Digital Smoking Cessation Intervention for Cancer Survivors: Analysis of Predictors and Moderators of Engagement and Outcome Alongside a Randomized Controlled Trial.

BACKGROUND: Recent studies have shown positive, though small, clinical effects of digital smoking cessation (SC) interventions for cancer survivors. However, research on associations among participant characteristics, intervention engagement, and outcomes is limited. OBJECTIVE: This study aimed to explore the predictors and moderators of engagement and outcome of MyCourse-Quit Smoking (in Dutch: "MijnKoers-Stoppen met Roken"), a digital minimally guided intervention for cancer survivors. METHODS: A secondary analysis of data from the randomized controlled trial was performed. The number of cigarettes smoked in the past 7 days at 6-month follow-up was the primary outcome measure. We analyzed interactions among participant characteristics (11 variables), intervention engagement (3 variables), and outcome using robust linear (mixed) modeling. RESULTS: In total, 165 participants were included in this study. Female participants accessed the intervention less often than male participants (B=-11.12; P=.004). A higher Alcohol Use Disorders Identification Test score at baseline was associated with a significantly higher number of logins (B=1.10; P<.001) and diary registrations (B=1.29; P<.001). A higher Fagerström Test for Nicotine Dependence score at baseline in the intervention group was associated with a significantly larger reduction in tobacco use after 6 months (B=-9.86; P=.002). No other associations and no moderating effects were found. CONCLUSIONS: Overall, a limited number of associations was found between participant characteristics, engagement, and outcome, except for gender, problematic alcohol use, and nicotine dependence. Future studies are needed to shed light on how this knowledge can be used to improve the effects of digital SC programs for cancer survivors. TRIAL REGISTRATION: Netherlands Trial register NTR6011/NL5434; https://onderzoekmetmensen.nl/nl/trial/22832.

Secondhand smoke exposure in public outdoor spaces in the Netherlands: The stronger the smell, the more exposure to nicotine.

INTRODUCTION: While secondhand smoke exposure in outdoor spaces has been investigated before, no data on outdoor secondhand smoke exposure have been collected in the Netherlands. Such data could help policymakers gain support for smoke-free outdoor public spaces. METHODS: Between May and November 2021, we visited 25 outdoor locations across the Netherlands. At each location, we conducted four measurements with smokers and one measurement without smokers. During each measurement, we counted the number of smokers present and we rated tobacco smell intensity on a five-point scale. Airborne nicotine and 3-ethenylpyridine (3-EP) data were collected through active sampling on thermal desorption tubes. The contents of these tubes were later analyzed using gas chromatography-mass spectrometry. Using linear mixed models, we investigated the association between levels of nicotine and the presence of smokers, the number of smokers, and the intensity of tobacco smell. We also investigated these association with levels of 3-EP. RESULTS: Nicotine levels were higher when smokers were present (B=1.40; 95% CI: 0.69-2.11, p<0.001). For each additional smoker present, we measured higher levels of nicotine (B=0.23; 95% CI: 0.10-0.37, p=0.001). When the smell of tobacco smoke was noted to be stronger by the researchers, higher levels of nicotine were measured through sampling (B=0.85; 95% CI: 0.44-1.26, p<0.001). We found similar results for 3-EP levels. CONCLUSIONS: This study showed that both nicotine and 3-EP are useful in quantifying levels of secondhand smoke in various outdoor locations. The level of nicotine exposure outdoors was positively associated with the number of smokers nearby. The intensity of the tobacco smell was also related to nicotine exposure: the stronger the smell of tobacco smoke, the more nicotine was measured in the air.

What do we not know (yet) about recovery colleges? A study protocol on their (cost-)effectiveness, mechanisms of action, fidelity and positioning.

BACKGROUND: Recovery Colleges (RCs) have spread across the globe as a new way of supporting people with mental vulnerabilities in their recovery journey. RCs focus on 'learning' rather than 'curing' and in that line facilitate a transition from being a passive, dependent patient/client to an active, empowered student learning to live life, despite vulnerabilities. Peer support and co-creation are central in RCs, as peers learn from each other by sharing personal experiences with mental vulnerabilities in an accessible, inspiring and stimulating atmosphere. The implementation of RCs is highly encouraged internationally, and as a result RCs and related self-help initiatives increasingly emerge. However, high-quality research on RCs is scarce and there is a call for thorough investigation of (cost-)effectiveness, mechanisms of action, cross-border fidelity and positioning of RCs. In response, this research project aims to fill these gaps. METHODS: This research project entails (1) a prospective quasi-experimental effectiveness study and economic evaluation, (2) a multifaceted qualitative study to elaborate on the mechanisms of action of RCs for those involved (3) a study to develop a (Dutch) Fidelity Measure of Recovery Colleges, and (4) an organisational case study to describe the positioning of RCs in relation to other mental health care services and community-based initiatives. Following the ideals of co-creation and empowerment in RCs we conduct this research project in co-creation with RC students from Enik Recovery College in Utrecht, the Netherlands. DISCUSSION: This research project will lead to one of the first longitudinal controlled quantitative evaluations of both cost-effectiveness and effectiveness of RC attendance in a broad sense (beyond attending courses alone). Moreover, we will gather data on a micro level (i.e., impact on RC students), meso level (i.e., organisational fidelity) and macro level (i.e., positioning in the care and support domain), capturing all important perspectives when scrutinizing the impact of complex systems. Finally, we will demonstrate the validity and value of embracing experiential knowledge in science as a complementary source of information, leading to a more profound understanding of what is researched. TRIAL REGISTRATION: The prospective quasi-experimental study has been pre-registered at clinicaltrails.gov (#NCT05620212).

Allelic expression imbalance in articular cartilage and subchondral bone refined genome-wide association signals in osteoarthritis.

OBJECTIVES: To present an unbiased approach to identify positional transcript single nucleotide polymorphisms (SNPs) of osteoarthritis (OA) risk loci by allelic expression imbalance (AEI) analyses using RNA sequencing of articular cartilage and subchondral bone from OA patients. METHODS: RNA sequencing from 65 articular cartilage and 24 subchondral bone from OA patients was used for AEI analysis. AEI was determined for all genes present in the 100 regions reported by the genome-wide association studies (GWAS) catalog that were also expressed in cartilage or bone. The count fraction of the alternative allele (φ) was calculated for each heterozygous individual with the risk SNP or with the SNP in linkage disequilibrium (LD) with it (r2 > 0.6). Furthermore, a meta-analysis was performed to generate a meta-φ (null hypothesis median φ = 0.49) and P-value for each SNP. RESULTS: We identified 30 transcript SNPs (28 in cartilage and two in subchondral bone) subject to AEI in 29 genes. Notably, 10 transcript SNPs were located in genes not previously reported in the GWAS catalog, including two long intergenic non-coding RNAs (lincRNAs), MALAT1 (meta-φ = 0.54, FDR = 1.7×10-4) and ILF3-DT (meta-φ = 0.6, FDR = 1.75×10-5). Moreover, 12 drugs were interacting with seven genes displaying AEI, of which seven drugs have been already approved. CONCLUSIONS: By prioritizing proxy transcript SNPs that mark AEI in cartilage and/or subchondral bone at loci harbouring GWAS signals, we present an unbiased approach to identify the most likely functional OA risk-SNP and gene. We identified 10 new potential OA risk genes ready for further translation towards underlying biological mechanisms.

Smart Continence Care for People With Profound Intellectual and Multiple Disabilities: Protocol for a Cluster Randomized Trial and Trial-Based Economic Evaluation.

BACKGROUND: People with profound intellectual and multiple disabilities (PIMD) cannot communicate the need to change their incontinence products. The smart continence care (SCC) product Abena Nova signals caregivers when change is needed. This provides the opportunity for more person-centered care, increased quality of life, and a decreased number of leakages. However, there is a need for evidence of the effectiveness and cost-effectiveness of such technology compared with regular continence care (RCC) for people with PIMD. OBJECTIVE: This paper presents the research protocol for an effectiveness and cost-effectiveness study with people with PIMD living in long-term care facilities in the Netherlands. METHODS: A cluster randomized trial will be conducted in 3 consecutive waves across 6 long-term care providers for people with disabilities and 160 participants with PIMD. Long-term care providers are randomized at a 1:1 ratio, resulting in an intervention group and a group continuing RCC. The intervention group will receive implementation guidance and use SCC for 3 months; the other group will continue their RCC as usual and then switch to SCC. This study consists of three components: effectiveness study, economic evaluation, and process evaluation. The primary outcome will be a change in the number of leakages. The secondary outcomes are quality of life, the difference in the number of changes, the work perception of caregivers, cost-effectiveness, and cost utility. Data collection will occur at T0 (baseline), T1 (6 weeks), T2 (12 weeks), and T3 (9-month follow-up) for the first 2 intervention groups. An intention-to-treat analysis will be performed. The economic evaluation will be conducted alongside the trial from the societal and long-term care provider perspectives. Qualitative data collection through interviews and field notes will complement these quantitative results and provide input for the process evaluation. RESULTS: This research was funded in December 2019 by ZonMw, the Netherlands Organization for Health Research and Development. As of June 2022, we enrolled 118 of the 160 participants. The enrollment of participants will continue in the third and fourth quarters of 2022. CONCLUSIONS: This study will provide insights into the effectiveness and cost-effectiveness of SCC for people with PIMD, allowing long-term care providers to make informed decisions about implementing such a technology. This is the first time that such a large-scale study is being conducted for people with PIMD. TRIAL REGISTRATION: ClinicalTrials.gov NCT05481840; https://clinicaltrials.gov/ct2/show/NCT05481840. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/42555.

Effectiveness of Resource Groups for Improving Empowerment, Quality of Life, and Functioning of People With Severe Mental Illness: A Randomized Clinical Trial.

Importance: Although the importance of recovery-oriented care for people with severe mental illness (SMI) is widely acknowledged, essential elements such as personalization and involvement of significant others are not adequately implemented in practice. Objective: To determine whether using resource groups (RGs) within flexible assertive community treatment (FACT) has favorable effects on empowerment and recovery-related outcomes in people with SMI. Design, Setting, and Participants: This assessor-blind, multisite randomized clinical trial was conducted from September 1, 2017, to September 30, 2020, with follow-up at 9 and 18 months. A total of 158 participants aged 18 to 65 years meeting the criteria for SMI were randomly allocated to FACT plus RG vs FACT as usual (1:1) in 20 FACT teams throughout the Netherlands. Data were analyzed from September 1, 2020, to January 31, 2021. The study was prespecified in the trial protocol and data from the intent-to-treat population were analyzed. Interventions: In the FACT plus RG condition, patients chose members from their informal and formal networks to form an RG that meets quarterly to discuss self-formulated recovery goals. The RG was integrated into the multidisciplinary support provided by the FACT team. In the FACT as-usual condition, empowerment (defined as overcoming powerlessness and gaining control of one's life) and involvement of significant others was also part of the provided care, but without the structure of the RG. Main Outcomes and Measures: The primary outcome was self-reported empowerment, measured with the Netherlands Empowerment List. Results: A total of 158 participants with SMI (median age, 38 [median absolute deviation, 13] years; 93 men [58.9%]) were randomized to FACT plus RG (n = 80) or FACT as usual (n = 78) care. Intention-to-treat analyses showed that randomization to the RG condition was associated with a clinically significant increase in empowerment (Cohen d, 0.54; 95% CI, 0.21-0.86) and improved outcomes with small to medium effect sizes in terms of quality of life (Cohen d, 0.25; 95% CI, -0.07 to 0.56), personal recovery (Cohen d, 0.38; 95% CI, 0.06-0.69), quality of social contact (Cohen d, 0.24; 95% CI, -0.07 to 0.56), disability (Cohen d, 0.29; 95% CI, -0.03 to 0.60), general functioning (Cohen d, 0.30; 95% CI, -0.01 to 0.62), and social functioning (Cohen d, 0.28; 95% CI, -0.04 to 0.59). No differences between conditions were found regarding psychopathological symptoms, attachment, frequency of social contact, and employment. Compared with FACT as usual, participants who stayed with the assigned treatment in the RG condition were more satisfied with treatment at 9 (Cohen d = 0.45; t135 = -2.62; P = .009) and 18 (Cohen d = 0.41; t116 = -2.22; P = .02) months. Conclusions and Relevance: These findings show that working with RGs improves empowerment and other mental health outcomes in people with SMI who receive community-based mental health services. This method of network-oriented care empowers people with SMI within their own environment. Trial Registration: Netherlands Trial Register Identifier: NL6548.

The human hepatocyte TXG-MAPr: gene co-expression network modules to support mechanism-based risk assessment.

Mechanism-based risk assessment is urged to advance and fully permeate into current safety assessment practices, possibly at early phases of drug safety testing. Toxicogenomics is a promising source of mechanisms-revealing data, but interpretative analysis tools specific for the testing systems (e.g. hepatocytes) are lacking. In this study, we present the TXG-MAPr webtool (available at https://txg-mapr.eu/WGCNA_PHH/TGGATEs_PHH/ ), an R-Shiny-based implementation of weighted gene co-expression network analysis (WGCNA) obtained from the Primary Human Hepatocytes (PHH) TG-GATEs dataset. The 398 gene co-expression networks (modules) were annotated with functional information (pathway enrichment, transcription factor) to reveal their mechanistic interpretation. Several well-known stress response pathways were captured in the modules, were perturbed by specific stressors and showed preservation in rat systems (rat primary hepatocytes and rat in vivo liver), with the exception of DNA damage and oxidative stress responses. A subset of 87 well-annotated and preserved modules was used to evaluate mechanisms of toxicity of endoplasmic reticulum (ER) stress and oxidative stress inducers, including cyclosporine A, tunicamycin and acetaminophen. In addition, module responses can be calculated from external datasets obtained with different hepatocyte cells and platforms, including targeted RNA-seq data, therefore, imputing biological responses from a limited gene set. As another application, donors' sensitivity towards tunicamycin was investigated with the TXG-MAPr, identifying higher basal level of intrinsic immune response in donors with pre-existing liver pathology. In conclusion, we demonstrated that gene co-expression analysis coupled to an interactive visualization environment, the TXG-MAPr, is a promising approach to achieve mechanistic relevant, cross-species and cross-platform evaluation of toxicogenomic data.

Pragmatic Quasi-Experimental Controlled Trial Evaluating the Outcomes of Blended CBT Compared to Face-to-Face CBT and Treatment as Usual for Adolescents with Depressive Disorders.

Depression is a major problem in youth mental health. Current treatment is on average effective, but adolescents are hesitant to seek help. Blended treatment could lower the barriers to seeking treatment. Evidence on effectiveness is, however, scarce. The present pragmatic quasi-experimental controlled trial aimed to compare the outcomes of blended cognitive behavioral therapy (CBT) to face-to-face CBT and treatment as usual. A total of 129 adolescents with clinical depression (82.2% female), aged 13-22 (M = 16.60, SD = 2.03) received blended CBT, face-to-face CBT or treatment as usual. Clinical diagnosis, depressive symptoms, and secondary outcomes were assessed at baseline, post-intervention, and six-months follow-up. Participants receiving blended CBT were, compared to participants receiving face-to-face CBT and treatment as usual, evenly likely to be in remission from their depressive disorder at post-intervention and at six-month follow-up. Depressive symptoms decreased significantly over time in all three conditions, and changes were not significantly different between conditions. Other secondary outcomes (suicide risk, internalizing and externalizing symptoms, severity of depression, and global functioning) did not differ between treatment conditions at post-intervention and six-month follow-up. Since there was no evidence for favorable outcomes for face-to-face therapies above blended CBT, blended CBT may also be an effective treatment format in clinical practice.

Accuracy of upper endoscopies with random biopsies to identify patients with gastric premalignant lesions who can safely be exempt from surveillance.

INTRODUCTION: Guidelines recommend endoscopy with biopsies to stratify patients with gastric premalignant lesions (GPL) to high and low progression risk. High-risk patients are recommended to undergo surveillance. We aimed to assess the accuracy of guideline recommendations to identify low-risk patients, who can safely be discharged from surveillance. METHODS: This study includes patients with GPL. Patients underwent at least two endoscopies with an interval of 1-6 years. Patients were defined 'low risk' if they fulfilled requirements for discharge, and 'high risk' if they fulfilled requirements for surveillance, according to European guidelines (MAPS-2012, updated MAPS-2019, BSG). Patients defined 'low risk' with progression of disease during follow-up (FU) were considered 'misclassified' as low risk. RESULTS: 334 patients (median age 60 years IQR11; 48.7% male) were included and followed for a median of 48 months. At baseline, 181/334 (54%) patients were defined low risk. Of these, 32.6% were 'misclassified', showing progression of disease during FU. If MAPS-2019 were followed, 169/334 (51%) patients were defined low risk, of which 32.5% were 'misclassified'. If BSG were followed, 174/334 (51%) patients were defined low risk, of which 32.2% were 'misclassified'. Seven patients developed gastric cancer (GC) or dysplasia, four patients were 'misclassified' based on MAPS-2012 and three on MAPS-2019 and BSG. By performing one additional endoscopy 72.9% (95% CI 62.4-83.3) of high-risk patients and all patients who developed GC or dysplasia were identified. CONCLUSION: One-third of patients that would have been discharged from GC surveillance, appeared to be 'misclassified' as low risk. One additional endoscopy will reduce this risk by 70%.

Identification and characterization of two consistent osteoarthritis subtypes by transcriptome and clinical data integration.

OBJECTIVE: To identify OA subtypes based on cartilage transcriptomic data in cartilage tissue and characterize their underlying pathophysiological processes and/or clinically relevant characteristics. METHODS: This study includes n = 66 primary OA patients (41 knees and 25 hips), who underwent a joint replacement surgery, from which macroscopically unaffected (preserved, n = 56) and lesioned (n = 45) OA articular cartilage were collected [Research Arthritis and Articular Cartilage (RAAK) study]. Unsupervised hierarchical clustering analysis on preserved cartilage transcriptome followed by clinical data integration was performed. Protein-protein interaction (PPI) followed by pathway enrichment analysis were done for genes significant differentially expressed between subgroups with interactions in the PPI network. RESULTS: Analysis of preserved samples (n = 56) resulted in two OA subtypes with n = 41 (cluster A) and n = 15 (cluster B) patients. The transcriptomic profile of cluster B cartilage, relative to cluster A (DE-AB genes) showed among others a pronounced upregulation of multiple genes involved in chemokine pathways. Nevertheless, upon investigating the OA pathophysiology in cluster B patients as reflected by differentially expressed genes between preserved and lesioned OA cartilage (DE-OA-B genes), the chemokine genes were significantly downregulated with OA pathophysiology. Upon integrating radiographic OA data, we showed that the OA phenotype among cluster B patients, relative to cluster A, may be characterized by higher joint space narrowing (JSN) scores and low osteophyte (OP) scores. CONCLUSION: Based on whole-transcriptome profiling, we identified two robust OA subtypes characterized by unique OA, pathophysiological processes in cartilage as well as a clinical phenotype. We advocate that further characterization, confirmation and clinical data integration is a prerequisite to allow for development of treatments towards personalized care with concurrently more effective treatment response.

Helicobacter pylori seroprevalence in six different ethnic groups living in Amsterdam: The HELIUS study.

BACKGROUND: Helicobacter pylori prevalence varies greatly worldwide. We explored the prevalence of H. pylori and CagA seropositivity among adults aged 18-44 years living in the Netherlands by ethnicity and migration status (first vs second generation). MATERIALS AND METHODS: Participants from six different ethnic groups were selected from the population-based multi-ethnic HELIUS study in Amsterdam, the Netherlands. Serum samples were tested for H. pylori antigens using a validated Luminex-based multiplex serology assay. Prevalence ratios were estimated using Poisson regression analysis. RESULTS: A total of 4683 participants aged 18-44 years were randomly selected based on sex, ethnicity, and age. H. pylori seroprevalence was highest in the Ghanaian group (84%), followed by Moroccan (81%), Turkish (66%), African Surinamese (51%), South-Asian Surinamese (48%), and Dutch (17%) participants. All ethnic minority groups had a significantly higher risk of being H. pylori seropositive compared to the Dutch group. This association was strongest among participants born outside the Netherlands (first generation), but was still significant and apparent among second-generation participants. Among first-generation participants, all groups, except the Moroccans, had a significantly higher proportion of individuals with a cagA + H. pylori strain compared to the Dutch participants. CONCLUSION: Helicobacter pylori seroprevalence among first-generation migrants is high in the Netherlands and remains elevated among second-generation migrants (ie, those born in the Netherlands). High exposure to H. pylori, and especially to the more virulent cagA+ strain, highlights the need for tailored prevention of gastric diseases (notably peptic ulcers and cancers) among migrants.

Increased WISP1 expression in human osteoarthritic articular cartilage is epigenetically regulated and decreases cartilage matrix production.

OBJECTIVES: Previously, we have shown the involvement of Wnt-activated protein Wnt-1-induced signaling protein 1 (WISP1) in the development of OA in mice. Here, we aimed to characterize the relation between WISP1 expression and human OA and its regulatory epigenetic determinants. METHODS: Preserved and lesioned articular cartilage from end-stage OA patients and non-OA-diagnosed individuals was collected. WISP1 expression was determined using immunohistochemistry and damage was classified using Mankin scoring. RNA expression and DNA methylation were assessed in silico from genome-wide datasets (microarray analysis and RNA sequencing, and 450 k-methylationarrays, respectively). Effects of WISP1 were tested in pellet cultures of primary human chondrocytes. RESULTS: WISP1 expression in cartilage of OA patients was increased compared with non-OA-diagnosed controls and, within OA patients, WISP1 was even higher in lesioned compared with preserved regions, with expression strongly correlating with Mankin score. In early symptomatic OA patients with disease progression, higher synovial WISP1 expression was observed as compared with non-progressors. Notably, increased WISP1 expression was inversely correlated with methylation levels of a positional CpG-dinucleotide (cg10191240), with lesioned areas showing strong hypomethylation for this CpG as compared with preserved cartilage. Additionally, we observed that methylation levels were allele-dependent for an intronic single-nucleotide polymorphism nearby cg10191240. Finally, addition of recombinant WISP1 to pellets of primary chondrocytes strongly inhibited deposition of extracellular matrix as reflected by decreased pellet circumference, proteoglycan content and decreased expression of matrix components. CONCLUSION: Increased WISP1 expression is found in lesioned human articular cartilage, and appears epigenetically regulated via DNA methylation. In vitro assays suggest that increased WISP1 is detrimental for cartilage integrity.

Surveillance of premalignant gastric lesions: a multicentre prospective cohort study from low incidence regions.

OBJECTIVE: International guidelines recommend endoscopic surveillance of premalignant gastric lesions. However, the diagnostic yield and preventive effect require further study. We therefore aimed to assess the incidence of neoplastic progression and to assess the ability of various tests to identify patients most at risk for progression. DESIGN: Patients from the Netherlands and Norway with a previous diagnosis of atrophic gastritis (AG), intestinal metaplasia (IM) or dysplasia were offered endoscopic surveillance. All histological specimens were assessed according to the updated Sydney classification and the operative link on gastric intestinal metaplasia (OLGIM) system. In addition, we measured serum pepsinogens (PG) and gastrin-17. RESULTS: 279 (mean age 57.9 years, SD 11.4, male/female 137/142) patients were included and underwent at least one surveillance endoscopy during follow-up. The mean follow-up time was 57 months (SD 36). Four subjects (1.4%) were diagnosed with high-grade adenoma/dysplasia or invasive neoplasia (ie, gastric cancer) during follow-up. Two of these patients were successfully treated with endoscopic submucosal dissection, while the other two underwent a total gastrectomy. Compared with patients with extended AG/IM (PGI/II≤3 and/or OGLIM stage III-IV), patients with limited AG/IM (PG I/II>3 and OLGIM stage 0-II) did not develop high-grade adenoma/dysplasia or invasive neoplasia during follow-up (p=0.02). CONCLUSION: In a low gastric cancer incidence area, a surveillance programme can detect gastric cancer at an early curable stage with an overall risk of neoplastic progression of 0.3% per year. Use of serological markers in endoscopic surveillance programmes may improve risk stratification.

Annotating Transcriptional Effects of Genetic Variants in Disease-Relevant Tissue: Transcriptome-Wide Allelic Imbalance in Osteoarthritic Cartilage.

OBJECTIVE: Multiple single-nucleotide polymorphisms (SNPs) conferring susceptibility to osteoarthritis (OA) mark imbalanced expression of positional genes in articular cartilage, reflected by unequally expressed alleles among heterozygotes (allelic imbalance [AI]). We undertook this study to explore the articular cartilage transcriptome from OA patients for AI events to identify putative disease-driving genetic variation. METHODS: AI was assessed in 42 preserved and 5 lesioned OA cartilage samples (from the Research Arthritis and Articular Cartilage study) for which RNA sequencing data were available. The count fraction of the alternative alleles among the alternative and reference alleles together (φ) was determined for heterozygous individuals. A meta-analysis was performed to generate a meta-φ and P value for each SNP with a false discovery rate (FDR) correction for multiple comparisons. To further validate AI events, we explored them as a function of multiple additional OA features. RESULTS: We observed a total of 2,070 SNPs that consistently marked AI of 1,031 unique genes in articular cartilage. Of these genes, 49 were found to be significantly differentially expressed (fold change <0.5 or >2, FDR <0.05) between preserved and paired lesioned cartilage, and 18 had previously been reported to confer susceptibility to OA and/or related phenotypes. Moreover, we identified notable highly significant AI SNPs in the CRLF1, WWP2, and RPS3 genes that were related to multiple OA features. CONCLUSION: We present a framework and resulting data set for researchers in the OA research field to probe for disease-relevant genetic variation that affects gene expression in pivotal disease-affected tissue. This likely includes putative novel compelling OA risk genes such as CRLF1, WWP2, and RPS3.

Characterisation of the NRF2 transcriptional network and its response to chemical insult in primary human hepatocytes: implications for prediction of drug-induced liver injury.

The transcription factor NRF2, governed by its repressor KEAP1, protects cells against oxidative stress. There is interest in modelling the NRF2 response to improve the prediction of clinical toxicities such as drug-induced liver injury (DILI). However, very little is known about the makeup of the NRF2 transcriptional network and its response to chemical perturbation in primary human hepatocytes (PHH), which are often used as a translational model for investigating DILI. Here, microarray analysis identified 108 transcripts (including several putative novel NRF2-regulated genes) that were both downregulated by siRNA targeting NRF2 and upregulated by siRNA targeting KEAP1 in PHH. Applying weighted gene co-expression network analysis (WGCNA) to transcriptomic data from the Open TG-GATES toxicogenomics repository (representing PHH exposed to 158 compounds) revealed four co-expressed gene sets or 'modules' enriched for these and other NRF2-associated genes. By classifying the 158 TG-GATES compounds based on published evidence, and employing the four modules as network perturbation metrics, we found that the activation of NRF2 is a very good indicator of the intrinsic biochemical reactivity of a compound (i.e. its propensity to cause direct chemical stress), with relatively high sensitivity, specificity, accuracy and positive/negative predictive values. We also found that NRF2 activation has lower sensitivity for the prediction of clinical DILI risk, although relatively high specificity and positive predictive values indicate that false positive detection rates are likely to be low in this setting. Underpinned by our comprehensive analysis, activation of the NRF2 network is one of several mechanism-based components that can be incorporated into holistic systems toxicology models to improve mechanistic understanding and preclinical prediction of DILI in man.

RNA sequencing data integration reveals an miRNA interactome of osteoarthritis cartilage.

OBJECTIVE: To uncover the microRNA (miRNA) interactome of the osteoarthritis (OA) pathophysiological process in the cartilage. METHODS: We performed RNA sequencing in 130 samples (n=35 and n=30 pairs for messenger RNA (mRNA) and miRNA, respectively) on macroscopically preserved and lesioned OA cartilage from the same patient and performed differential expression (DE) analysis of miRNA and mRNAs. To build an OA-specific miRNA interactome, a prioritisation scheme was applied based on inverse Pearson's correlations and inverse DE of miRNAs and mRNAs. Subsequently, these were filtered by those present in predicted (TargetScan/microT-CDS) and/or experimentally validated (miRTarBase/TarBase) public databases. Pathway enrichment analysis was applied to elucidate OA-related pathways likely mediated by miRNA regulatory mechanisms. RESULTS: We found 142 miRNAs and 2387 mRNAs to be differentially expressed between lesioned and preserved OA articular cartilage. After applying prioritisation towards likely miRNA-mRNA targets, a regulatory network of 62 miRNAs targeting 238 mRNAs was created. Subsequent pathway enrichment analysis of these mRNAs (or genes) elucidated that genes within the 'nervous system development' are likely mediated by miRNA regulatory mechanisms (familywise error=8.4×10-5). Herein NTF3 encodes neurotrophin-3, which controls survival and differentiation of neurons and which is closely related to the nerve growth factor. CONCLUSIONS: By an integrated approach of miRNA and mRNA sequencing data of OA cartilage, an OA miRNA interactome and related pathways were elucidated. Our functional data demonstrated interacting levels at which miRNA affects expression of genes in the cartilage and exemplified the complexity of functionally validating a network of genes that may be targeted by multiple miRNAs.

Genome-wide analyses identify a role for SLC17A4 and AADAT in thyroid hormone regulation.

Thyroid dysfunction is an important public health problem, which affects 10% of the general population and increases the risk of cardiovascular morbidity and mortality. Many aspects of thyroid hormone regulation have only partly been elucidated, including its transport, metabolism, and genetic determinants. Here we report a large meta-analysis of genome-wide association studies for thyroid function and dysfunction, testing 8 million genetic variants in up to 72,167 individuals. One-hundred-and-nine independent genetic variants are associated with these traits. A genetic risk score, calculated to assess their combined effects on clinical end points, shows significant associations with increased risk of both overt (Graves' disease) and subclinical thyroid disease, as well as clinical complications. By functional follow-up on selected signals, we identify a novel thyroid hormone transporter (SLC17A4) and a metabolizing enzyme (AADAT). Together, these results provide new knowledge about thyroid hormone physiology and disease, opening new possibilities for therapeutic targets.

ANP32A regulates ATM expression and prevents oxidative stress in cartilage, brain, and bone.

Osteoarthritis is the most common joint disorder with increasing global prevalence due to aging of the population. Current therapy is limited to symptom relief, yet there is no cure. Its multifactorial etiology includes oxidative stress and overproduction of reactive oxygen species, but the regulation of these processes in the joint is insufficiently understood. We report that ANP32A protects the cartilage against oxidative stress, preventing osteoarthritis development and disease progression. ANP32A is down-regulated in human and mouse osteoarthritic cartilage. Microarray profiling revealed that ANP32A protects the joint by promoting the expression of ATM, a key regulator of the cellular oxidative defense. Antioxidant treatment reduced the severity of osteoarthritis, osteopenia, and cerebellar ataxia features in Anp32a-deficient mice, revealing that the ANP32A/ATM axis discovered in cartilage is also present in brain and bone. Our findings indicate that modulating ANP32A signaling could help manage oxidative stress in cartilage, brain, and bone with therapeutic implications for osteoarthritis, neurological disease, and osteoporosis.

Helicobacter pylori colonization and obesity - a Mendelian randomization study.

Obesity is associated with substantial morbidity, costs, and decreased life expectancy, and continues to rise worldwide. While etiological understanding is needed for prevention, epidemiological studies indicated that colonization with Helicobacter pylori (H. pylori) may affect body mass index (BMI), but with inconsistent results. Here, we examine the relationship between H. pylori colonization and BMI/obesity. Cross-sectional analyses were performed in two independent population-based cohorts of elderly from the Netherlands and Germany (n = 13,044). Genetic risk scores were conducted based on genetic loci associated with either H. pylori colonization or BMI/obesity. We performed a bi-directional Mendelian randomization. Meta-analysis of cross-sectional data revealed no association between anti-H. pylori IgG titer and BMI, nor of H. pylori positivity and BMI. Anti-H. pylori IgG titer was negatively associated with obesity (OR 0.99972; 95% CI 0.99946-0.99997, p = 0.03) and with obesity classes (Beta -6.91 •10-5; 95% CI -1.38•10-4, -5.49•10-7, p = 0.048), but the magnitude of these effects was limited. Mendelian randomization showed no causal relation between H. pylori genetic risk score and BMI/obesity, nor between BMI or obesity genetic risk scores and H. pylori positivity. This study provides no evidence for a clinically relevant association between H. pylori and BMI/obesity.

Genome-wide association and functional studies identify a role for matrix Gla protein in osteoarthritis of the hand.

OBJECTIVE: Osteoarthritis (OA) is the most common form of arthritis and the leading cause of disability in the elderly. Of all the joints, genetic predisposition is strongest for OA of the hand; however, only few genetic risk loci for hand OA have been identified. Our aim was to identify novel genes associated with hand OA and examine the underlying mechanism. METHODS: We performed a genome-wide association study of a quantitative measure of hand OA in 12 784 individuals (discovery: 8743, replication: 4011). Genome-wide significant signals were followed up by analysing gene and allele-specific expression in a RNA sequencing dataset (n=96) of human articular cartilage. RESULTS: We found two significantly associated loci in the discovery set: at chr12 (p=3.5 × 10-10) near the matrix Gla protein (MGP) gene and at chr12 (p=6.1×10-9) near the CCDC91 gene. The DNA variant near the MGP gene was validated in three additional studies, which resulted in a highly significant association between the MGP variant and hand OA (rs4764133, Betameta=0.83, Pmeta=1.8*10-15). This variant is high linkage disequilibrium with a coding variant in MGP, a vitamin K-dependent inhibitor of cartilage calcification. Using RNA sequencing data from human primary cartilage tissue (n=96), we observed that the MGP RNA expression of the hand OA risk allele was significantly lowercompared with the MGP RNA expression of the reference allele (40.7%, p<5*10-16). CONCLUSIONS: Our results indicate that the association between the MGP variant and increased risk for hand OA is caused by a lower expression of MGP, which may increase the burden of hand OA by decreased inhibition of cartilage calcification.