Observation of an Estuarine Turbidity Maximum in the Highly Impacted Capibaribe Estuary, Brazil

Background: Alterations in insulin-like growth factor I (IGF-I) signaling have been associated with dementia and Alzheimer's disease (AD). Studies on the association between IGF-I levels and dementia risk have been inconclusive. We reported earlier that higher levels of IGF-I receptor stimulating activity are associated with a higher prevalence and incidence of dementia. Objective: In the present study, we test the robustness of the association between IGF-I receptor stimulating activity and dementia by extending the follow-up period to 16 years and investigate possible effect modification by apolipoprotein E (ApoE). Methods: At baseline, circulating IGF-I receptor stimulating activity was determined by the IGF-I kinase receptor activation (KIRA) assay in 1,014 elderly from the Rotterdam Study. Dementia was assessed from baseline (1997-1999) to follow-up in January 2015. Associations of IGF-I receptor stimulating activity and incident dementia were assessed with Cox proportional hazards models. Results: During 10,752 person-years of follow-up, 174 people developed dementia. In the extended follow-up we no longer observed a dose-response relationship between IGF-I receptor stimulating activity and risk of dementia [adjusted odds ratio 1.11; 95% confidence interval (CI) 0.97-1.28]. Interestingly, we found evidence of an interaction between ApoE-ε4 and tertiles of IGF-I receptor stimulating activity. IGF-I receptor stimulating activity in the median and top tertiles was related to increased dementia incidence in hetero- and homozygotes of the ApoE-ε4 allele, but did not show any association with dementia risk in people without the ApoE-ε4 allele (adjusted odds ratio medium vs. low IGF-I receptor stimulating activity in ApoE-ε4 carriers: 1.45; 95% CI 1.00-2.12). These findings suggest a threshold effect in ApoE-ε4 carriers. In line with the hypothesis that downregulation of IGF-I signaling is associated with increased dementia risk, ApoE-ε4 homozygotes without prevalent dementia displayed lower levels of IGF-I receptor stimulating activity than heterozygotes and non-carriers. Conclusion: The findings shed new light on the association between IGF-I signaling and the neuropathology of dementia and ask for replication in other cohorts, using measures of IGF-I receptor stimulating activity rather than total serum levels as putative markers of dementia risk

Revisiting the Role of Insulin-Like Growth Factor-I Receptor Stimulating Activity and the Apolipoprotein E in Alzheimer’s Disease

Background: Alterations in insulin-like growth factor I (IGF-I) signaling have been associated with dementia and Alzheimer’s disease (AD). Studies on the association between IGF-I levels and dementia risk have been inconclusive. We reported earlier that higher levels of IGF-I receptor stimulating activity are associated with a higher prevalence and incidence of dementia.Objective: In the present study, we test the robustness of the association between IGF-I receptor stimulating activity and dementia by extending the follow-up period to 16 years and investigate possible effect modification by apolipoprotein E (ApoE).Methods: At baseline, circulating IGF-I receptor stimulating activity was determined by the IGF-I kinase receptor activation (KIRA) assay in 1,014 elderly from the Rotterdam Study. Dementia was assessed from baseline (1997–1999) to follow-up in January 2015. Associations of IGF-I receptor stimulating activity and incident dementia were assessed with Cox proportional hazards models.Results: During 10,752 person-years of follow-up, 174 people developed dementia. In the extended follow-up we no longer observed a dose-response relationship between IGF-I receptor stimulating activity and risk of dementia [adjusted odds ratio 1.11; 95% confidence interval (CI) 0.97–1.28]. Interestingly, we found evidence of an interaction between ApoE-ε4 and tertiles of IGF-I receptor stimulating activity. IGF-I receptor stimulating activity in the median and top tertiles was related to increased dementia incidence in hetero- and homozygotes of the ApoE-ε4 allele, but did not show any association with dementia risk in people without the ApoE-ε4 allele (adjusted odds ratio medium vs. low IGF-I receptor stimulating activity in ApoE-ε4 carriers: 1.45; 95% CI 1.00–2.12). These findings suggest a threshold effect in ApoE-ε4 carriers. In line with the hypothesis that downregulation of IGF-I signaling is associated with increased dementia risk, ApoE-ε4 homozygotes without prevalent dementia displayed lower levels of IGF-I receptor stimulating activity than heterozygotes and non-carriers.Conclusion: The findings shed new light on the association between IGF-I signaling and the neuropathology of dementia and ask for replication in other cohorts, using measures of IGF-I receptor stimulating activity rather than total serum levels as putative markers of dementia risk

Revisiting the role of insulin-like growth factor-I receptor stimulating activity and the apolipoprotein E in Alzheimer's disease

__Background:__ Alterations in insulin-like growth factor I (IGF-I) signaling have been associated with dementia and Alzheimer's disease (AD). Studies on the association between IGF-I levels and dementia risk have been inconclusive. We reported earlier that higher levels of IGF-I receptor stimulating activity are associated with a higher prevalence and incidence of dementia. __Objective:__ In the present study, we test the robustness of the association between IGF-I receptor stimulating activity and dementia by extending the follow-up period to 16 years and investigate possible effect modification by apolipoprotein E (ApoE). __Methods:__ At baseline, circulating IGF-I receptor stimulating activity was determined by the IGF-I kinase receptor activation (KIRA) assay in 1,014 elderly from the Rotterdam Study. Dementia was assessed from baseline (1997-1999) to follow-up in January 2015. Associations of IGF-I receptor stimulating activity and incident dementia were assessed with Cox proportional hazards models. __Results:__ During 10,752 person-years of follow-up, 174 people developed dementia. In the extended follow-up we no longer observed a dose-response relationship between IGF-I receptor stimulating activity and risk of dementia [adjusted odd

Afstudeerwerk

Preface In nummer 2 van 2022 introduceerde het Bulletin KNOB een tweejaarlijkse rubriek ‘afstudeerwerk’, waarin de studenten die hadden meegedongen naar de KNOB Stimuleringsprijs 2021 hun onderzoek presenteerden. In dit nummer vindt u de tweede editie van die rubriek. Het bevat samenvattingen van scripties ingezonden voor de KNOB Stimuleringsprijs 2023. De zestien scripties zijn geschreven aan twee Belgische universiteiten (Katholieke Universiteit Leuven en Vrije Universiteit Brussel), vier Nederlandse (Rijksuniversiteit Groningen, Technische Universiteit Delft, Universiteit Utrecht, Universiteit van Amsterdam) en een hogeschool (Inholland Delft). Ze behandelen herkenbare architectuurhistorische thema’s als de negentiendeeeuwse arbeiderswoning, plafondontwerpen van Daniel Marot en historisch glas-in-lood, maar ook aanverwante onderwerpen als de ‘soundscape’ van de kerken van Christopher Wren, archeologisch erfgoed als herinneringsplaats, en – op het snijvlak van de architectuurhistorie en de sociale geschiedenis – de speeltuin tussen 1878 en 1978. De KNOB Stimuleringsprijs leidt tot meer. Het afstudeeronderzoek van Sara Duisters over kunststof gevels resulteerde al in een publicatie in het recente themanummer Post 65. Winnaar van de Stimuleringsprijs 2023 Lara Reyniers schreef voortbouwend op haar afstudeeronderzoek voor het huidige nummer samen met Stephanie Van de Voorde en Ine Wouters een artikel over de omgang met afbraakmaterialen in Brussel in de periode 1860-1940. Daarmee is dit nummer bijna volledig gevuld met het werk van jonge vakgenoten. In de bijdrage van Reyniers et al staan nu eens niet de creatie en bouw van architectuur centraal, maar de afbraak ervan, en dan met name het beleid ten aanzien van het sloopafval. De behandelde periode was er een van grootschalige stedelijke vernieuwing die veel afval opleverde, waaronder puin, bijzondere bouwfragmenten en van alles daar tussenin. Hoe de Brusselse overheid hiermee omging is interessant, zeker ook in het huidige tijdsgewricht, waarin sloop en sloopafval – nu vanuit een duurzaamheidsoogpunt – opnieuw in de aandacht staan. De redactieVoorwoord In nummer 2 van 2022 introduceerde het Bulletin KNOB een tweejaarlijkse rubriek ‘afstudeerwerk’, waarin de studenten die hadden meegedongen naar de KNOB Stimuleringsprijs 2021 hun onderzoek presenteerden. In dit nummer vindt u de tweede editie van die rubriek. Het bevat samenvattingen van scripties ingezonden voor de KNOB Stimuleringsprijs 2023. De zestien scripties zijn geschreven aan twee Belgische universiteiten (Katholieke Universiteit Leuven en Vrije Universiteit Brussel), vier Nederlandse (Rijksuniversiteit Groningen, Technische Universiteit Delft, Universiteit Utrecht, Universiteit van Amsterdam) en een hogeschool (Inholland Delft). Ze behandelen herkenbare architectuurhistorische thema’s als de negentiendeeeuwse arbeiderswoning, plafondontwerpen van Daniel Marot en historisch glas-in-lood, maar ook aanverwante onderwerpen als de ‘soundscape’ van de kerken van Christopher Wren, archeologisch erfgoed als herinneringsplaats, en – op het snijvlak van de architectuurhistorie en de sociale geschiedenis – de speeltuin tussen 1878 en 1978. De KNOB Stimuleringsprijs leidt tot meer. Het afstudeeronderzoek van Sara Duisters over kunststof gevels resulteerde al in een publicatie in het recente themanummer Post 65. Winnaar van de Stimuleringsprijs 2023 Lara Reyniers schreef voortbouwend op haar afstudeeronderzoek voor het huidige nummer samen met Stephanie Van de Voorde en Ine Wouters een artikel over de omgang met afbraakmaterialen in Brussel in de periode 1860-1940. Daarmee is dit nummer bijna volledig gevuld met het werk van jonge vakgenoten. In de bijdrage van Reyniers et al staan nu eens niet de creatie en bouw van architectuur centraal, maar de afbraak ervan, en dan met name het beleid ten aanzien van het sloopafval. De behandelde periode was er een van grootschalige stedelijke vernieuwing die veel afval opleverde, waaronder puin, bijzondere bouwfragmenten en van alles daar tussenin. Hoe de Brusselse overheid hiermee omging is interessant, zeker ook in het huidige tijdsgewricht, waarin sloop en sloopafval – nu vanuit een duurzaamheidsoogpunt – opnieuw in de aandacht staan. De redacti

Loss of DPP6 in neurodegenerative dementia : a genetic player in the dysfunction of neuronal excitability

Emerging evidence suggested a converging mechanism in neurodegenerative brain diseases (NBD) involving early neuronal network dysfunctions and alterations in the homeostasis of neuronal firing as culprits of neurodegeneration. In this study, we used paired-end short-read and direct long-read whole genome sequencing to investigate an unresolved autosomal dominant dementia family significantly linked to 7q36. We identified and validated a chromosomal inversion of ca. 4Mb, segregating on the disease haplotype and disrupting the coding sequence of dipeptidyl-peptidase 6 gene (DPP6). DPP6 resequencing identified significantly more rare variants-nonsense, frame-shift, and missense-in early-onset Alzheimer's disease (EOAD, p value = 0.03, OR = 2.21 95% CI 1.05-4.82) and frontotemporal dementia (FTD, p = 0.006, OR = 2.59, 95% CI 1.28-5.49) patient cohorts. DPP6 is a type II transmembrane protein with a highly structured extracellular domain and is mainly expressed in brain, where it binds to the potassium channel K(v)4.2 enhancing its expression, regulating its gating properties and controlling the dendritic excitability of hippocampal neurons. Using in vitro modeling, we showed that the missense variants found in patients destabilize DPP6 and reduce its membrane expression (p < 0.001 and p < 0.0001) leading to a loss of protein. Reduced DPP6 and/or K(v)4.2 expression was also detected in brain tissue of missense variant carriers. Loss of DPP6 is known to cause neuronal hyperexcitability and behavioral alterations in Dpp6-KO mice. Taken together, the results of our genomic, genetic, expression and modeling analyses, provided direct evidence supporting the involvement of DPP6 loss in dementia. We propose that loss of function variants have a higher penetrance and disease impact, whereas the missense variants have a variable risk contribution to disease that can vary from high to low penetrance. Our findings of DPP6, as novel gene in dementia, strengthen the involvement of neuronal hyperexcitability and alteration in the homeostasis of neuronal firing as a disease mechanism to further investigate

Strengthening the reporting of genetic risk prediction studies (GRIPS): explanation and elaboration

The rapid and continuing progress in gene discovery for complex diseases is fuelling interest in the potential application of genetic risk models for clinical and public health practice. The number of studies assessing the predictive ability is steadily increasing, but they vary widely in completeness of reporting and apparent quality. Transparent reporting of the strengths and weaknesses of these studies is important to facilitate the accumulation of evidence on genetic risk prediction. A multidisciplinary workshop sponsored by the Human Genome Epidemiology Network developed a checklist of 25 items recommended for strengthening the reporting of Genetic RIsk Prediction Studies (GRIPS), building on the principles established by prior reporting guidelines. These recommendations aim to enhance the transparency, quality and completeness of study reporting, and thereby to improve the synthesis and application of information from multiple studies that might differ in design, conduct or analysis

Improved imputation quality of low-frequency and rare variants in European samples using the ‘Genome of The Netherlands'

Although genome-wide association studies (GWAS) have identified many common variants associated with complex traits, low-frequency and rare variants have not been interrogated in a comprehensive manner. Imputation from dense reference panels, such as the 1000 Genomes Project (1000G), enables testing of ungenotyped variants for association. Here we present the results of imputation using a large, new population-specific panel: the Genome of The Netherlands (GoNL). We benchmarked the performance of the 1000G and GoNL reference sets by comparing imputation genotypes with ‘true' genotypes typed on ImmunoChip in three European populations (Dutch, British, and Italian). GoNL showed significant improvement in the imputation quality for rare variants (MAF 0.05–0.5%) compared with 1000G. In Dutch samples, the mean observed Pearson correlation, r2, increased from 0.61 to 0.71. We also saw improved imputation accuracy for other European populations (in the British samples, r2 improved from 0.58 to 0.65, and in the Italians from 0.43 to 0.47). A combined reference set comprising 1000G and GoNL improved the imputation of rare variants even further. The Italian samples benefitted the most from this combined reference (the mean r2 increased from 0.47 to 0.50). We conclude that the creation of a large population-specific reference is advantageous for imputing rare variants and that a combined reference panel across multiple populations yields the best imputation results

The Genome of the Netherlands:design, and project goals

Within the Netherlands a national network of biobanks has been established (Biobanking and Biomolecular Research Infrastructure-Netherlands (BBMRI-NL)) as a national node of the European BBMRI. One of the aims of BBMRI-NL is to enrich biobanks with different types of molecular and phenotype data. Here, we describe the Genome of the Netherlands (GoNL), one of the projects within BBMRI-NL. GoNL is a whole-genome-sequencing project in a representative sample consisting of 250 trio-families from all provinces in the Netherlands, which aims to characterize DNA sequence variation in the Dutch population. The parent-offspring trios include adult individuals ranging in age from 19 to 87 years (mean = 53 years; SD = 16 years) from birth cohorts 1910-1994. Sequencing was done on blood-derived DNA from uncultured cells and accomplished coverage was 14-15x. The family-based design represents a unique resource to assess the frequency of regional variants, accurately reconstruct haplotypes by family-based phasing, characterize short indels and complex structural variants, and establish the rate of de novo mutational events. GoNL will also serve as a reference panel for imputation in the available genome-wide association studies in Dutch and other cohorts to refine association signals and uncover population-specific variants. GoNL will create a catalog of human genetic variation in this sample that is uniquely characterized with respect to micro-geographic location and a wide range of phenotypes. The resource will be made available to the research and medical community to guide the interpretation of sequencing projects. The present paper summarizes the global characteristics of the project.</p

A Methodological Perspective on Genetic Risk Prediction Studies in Type 2 Diabetes: Recommendations for Future Research

Fueled by the successes of genome-wide association studies, numerous studies have investigated the predictive ability of genetic risk models in type 2 diabetes. In this paper, we review these studies from a methodological perspective, focusing on the variables included in the risk models as well as the study designs and populations investigated. We argue and show that differences in study design and characteristics of the study population have an impact on the observed predictive ability of risk models. This observation emphasizes that genetic risk prediction studies should be conducted in those populations in which the prediction models will ultimately be applied, if proven useful. Of all genetic risk prediction studies to date, only a few were conducted in populations that might be relevant for targeting preventive interventions

Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization.

The QT interval, an electrocardiographic measure reflecting myocardial repolarization, is a heritable trait. QT prolongation is a risk factor for ventricular arrhythmias and sudden cardiac death (SCD) and could indicate the presence of the potentially lethal mendelian long-QT syndrome (LQTS). Using a genome-wide association and replication study in up to 100,000 individuals, we identified 35 common variant loci associated with QT interval that collectively explain ∼8-10% of QT-interval variation and highlight the importance of calcium regulation in myocardial repolarization. Rare variant analysis of 6 new QT interval-associated loci in 298 unrelated probands with LQTS identified coding variants not found in controls but of uncertain causality and therefore requiring validation. Several newly identified loci encode proteins that physically interact with other recognized repolarization proteins. Our integration of common variant association, expression and orthogonal protein-protein interaction screens provides new insights into cardiac electrophysiology and identifies new candidate genes for ventricular arrhythmias, LQTS and SCD