Paediatrics (RCH) - Research Publications
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ItemIdentification of highly conserved putative developmental enhancers bound by SOX3 in neural progenitors using ChIP-Seq.(Public Library of Science (PLoS), 2014)The transcription factor SOX3 is expressed within most neural progenitor (NP) cells of the vertebrate central nervous system (CNS) and is essential for normal brain development in mice and humans. However, despite the widespread expression of Sox3, CNS defects in null mice are relatively mild due to functional redundancy with the other SOXB1 sub-group members Sox1 and Sox2. To further understand the molecular function of SOX3, we investigated the genome-wide binding profile of endogenous SOX3 in NP cells using ChIP-seq. SOX3 binding was identified at over 8,000 sites, most of which were intronic or intergeneic and were significantly associated with neurodevelopmental genes. The majority of binding sites were moderately or highly conserved (phastCons scores >0.1 and 0.5, respectively) and included the previously characterised, SOXB1-binding Nestin NP cell enhancer. Comparison of SOX3 and published ChIP-Seq data for the co-activator P300 in embryonic brain identified hundreds of highly conserved putative enhancer elements. In addition, we identified a subset of highly conserved putative enhancers for CNS development genes common to SOXB1 members in NP cells, all of which contained the SOX consensus motif (ACAAWR). Together these data implicate SOX3 in the direct regulation of hundreds of NP genes and provide molecular insight into the overlapping roles of SOXB1 proteins in CNS development.
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ItemDbx1 is a direct target of SOX3 in the spinal cord.(Public Library of Science (PLoS), 2014)SoxB1 sub-family of transcriptional regulators are expressed in progenitor (NP) cells throughout the neuroaxis and are generally downregulated during neuronal differentiation. Gain- and loss-of-function studies indicate that Sox1, Sox2 and Sox3 are key regulators of NP differentiation and that their roles in CNS development are largely redundant. Nevertheless, mutation of each SoxB1 individually results in a different array of CNS defects, raising the possibility that SoxB1 proteins have subtly different functions in NP cells. To explore the mechanism of SOXB1 functional redundancy, and to identify genes that are most sensitive to loss of the Sox3 gene, we performed genome wide expression profiling of Sox3 null NP cells. Nineteen genes with abnormal expression were identified, including the homeobox gene Dbx1. Analysis of Sox3 null embryos revealed that Dbx1 was significantly reduced in the neural tube and developing brain and that SOX3 bound directly to conserved elements associated with this gene in cultured NP cells and in vivo. These data define Dbx1 as a direct SOX3 target gene whose expression, intriguingly, is not fully rescued by other SOXB1 transcription factors, suggesting that there are inherent differences in SOXB1 protein activity.
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ItemHealth and wealth in children and adolescents with chronic kidney disease (K-CAD study).(Springer Science and Business Media LLC, 2014-04-04)BACKGROUND: The impact of reduced kidney function in children is substantial. End-stage kidney disease (ESKD), the most severe form of chronic kidney disease (CKD), is a devastating illness associated with substantially increased mortality, impaired growth and psychosocial maladjustment in children. Understanding how to address the complex causes of mortality and morbidity in children with CKD requires explicit information about the risk factors that lead to adverse outcomes. In addition to biological influences, the socioeconomic circumstances of caregivers may play a significant role in the health and well-being of children with CKD. METHODS/DESIGN: A prospective cohort study (n=380 children and n=380 caregivers) will be conducted to determine the prevalence of economic hardship among caregivers of children with CKD. All participants will be followed biennially over a period of 5 years to determine the association between the changing socioeconomic status of the caregivers and the health and overall well-being of school-aged children with CKD. Face to face, semi-structured interviews with the caregivers (n=45) will also be conducted to understand their perspectives on the economic, financial and psychosocial impact of CKD and how this affects the health outcomes of their child with CKD. The primary outcomes of the study are the effects of the socioeconomic status of the caregivers and self-reported health status of the children. Secondary outcomes included the prevalence of economic hardship and the distribution of wealth among the caregivers of children with CKD. DISCUSSION: Findings from this study presents not only a snapshot of the current economic and social situation of the caregivers of children and adolescents with CKD but will also provide definitive evidence of determining whether a link between socioeconomic status of caregivers and outcomes of children with CKD exists.
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ItemComparing the feasibility, acceptability, clinical-, and cost-effectiveness of mental health e-screening to paper-based screening on the detection of depression, anxiety, and psychosocial risk in pregnant women: a study protocol of a randomized, parallel-group, superiority trial(BIOMED CENTRAL LTD, 2014-01-02)BACKGROUND: Stress, depression, and anxiety affect 15% to 25% of pregnant women. However, substantial barriers to psychosocial assessment exist, resulting in less than 20% of prenatal care providers assessing and treating mental health problems. Moreover, pregnant women are often reluctant to disclose their mental health concerns to a healthcare provider. Identifying screening and assessment tools and procedures that are acceptable to both women and service providers, cost-effective, and clinically useful is needed. METHODS/DESIGN: The primary objective of this randomized, parallel-group, superiority trial is to evaluate the feasibility and acceptability of a computer tablet-based prenatal psychosocial assessment (e-screening) compared to paper-based screening. Secondary objectives are to compare the two modes of screening on: (1) the level of detection of prenatal depression and anxiety symptoms and psychosocial risk; (2) the level of disclosure of symptoms; (3) the factors associated with feasibility, acceptability, and disclosure; (4) the psychometric properties of the e-version of the assessment tools; and (5) cost-effectiveness. A sample of 542 women will be recruited from large, primary care maternity clinics and a high-risk antenatal unit in an urban Canadian city. Pregnant women are eligible to participate if they: (1) receive care at one of the recruitment sites; (2) are able to speak/read English; (3) are willing to be randomized to e-screening; and (4) are willing to participate in a follow-up diagnostic interview within 1 week of recruitment. Allocation is by computer-generated randomization. Women in the intervention group will complete an online psychosocial assessment on a computer tablet, while those in the control group will complete the same assessment in paper-based form. All women will complete baseline questionnaires at the time of recruitment and will participate in a diagnostic interview within 1 week of recruitment. Research assistants conducting diagnostic interviews and physicians will be blinded. A qualitative descriptive study involving healthcare providers from the recruitment sites and women will provide data on feasibility and acceptability of the intervention. We hypothesize that mental health e-screening in primary care maternity settings and high-risk antenatal units will be as or more feasible, acceptable, and capable of detecting depression, anxiety, and psychosocial risk compared to paper-based screening. TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT01899534.
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ItemStudy protocol for a randomized, controlled, superiority trial comparing the clinical and cost-effectiveness of integrated online mental health assessment-referral-care in pregnancy to usual prenatal care on prenatal and postnatal mental health and infant health and development: the Integrated Maternal Psychosocial Assessment to Care Trial (IMPACT)(BMC, 2014-03-06)BACKGROUND: Stress, depression, and anxiety affect 15 to 25% of pregnant women. However, fewer than 20% of prenatal care providers assess and treat mental health problems and fewer than 20% of pregnant women seek mental healthcare. For those who seek treatment, the lack of health system integration and existing barriers frequently prevent treatment access. Without treatment, poor prenatal mental health can persist for years and impact future maternal, child, and family well-being. METHODS/DESIGN: The purpose of this randomized controlled trial is to evaluate the effectiveness of an integrated process of online psychosocial assessment, referral, and cognitive behavior therapy (CBT) for pregnant women compared to usual prenatal care (no formal screening or specialized care). The primary outcome is self-reported prenatal depression, anxiety, and stress symptoms at 6 to 8 weeks postrandomization. Secondary outcomes are postpartum depression, anxiety, and stress symptoms; self-efficacy; mastery; self-esteem; sleep; relationship quality; coping; resilience; Apgar score; gestational age; birth weight; maternal-infant attachment; infant behavior and development; parenting stress/competence; and intervention cost-effectiveness, efficiency, feasibility, and acceptability. Pregnant women are eligible if they: 1) are <28 weeks gestation; 2) speak/read English; 3) are willing to complete email questionnaires; 4) have no, low, or moderate psychosocial risk on screening at recruitment; and 5) are eligible for CBT. A sample of 816 women will be recruited from large, urban primary care clinics and allocation is by computer-generated randomization. Women in the intervention group will complete an online psychosocial assessment, and those with mild or moderate depression, anxiety, or stress symptoms then complete six interactive cognitive behavior therapy modules. All women will complete email questionnaires at 6 to 8 weeks postrandomization and at 3, 6, and 12 months postpartum. Clinic-based providers and researchers conducting chart abstraction and analysis are blinded. Qualitative interviews with 8 to 10 healthcare providers and 15 to 30 intervention group women will provide data on feasibility and acceptability of the intervention. Results of this trial will determine the feasibility and effectiveness of an integrated approach to prenatal mental healthcare and the use of highly accessible computer-based psychosocial assessment and CBT on maternal, infant, and family-based outcomes. TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT01901796.
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ItemDiagnosis of Whooping Cough in Switzerland: Differentiating Bordetella pertussis from Bordetella holmesii by Polymerase Chain Reaction(PUBLIC LIBRARY SCIENCE, 2014-02-19)Bordetella holmesii, an emerging pathogen, can be misidentified as Bordetella pertussis by routine polymerase chain reaction (PCR). In some reports, up to 29% of the patients diagnosed with pertussis have in fact B. holmesii infection and invasive, non-respiratory B. holmesii infections have been reported worldwide. This misdiagnosis undermines the knowledge of pertussis' epidemiology, and may lead to misconceptions on pertussis vaccine's efficacy. Recently, the number of whooping cough cases has increased significantly in several countries. The aim of this retrospective study was to determine whether B. holmesii was contributing to the increase in laboratory-confirmed cases of B. pertussis in Switzerland. A multiplex species-specific quantitative PCR assay was performed on 196 nasopharyngeal samples from Swiss patients with PCR-confirmed Bordetella infection (median age: 6 years-old, minimum 21 days-old, maximum 86 years-old), formerly diagnosed as Bordetella pertussis (IS481+). No B. holmesii (IS481+, IS1001-, hIS1001+) was identified. We discuss whether laboratories should implement specific PCR to recognize different Bordetella species. We conclude that in Switzerland B. holmesii seems to be circulating less than in neighboring countries and that specific diagnostic procedures are not necessary routinely. However, as the epidemiological situation may change rapidly, periodic reevaluation is suggested.
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ItemControlling Expansion and Cardiomyogenic Differentiation of Human Pluripotent Stem Cells in Scalable Suspension Culture(CELL PRESS, 2014-12-09)To harness the potential of human pluripotent stem cells (hPSCs), an abundant supply of their progenies is required. Here, hPSC expansion as matrix-independent aggregates in suspension culture was combined with cardiomyogenic differentiation using chemical Wnt pathway modulators. A multiwell screen was scaled up to stirred Erlenmeyer flasks and subsequently to tank bioreactors, applying controlled feeding strategies (batch and cyclic perfusion). Cardiomyogenesis was sensitive to the GSK3 inhibitor CHIR99021 concentration, whereas the aggregate size was no prevailing factor across culture platforms. However, in bioreactors, the pattern of aggregate formation in the expansion phase dominated subsequent differentiation. Global profiling revealed a culture-dependent expression of BMP agonists/antagonists, suggesting their decisive role in cell-fate determination. Furthermore, metallothionein was discovered as a potentially stress-related marker in hPSCs. In 100 ml bioreactors, the production of 40 million predominantly ventricular-like cardiomyocytes (up to 85% purity) was enabled that were directly applicable to bioartificial cardiac tissue formation.
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ItemComparison of cancer diagnostic intervals before and after implementation of NICE guidelines: analysis of data from the UK General Practice Research Database(NATURE PUBLISHING GROUP, 2014-02-04)BACKGROUND: The primary aim was to use routine data to compare cancer diagnostic intervals before and after implementation of the 2005 NICE Referral Guidelines for Suspected Cancer. The secondary aim was to compare change in diagnostic intervals across different categories of presenting symptoms. METHODS: Using data from the General Practice Research Database, we analysed patients with one of 15 cancers diagnosed in either 2001-2002 or 2007-2008. Putative symptom lists for each cancer were classified into whether or not they qualified for urgent referral under NICE guidelines. Diagnostic interval (duration from first presented symptom to date of diagnosis in primary care records) was compared between the two cohorts. RESULTS: In total, 37,588 patients had a new diagnosis of cancer and of these 20,535 (54.6%) had a recorded symptom in the year prior to diagnosis and were included in the analysis. The overall mean diagnostic interval fell by 5.4 days (95% CI: 2.4-8.5; P<0.001) between 2001-2002 and 2007-2008. There was evidence of significant reductions for the following cancers: (mean, 95% confidence interval) kidney (20.4 days, -0.5 to 41.5; P=0.05), head and neck (21.2 days, 0.2-41.6; P=0.04), bladder (16.4 days, 6.6-26.5; P≤0.001), colorectal (9.0 days, 3.2-14.8; P=0.002), oesophageal (13.1 days, 3.0-24.1; P=0.006) and pancreatic (12.6 days, 0.2-24.6; P=0.04). Patients who presented with NICE-qualifying symptoms had shorter diagnostic intervals than those who did not (all cancers in both cohorts). For the 2007-2008 cohort, the cancers with the shortest median diagnostic intervals were breast (26 days) and testicular (44 days); the highest were myeloma (156 days) and lung (112 days). The values for the 90th centiles of the distributions remain very high for some cancers. Tests of interaction provided little evidence of differences in change in mean diagnostic intervals between those who did and did not present with symptoms specifically cited in the NICE Guideline as requiring urgent referral. CONCLUSION: We suggest that the implementation of the 2005 NICE Guidelines may have contributed to this reduction in diagnostic intervals between 2001-2002 and 2007-2008. There remains considerable scope to achieve more timely cancer diagnosis, with the ultimate aim of improving cancer outcomes.
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ItemAutoantibodies against C1q as a Diagnostic Measure of Lupus Nephritis: Systematic Review and Meta-analysis.(OMICS Publishing Group, 2014-04-22)OBJECTIVES: To evaluate the diagnostic accuracy of C1q autoantibodies in identifying lupus nephritis (LN) in patients with systemic lupus erythematosus (SLE). DATA SOURCES AND METHODS: Citation indexes were searched and 370 articles published from 1977 to 2013 were evaluated. The 31 selected studies included in the meta-analysis were cross-sectional in design. Among the 31 studies, 28 compared anti-C1q antibodies in 2769 SLE patients with (n=1442) and without a history of LN (n=1327). Nine studies examined anti-C1q in 517 SLE patients with active (n=249) and inactive LN (n=268). Hierarchical summary receiver operating characteristic (HSROC) random effects models were fitted to pool estimates of accuracy across the studies. RESULTS: Anti-C1q antibodies discriminated between patients with and without a history of LN, with a median specificity of 73.5%. The HSROC model estimated the corresponding sensitivity to be 70.4%. A hypothetical patient with a 55% prior probability of having a history of LN as opposed to no history (the median prevalence across 28 eligible studies) would have a post-test probability of 76.4% following a positive test result (positive predictive value) or 33.0% following a negative test result (negative predictive value). For discriminating active from inactive LN the median specificity of anti-C1q antibodies was 80%, with a corresponding estimated sensitivity value 75.7% based on the HSROC model. A hypothetical patient with a 56% prior probability of active as opposed to inactive LN (the median prevalence across the 9 eligible studies) would have a post-test probability of 82.8% following a positive test result or 27.9% following a negative test result. CONCLUSIONS: Although C1q antibodies are associated with lupus nephritis the post-test probabilities are not sufficiently convincing to provide reasonable certainty of the presence or absence of history of disease/active disease.
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ItemThe Devon Active Villages Evaluation (DAVE) trial of a community-level physical activity intervention in rural south-west England: a stepped wedge cluster randomised controlled trial(BMC, 2014-07-18)BACKGROUND: The majority of adults are not meeting the guidelines for physical activity despite activity being linked with numerous improvements to long-term health. In light of this, researchers have called for more community-level interventions. The main objective of the present study was to evaluate whether a community-level physical activity intervention increased the activity levels of rural communities. METHODS: 128 rural villages (clusters) were randomised to receive the intervention in one of four time periods between April 2011 and December 2012. The Devon Active Villages intervention provided villages with 12 weeks of physical activity opportunities for all age groups, including at least three different types of activities per village. Each village received an individually tailored intervention, incorporating a local needs-led approach. Support was provided for a further 12 months following the intervention. The evaluation study used a stepped wedge cluster randomised controlled trial design. All 128 villages were measured at each of five data collection periods using a postal survey. The primary outcome of interest was the proportion of adults reporting sufficient physical activity to meet internationally recognised guidelines. Minutes spent in moderate-and-vigorous activity per week was analysed as a secondary outcome. To compare between intervention and control modes, random effects linear regression and marginal logistic regression models were implemented for continuous and binary outcomes respectively. RESULTS: 10,412 adults (4693 intervention, 5719 control) completed the postal survey (response rate 32.2%). The intervention did not increase the odds of adults meeting the physical activity guideline (adjusted OR 1.02, 95% CI: 0.88 to 1.17; P = 0.80), although there was weak evidence of an increase in minutes of moderate-and-vigorous-intensity activity per week (adjusted mean difference = 171, 95% CI: -16 to 358; P = 0.07). The ineffectiveness of the intervention may have been due to its low penetration-only 16% of intervention mode participants reported awareness of the intervention and just 4% reported participating in intervention events. CONCLUSIONS: A community-level physical activity intervention providing tailored physical activity opportunities to rural villages did not improve physical activity levels in adults. Greater penetration of such interventions must be achieved if they are to increase physical activity prevalence at the community level. TRIAL REGISTRATION: Current Controlled Trials ISRCTN37321160.