Thromboembolic complications remain a major public health burden, making antithrombotic agents one of the most widely prescribed groups of medication, but the treatment is often challenging as it... Show moreThromboembolic complications remain a major public health burden, making antithrombotic agents one of the most widely prescribed groups of medication, but the treatment is often challenging as it at the same time increases risk of bleeding. With nationwide data from Statistics Netherlands, antithrombotic therapy and relevant clinical outcomes were comprehensively examined in the patient population of atrial fibrillation, overall or among those with comorbid cancer. The results suggest the patient population was increasingly receiving anticoagulants, driven by the newly introduced medication- direct oral anticoagulant and guided by the CHA2DS2-VASc score, and meanwhile the patient population experienced fewer ischemic stroke and major bleeding. In spite of these promising changes, suboptimal medication adherence and potential underuse of anticoagulants remain directions for further improvement. Antithrombotic agent use during pregnancy was also examined in the general Dutch pregnant population, which featured a surge in antiplatelet prescriptions, and risk of preeclampsia/eclampsia decreased and several newborn outcomes improved simultaneously. Together, the studies presented in this thesis provide an overview of antithrombotic therapy in the Netherlands in recent years, providing insights for further improving this treatment and relevant patient outcomes. Show less
Background: Colorectal cancer (CRC) is the third most prevalent cancer type. CRC-patients are at increased risk of venous and arterial thromboembolism (TE), but the magnitude of the risks, their... Show moreBackground: Colorectal cancer (CRC) is the third most prevalent cancer type. CRC-patients are at increased risk of venous and arterial thromboembolism (TE), but the magnitude of the risks, their predictors and consequences are not exactly known.Objectives: We aimed to determine incidence, predictors and prognosis of TE after incident CRC in a large, unselected population. Methods: Using data from Statistics Netherlands and the Netherlands Comprehensive Cancer Organization, all incident CRC-patients were identified between 2013 and 2018 plus a sample of 1:2 age- and sex-matched control subjects. Incidence rates and cumulative incidences for TE were estimated. Predictor variables for TE were explored by univariable Cox regression. The association between TE and all-cause mortality was evaluated by multivariable time-dependent Cox regression.Results: 68,238 incident CRC-patients were matched to 136,476 controls. CRC-patients had a 1-year cumulative venous TE (VTE) incidence of 1.93 % (95%CI 1.83-2.04), versus 0.24 % (95%CI 0.21-0.27) in controls (HR 8.85; 95%CI 7.83-9.99). For arterial TE (ATE), this was 2.74 % (95%CI 2.62-2.87) in CRC versus 1.88 % (95%CI 1.81-1.95) in controls (HR 1.57; 95%CI 1.47-1.66). Cancer stage, surgery, chemotherapy and asthma were predictors for VTE, whereas age, prior ATE and Parkinson's disease were predictors for ATE. CRC patients with TE had an increased risk of all-cause mortality (VTE HR; 3.68 (95%CI 3.30-4.10, ATE HR; 3.05 (95%CI 2.75-3.39)) compared with CRC-patients without TE.Conclusions: This Dutch nationwide cohort study adds detailed knowledge on the risk of VTE and ATE, their predictors and prognosis in CRC-patients. These findings may drive TE prophylactic management decisions. Show less
Chen, Q.; Timmermans, J.; Wen, W.; Bodegom, P.M. van 2023
Large topologically associated domains (TADs) contain irregularly spaced nucleosome clutches, and interactions between such clutches are thought to aid the compaction of these domains. Here, we... Show moreLarge topologically associated domains (TADs) contain irregularly spaced nucleosome clutches, and interactions between such clutches are thought to aid the compaction of these domains. Here, we reconstituted TAD-sized chromatin fibers containing hundreds of nucleosomes on native source human and lambda-phage DNA and compared their mechanical properties at the single-molecule level with shorter '601' arrays with various nucleosome repeat lengths. Fluorescent imaging showed increased compaction upon saturation of the DNA with histones and increasing magnesium concentration. Nucleosome clusters and their structural fluctuations were visualized in confined nanochannels. Force spectroscopy revealed not only similar mechanical properties of the TAD-sized fibers as shorter fibers but also large rupture events, consistent with breaking the interactions between distant clutches of nucleosomes. Though the arrays of native human DNA, lambda-phage and '601' DNA featured minor differences in reconstitution yield and nucleosome stability, the fibers' global structural and mechanical properties were similar, including the interactions between nucleosome clutches. These single-molecule experiments quantify the mechanical forces that stabilize large TAD-sized chromatin domains consisting of disordered, dynamically interacting nucleosome clutches and their effect on the condensation of large chromatin domains. Show less
Telomeres, the ends of eukaryotic chromosomes, play pivotal parts in ageing and cancer and are targets of DNA damage and the DNA damage response1-5. Little is known about the structure of telomeric... Show moreTelomeres, the ends of eukaryotic chromosomes, play pivotal parts in ageing and cancer and are targets of DNA damage and the DNA damage response1-5. Little is known about the structure of telomeric chromatin at the molecular level. Here we used negative stain electron microscopy and single-molecule magnetic tweezers to characterize 3-kbp-long telomeric chromatin fibres. We also obtained the cryogenic electron microscopy structure of the condensed telomeric tetranucleosome and its dinucleosome unit. The structure displayed close stacking of nucleosomes with a columnar arrangement, and an unusually short nucleosome repeat length that comprised about 132 bp DNA wound in a continuous superhelix around histone octamers. This columnar structure is primarily stabilized by the H2A carboxy-terminal and histone amino-terminal tails in a synergistic manner. The columnar conformation results in exposure of the DNA helix, which may make it susceptible to both DNA damage and the DNA damage response. The conformation also exists in an alternative open state, in which one nucleosome is unstacked and flipped out, which exposes the acidic patch of the histone surface. The structural features revealed in this work suggest mechanisms by which protein factors involved in telomere maintenance can access telomeric chromatin in its compact form. Show less
Understanding the genomic basis of memory processes may help in combating neurodegenerative disorders. Hence, we examined the associations of common genetic variants with verbal short-term memory... Show moreUnderstanding the genomic basis of memory processes may help in combating neurodegenerative disorders. Hence, we examined the associations of common genetic variants with verbal short-term memory and verbal learning in adults without dementia or stroke (N = 53,637). We identified novel loci in the intronic region of CDH18, and at 13q21 and 3p21.1, as well as an expected signal in the APOE/APOC1/TOMM40 region. These results replicated in an independent sample. Functional and bioinformatic analyses supported many of these loci and further implicated POC1. We showed that polygenic score for verbal learning associated with brain activation in right parieto-occipital region during working memory task. Finally, we showed genetic correlations of these memory traits with several neurocognitive and health outcomes. Our findings suggest a role of several genomic loci in verbal memory processes. Show less
Chen, Q.; Timmermans, J.; Wen, W.; Bodegom, P.M. van 2022
Drought impact monitoring is of crucial importance in light of climate change. However, we lack an understanding of the concomitant responses of ecosystems to a variety of drought characteristics... Show moreDrought impact monitoring is of crucial importance in light of climate change. However, we lack an understanding of the concomitant responses of ecosystems to a variety of drought characteristics and the links between drought and ecosystem anomaly characteristics for a comprehensive set of vegetation types to provide needed information for water management. In response, this study presents a new framework that allows us to explore the relationship between drought and its impact on ecosystems in greater detail. Specifically, our framework focuses on estimating jointly the hydrological and ecosystem temporal evolution and anomalies around a drought event using four pairs of metrics: onset-onset, duration-duration, intensity-intensity, and severity-severity of drought and vegetation damage. Additionally, we incorporated a metric on vegetation vulnerability based on changes in damage severity along a gradient of increasing drought severity. Based on this framework, we evaluated drought vulnerability patterns of various vegetation types across the Netherlands and Belgium in 2018 at high spatiotemporal resolution. Our results reveal a differential vulnerability of vegetation between ecosystems with increasing drought severity, which could aid future drought impact predictions. In particular, mosaic grasslands and tree/shrub croplands are highly sensitive to increasing drought severity. Individual characteristics (onset, duration, intensity and severity) of drought and vegetation damage behave differently in various vegetation types. For instance, broadleaved forests respond faster than other forests, while mixed forests suffer less damage than other types. The early warning threshold to drought for most vegetation types is around a Standardized Precipitation Evapotranspiration Index (SPEI) value of -1. The characterization of a suite of drought response characteristics through our impact analysis framework can be used in a wide variety of regions to understand current and possible future responses to drought. Show less
In vivo data are rare but essential for establishing the clinical potential of ruthenium-based photoactivated chemotherapy (PACT) compounds, a new family of phototherapeutic drugs that are... Show moreIn vivo data are rare but essential for establishing the clinical potential of ruthenium-based photoactivated chemotherapy (PACT) compounds, a new family of phototherapeutic drugs that are activated via ligand photosubstitution. Here a novel trisheteroleptic ruthenium complex [Ru(dpp)(bpy)(mtmp)](PF6)2 ([2](PF6)2, dpp = 4,7-diphenyl-1,10-phenanthroline, bpy = 2,2'-bipyridine, mtmp = 2-methylthiomethylpyridine) was synthesized and its light-activated anticancer properties were validated in cancer cell monolayers, 3D tumor spheroids, and in embryonic zebrafish cancer models. Upon green light irradiation, the non-toxic mtmp ligand is selectively cleaved off, thereby releasing a phototoxic ruthenium-based photoproduct capable notably of binding to nuclear DNA and triggering DNA damage and apoptosis within 24-48 h. In vitro, fifteen minutes of green light irradiation (21 mW cm-2, 19 J cm-2, 520 nm) were sufficient to generate high phototherapeutic indexes (PI) for this compound in a range of cancer cell lines including lung (A549), prostate (PC3Pro4), conjunctival melanoma (CRMM1, CRMM2, CM2005.1) and uveal melanoma (OMM1, OMM2.5, Mel270) cancer cell lines. The therapeutic potential of [2](PF6)2 was further evaluated in zebrafish embryo ectopic (PC3Pro4) or orthotopic (CRMM1, CRMM2) tumour models. The ectopic model consisted of red fluorescent PC3Pro4-mCherry cells injected intravenously (IV) into zebrafish, that formed perivascular metastatic lesions at the posterior ventral end of caudal hematopoietic tissue (CHT). By contrast, in the orthotopic model, CRMM1- and CRMM2-mCherry cells were injected behind the eye where they developed primary lesions. The maximally-tolerated dose (MTD) of [2](PF6)2 was first determined for three different modes of compound administration: (i) incubating the fish in prodrug-containing water (WA); (ii) injecting the prodrug intravenously (IV) into the fish; or (iii) injecting the prodrug retro-orbitally (RO) into the fish. To test the anticancer efficiency of [2](PF6)2, the embryos were treated 24 h after engraftment at the MTD. Optimally, four consecutive PACT treatments were performed on engrafted embryos using 60 min drug-to-light intervals and 90 min green light irradiation (21 mW cm-2, 114 J cm-2, 520 nm). Most importantly, this PACT protocol was not toxic to the zebrafish. In the ectopic prostate tumour models, where [2](PF6)2 showed the highest photoindex in vitro (PI > 31), the PACT treatment did not significantly diminish the growth of primary lesions, while in both conjunctival melanoma orthotopic tumour models, where [2](PF6)2 showed more modest photoindexes (PI ∼ 9), retro-orbitally administered PACT treatment significantly inhibited growth of the engrafted tumors. Overall, this study represents the first demonstration in zebrafish cancer models of the clinical potential of ruthenium-based PACT, here against conjunctival melanoma. Show less
Background Non-valvular atrial fibrillation (NVAF) patients are advised to switch from a vitamin K antagonist (VKA) to direct oral anticoagulant (DOAC) when time in therapeutic range (TTR) is low.... Show moreBackground Non-valvular atrial fibrillation (NVAF) patients are advised to switch from a vitamin K antagonist (VKA) to direct oral anticoagulant (DOAC) when time in therapeutic range (TTR) is low. Objective To examine if pre-switch TTR determines persistence patterns in NVAF patients who are switched from a VKA to DOAC. Patients/Methods Adult NVAF patients from three Dutch anticoagulation clinics who were newly switched from a VKA to DOAC between July 1, 2013 and September 30, 2018 were stratified by pre-switch TTR levels. DOAC prescription records were examined to determine persistence patterns according to a 100-day prescription gap. Cumulative incidences of non-persistence to DOAC were estimated using the cumulative incidence competing risk method. The association of pre-switch TTR levels with DOAC non-persistence was evaluated by Cox regression models. Results A total of 3696 NVAF patients were included, of whom 690 (18.7%) had a pre-switch TTR <= 45%. After switching from VKA to DOAC, 14.0% (95% confidence interval [CI] 11.3-17.0%) of the patients with a pre-switch TTR <= 45% became non-persistent to DOAC within 1 year, while 9.8% (95% CI 8.7-11.0%) did in those with a pre-switch TTR > 45%. In a multivariable model, a pre-switch TTR <= 45% was associated with a higher risk of non-persistence to DOAC (adjusted hazard ratio 1.55, 95% CI 1.22-1.97). Results were similar when using other cut-off points (60% or 70%) to define a low TTR. Conclusion NVAF patients switching from VKA to DOAC due to a low pre-switch TTR saw a worse persistence pattern to DOAC after the switch compared to patients with a high pre-switch TTR. Show less
Background Non-valvular atrial fibrillation (NVAF) patients are advised to switch from a vitamin K antagonist (VKA) to direct oral anticoagulant (DOAC) when time in therapeutic range (TTR) is low.... Show moreBackground Non-valvular atrial fibrillation (NVAF) patients are advised to switch from a vitamin K antagonist (VKA) to direct oral anticoagulant (DOAC) when time in therapeutic range (TTR) is low. Objective To examine if pre-switch TTR determines persistence patterns in NVAF patients who are switched from a VKA to DOAC. Patients/Methods Adult NVAF patients from three Dutch anticoagulation clinics who were newly switched from a VKA to DOAC between July 1, 2013 and September 30, 2018 were stratified by pre-switch TTR levels. DOAC prescription records were examined to determine persistence patterns according to a 100-day prescription gap. Cumulative incidences of non-persistence to DOAC were estimated using the cumulative incidence competing risk method. The association of pre-switch TTR levels with DOAC non-persistence was evaluated by Cox regression models. Results A total of 3696 NVAF patients were included, of whom 690 (18.7%) had a pre-switch TTR <= 45%. After switching from VKA to DOAC, 14.0% (95% confidence interval [CI] 11.3-17.0%) of the patients with a pre-switch TTR <= 45% became non-persistent to DOAC within 1 year, while 9.8% (95% CI 8.7-11.0%) did in those with a pre-switch TTR > 45%. In a multivariable model, a pre-switch TTR <= 45% was associated with a higher risk of non-persistence to DOAC (adjusted hazard ratio 1.55, 95% CI 1.22-1.97). Results were similar when using other cut-off points (60% or 70%) to define a low TTR. Conclusion NVAF patients switching from VKA to DOAC due to a low pre-switch TTR saw a worse persistence pattern to DOAC after the switch compared to patients with a high pre-switch TTR. Show less
The temporal decision model of procrastination has proposed that outcome value and task aversiveness are two separate aspects accounting for procrastination. If true, the human brain is likely to... Show moreThe temporal decision model of procrastination has proposed that outcome value and task aversiveness are two separate aspects accounting for procrastination. If true, the human brain is likely to implicate separate neural pathways to mediate the effect of outcome value and task aversiveness on procrastination. Outcome value is plausibly constructed via a hippocampus-based pathway because of the hippocampus's unique role in episodic prospection. In contrast, task aversiveness might be represented through an amygdala-involved pathway. In the current study, participants underwent fMRI scanning when viewing both tasks and future outcomes, without any experimental instruction imposed. The results revealed that outcome value increased activations in the caudate, and suppressed procrastination through a hippocampus-caudate pathway. In contrast, task aversiveness increased activations in the anterior insula, and increased procrastination via an amygdala-insula pathway. In sum, this study demonstrates that people can incorporate both outcome value and task aversiveness into task valuation to decide whether to procrastinate or not; and it elucidates the separate neural pathways via which this occurs. Show less
Lee, A.; Shi, M.; Chen, Q.; Horsley, J.P.; Schaefer, K.; Creemers, R.J.E.H.; Webster, G. 2021
In this thesis, we will utilize embryonic zebrafish tumour models to understand the interaction between engrafted human cancer cells and macrophages from the host, test drug administration... Show moreIn this thesis, we will utilize embryonic zebrafish tumour models to understand the interaction between engrafted human cancer cells and macrophages from the host, test drug administration modalities and anti-cancer efficacies of newly-developed PDT and PACT compounds, and test a light-triggered liposomal system for targeted drug delivery specifically to cancer cells in vivo. In chapter 2, we investigate the role of macrophages in tumour-induced angiogenesis. We show that macrophage-dependent angiogenesis is driven by macrophage recruitment to lactic acid secreted by glycolytic B16 melanoma cells. Chemical inhibition of macrophages and glycolysis blocks the initiation of angiogenesis in these models, suggesting that macrophages attracted to glycolytic melanoma cells contribute to the tumour-induced angiogenesis process.In chapters 3 and 4, we explore novel PDT and PACT compounds, respectively, for treatment of conjunctival melanoma in zebrafish. We inject conjunctival melanoma cells into the retro-orbital site to establish an orthotopic model and into the Duct of Cuvier to generate an ectopic model. Our results prove that zebrafish provides a fast vertebrate cancer model to test the optimal administration regimen of drugs, conditions of light irradiation, host toxicity and anti-cancer efficacy of PDT and PACT drugs against conjunctival melanoma.In chapter 5, we focus on modifying liposomes to be light triggered in order to deliver drugs specifically to cancer cells. We inject MDA231 breast cancer cells into the Duct of Cuvier at 2 days post fertilization (dpf) to initiate metastasis to the CHT. We successfully demonstrate that light-triggered, cell-specific delivery of liposome-encapsulated doxorubicin reduces the xenograft cancer cell burden without enhanced cytotoxicity of the zebrafish embryos. In chapter 6, we summarize the novel anti-cancer strategies, which we have developed using zebrafish xenograft models. In the same chapter, we frame our findings in the current scientific landscape and discuss future perspectives. Show less
The cerebral cortex underlies our complex cognitive capabilities, yet little is known about the specific genetic loci that influence human cortical structure. To identify genetic variants that... Show moreThe cerebral cortex underlies our complex cognitive capabilities, yet little is known about the specific genetic loci that influence human cortical structure. To identify genetic variants that affect cortical structure, we conducted a genome-wide association meta-analysis of brain magnetic resonance imaging data from 51,665 individuals. We analyzed the surface area and average thickness of the whole cortex and 34 regions with known functional specializations. We identified 199 significant loci and found significant enrichment for loci influencing total surface area within regulatory elements that are active during prenatal cortical development, supporting the radial unit hypothesis. Loci that affect regional surface area cluster near genes in Wnt signaling pathways, which influence progenitor expansion and areal identity. Variation in cortical structure is genetically correlated with cognitive function, Parkinson's disease, insomnia, depression, neuroticism, and attention deficit hyperactivity disorder. Show less
Multi-spanning membrane proteins usually require solubilization to allow proper purification and characterization, which generally impairs their structural and functional integrity. We have tested... Show moreMulti-spanning membrane proteins usually require solubilization to allow proper purification and characterization, which generally impairs their structural and functional integrity. We have tested the efficacy of several commonly used detergents and membrane-mimicking nanodiscs with respect to solubilization, spectral properties, thermal stability and oligomeric profile of two membrane proteins from the eubacterial rhodopsin family, green proteorhodopsin (PR) and Gloeobacter violaceus rhodopsin (GR). Good solubilization was observed for the detergents TritonX-100 and dodecylphosphocholine (DPC), but DPC in particular strongly affected the thermal stability of PR and especially GR. The least deleterious effects were obtained with n-dodecyl-β-D-maltopyranoside (DDM) and octyl glucose neopentyl glycol (OGNG), which adequately stabilized the native oligomeric and monomeric state of PR and GR, respectively. The transition from the oligomeric to the monomeric state is accompanied by a small red-shift. Both GR and PR were rather unstable in SMA-nanodiscs, but the highest thermal stability was realized by the MSP-nanodisc environment. The size of the MSP-nanodisc was too small to fit the PR hexamer, but large enough to contain the PR monomer and GR trimer. This permitted the comparison of the photocycle of trimeric GR in a membrane-mimicking (MSP-nanodisc) and a detergent (DDM) environment. The ultrarapid early phase of the photocycle (femto- to picosecond lifetimes) showed very similar kinetics in either environment, but the slower part, initiated with proton transfer and generation of the M intermediate, proceeded faster in the nanodisc environment. The implications of our results for the biophysical characterization of PR and GR are discussed. Show less
Kong L.; Chen, Q.; Campbell, F.; Snaar‐Jagalska, E.; Kros, A. 2020
Subcortical brain structures are integral to motion, consciousness, emotions and learning. We identified common genetic variation related to the volumes of the nucleus accumbens, amygdala,... Show moreSubcortical brain structures are integral to motion, consciousness, emotions and learning. We identified common genetic variation related to the volumes of the nucleus accumbens, amygdala, brainstem, caudate nucleus, globus pallidus, putamen and thalamus, using genome-wide association analyses in almost 40,000 individuals from CHARGE, ENIGMA and UK Biobank. We show that variability in subcortical volumes is heritable, and identify 48 significantly associated loci (40 novel at the time of analysis). Annotation of these loci by utilizing gene expression, methylation and neuropathological data identified 199 genes putatively implicated in neurodevelopment, synaptic signaling, axonal transport, apoptosis, inflammation/infection and susceptibility to neurological disorders. This set of genes is significantly enriched for Drosophila orthologs associated with neurodevelopmental phenotypes, suggesting evolutionarily conserved mechanisms. Our findings uncover novel biology and potential drug targets underlying brain development and disease. Show less
Multi-spanning membrane proteins usually require solubilization to allow proper purification and characterization, which generally impairs their structural and functional integrity. We have tested... Show moreMulti-spanning membrane proteins usually require solubilization to allow proper purification and characterization, which generally impairs their structural and functional integrity. We have tested the efficacy of several commonly used detergents and membrane-mimicking nanodiscs with respect to solubilization, spectral properties, thermal stability and oligomeric profile of two membrane proteins from the eubacterial rhodopsin family, green proteorhodopsin (PR) and Gloeobacter violaceus rhodopsin (GR). Good solubilization was observed for the detergents TritonX-100 and dodecylphosphocholine (DPC), but DPC in particular strongly affected the thermal stability of PR and especially GR. The least deleterious effects were obtained with n-dodecyl-β-D-maltopyranoside (DDM) and octyl glucose neopentyl glycol (OGNG), which adequately stabilized the native oligomeric and monomeric state of PR and GR, respectively. The transition from the oligomeric to the monomeric state is accompanied by a small red-shift. Both GR and PR were rather unstable in SMA-nanodiscs, but the highest thermal stability was realized by the MSP-nanodisc environment. The size of the MSP-nanodisc was too small to fit the PR hexamer, but large enough to contain the PR monomer and GR trimer. This permitted the comparison of the photocycle of trimeric GR in a membrane-mimicking (MSP-nanodisc) and a detergent (DDM) environment. The ultrarapid early phase of the photocycle (femto- to picosecond lifetimes) showed very similar kinetics in either environment, but the slower part, initiated with proton transfer and generation of the M intermediate, proceeded faster in the nanodisc environment. The implications of our results for the biophysical characterization of PR and GR are discussed. Show less
