES) exposure increases the risk for later-life diseases, such as Alzheimers disease (AD). Accordingly, we and others have shown that ES aggravates the development of, and response to, amyloid-beta (A{beta}) pathology in animal models. Moreover, ES-exposed transgenic APP/PS1 mice display deficits in both cognitive flexibility and synaptic function. As the mechanisms behind these changes were unclear, we here investigated how exposure to ES, using the limited nesting and bedding model, affects the synaptic proteome across 2 different ages in both wildtype and APP/PS1 transgenic mice. We found that, compared to wildtype mice, the hippocampal synaptosomes of APP/PS1 mice at an early pathological stage (4 months) showed a higher abundance of mitochondrial proteins and lower levels of proteins involved in actin dynamics. Interestingly, ES exposure in wildtype mice had similar effects on the level of mitochondrial and actin-related synaptosomal proteins at this age, whereas ES exposure had no additional effect on the synaptosomal proteome of early-stage APP/PS1 mice. Accordingly, ultrastructural analysis of the synapse using electron microscopy in a follow-up cohort showed fewer mitochondria in pre- and post-synaptic compartments of APP/PS1 and ES-exposed mice, respectively. At a later pathological stage (10 months), the hippocampal synaptic proteome of APP/PS1 mice revealed an upregulation of proteins related to A{beta} processing, that was accompanied by a downregulation of proteins related to postsynaptic receptor endocytosis. ES exposure no longer affected the synaptic proteome of wildtype animals by this age, whereas it affected the expression of astrocytic proteins involved in lipid metabolism in APP/PS1 mice. We confirmed a dysregulation of astrocyte protein expression in a separate cohort of 12-month-old mice, by immunostaining for the alpha subunit of the mitochondrial trifunctional protein and fatty acid synthase in astrocytes. In conclusion, our data suggest that ES and amyloidosis share pathogenic pathways involving synaptic mitochondrial dysfunction and astrocytic lipid metabolism. These pathways might be underlying contributors to the long-term aggravation of the APP/PS1 phenotype by ES, as well as to the ES-associated risk for AD progression. These data are publicly accessible online as a web app via https://amsterdamstudygroup.shinyapps.io/ES_Synaptosome_Proteomics_Visualizer/.

neuroscience↗

bioRxiv2022

Transcriptional diversity in synaptic gene sets is sufficient to discriminate cortical neuronal identity

Synapse diversity has been described from different perspectives, ranging from the specific neurotransmitters released, to their diverse biophysical properties and proteome profiles. However, synapse diversity at the transcriptional level has not been systematically identified across all synapse populations in the brain. To quantify postsynaptic and identify specific synaptic features of neuronal cell types we combined the SynGO (Synaptic Gene Ontology) database with single-cell RNA sequencing data of the mouse neocortex. We show that cell types can be discriminated by synaptic genes alone with the same power as all genes. The cell type discriminatory power is not equally distributed across synaptic genes as we could identify functional categories and synaptic compartments with greater cell type specific expression. Synaptic genes, and specific SynGO categories, belonged to three different types of gene modules: gradient expression over all cell types, gradient expression in selected cell types and cell class- or type-specific profiles. This data provides a deeper understanding of synapse diversity in the neocortex and identifies potential markers to selectively identify synapses from specific neuronal populations.

neuroscience↗

bioRxiv2022

Proximity of astrocyte leaflets to the synapse determines memory strength

SummaryAstrocyte distal processes, known as leaflets or perisynaptic astrocyte processes (PAPs), fine-tune synaptic activity by clearing neurotransmitters and limiting extrasynaptic glutamate diffusion. While learning and memory depends on orchestrated synaptic activity of neuronal ensembles within the hippocampus, it is becoming increasingly evident that astrocytes residing in the environment of these synapses play a central role in shaping memories. However, how astroglial synaptic coverage contributes to mnemonic processing remains largely unknown. Here, we targeted astrocyte leaflet structure in vivo by depleting Ezrin, an integral leaflet-structural protein, in astrocytes of the adult hippocampal CA1 using a CRISPR-Cas9 genetic approach. This resulted in significantly smaller astrocyte territories and reduced astroglial synaptic coverage. In addition, using genetically encoded glutamate sensors and whole-cell patch-clamp recordings from pyramidal neurons, we found that Ezrin deletion and the resultant manipulation of leaflet structure boosted extrasynaptic glutamate diffusion and NMDA-receptor activation. Importantly, these cellular phenotypes translated to enhanced fear memory expression that was accompanied by increased activation of CA1 pyramidal neurons in the days after learning occurred. We show that Ezrin is critical for astrocyte morphology as well as for adult hippocampal synapse integrity and function. Our data show that astrocyte leaflet structure gates memory strength by regulating glutamate spillover in the vicinity of memory-related synaptic activity.

neuroscience↗

bioRxiv2021

β-amyloid-driven synaptic depression requires PDZ protein interaction at AMPA-receptor subunit GluA3

Soluble oligomeric amyloid-{beta} (A{beta}) is a prime suspect to cause cognitive deficits in Alzheimers disease and weakens synapses by removing AMPA-type glutamate receptors (AMPARs). We show that synapses of CA1 pyramidal neurons become vulnerable to A{beta} when they express AMPAR subunit GluA3. We found that A{beta}-oligomers reduce the levels of GluA3 immobilized at spines, indicating they deplete GluA3-containing AMPARs from synapses. These A{beta}-driven effects critically depended on the PDZ-binding motif of GluA3. When GluA3 was expressed with a single amino acid mutation in its PDZ-binding motif that prevents GRIP binding, it did not end up at spines and A{beta} failed to trigger synaptic depression. GluA3 with a different point mutation in the PDZ-motif that leaves GRIP-binding intact but prevents its endocytosis, was present at spines in normal amounts but was fully resistant to effects of A{beta}. Our data indicate that A{beta}-mediated synaptic depression requires the removal of GluA3 from synapses. We propose that GRIP-detachment from GluA3 is a critical early step in the cascade of events through which A{beta} accumulation causes a loss of synapse.

neuroscience↗

bioRxiv2018

Inducing controlled cell cycle arrest and re-entry during asexual proliferation of Plasmodium falciparum malaria parasites.

The life cycle of the malaria parasite Plasmodium falciparum is tightly regulated, oscillating between stages of intense proliferation and quiescence. Cyclic 48-hour asexual replication of Plasmodium is markedly different from cell division in higher eukaryotes, and mechanistically poorly understood. Here, we report tight synchronisation of malaria parasites during the early phases of the cell cycle by exposure to DL--difluoromethylornithine (DFMO), which results in the depletion of polyamines. This induces an inescapable cell cycle arrest in G1 (~15 hours post-invasion) by blocking G1/S transition. Cell cycle-arrested parasites enter a quiescent G0-like state but, upon addition of exogenous polyamines, re-initiate their cell cycle in a coordinated fashion. This ability to halt malaria parasites at a specific point in their cell cycle, and to subsequently trigger re-entry into the cell cycle, provides a valuable framework to investigate cell cycle regulation in these parasites. We therefore used gene expression analyses to show that re-entry into the cell cycle involves expression of Ca2+-sensitive (cdpk4 and pk2) and mitotic kinases (nima and ark2), with deregulation of the pre-replicative complex associated with expression of pk2. Changes in gene expression could be driven through transcription factors MYB1 and two ApiAP2 family members. This new approach to parasite synchronisation therefore expands our currently limited toolkit to investigate cell cycle regulation in malaria parasites.

cell biology↗