Transcriptome Analysis of CD4+ T Cells in Coeliac Disease Reveals Imprint of BACH2 and IFNγ Regulation

peer-reviewedData Availability: The raw sequencing reads (FASTQ files) and sequence read counts mapped to UCSC hg19 for each of the 74 transcriptomes sequenced in this study have been deposited at Gene Expression Omnibus (GEO) accession GSE69549.This project was funded by Science Foundation Ireland Grant number 09/IN.1/B2640 to RM.Genetic studies have to date identified 43 genome wide significant coeliac disease susceptibility (CD) loci comprising over 70 candidate genes. However, how altered regulation of such disease associated genes contributes to CD pathogenesis remains to be elucidated. Recently there has been considerable emphasis on characterising cell type specific and stimulus dependent genetic variants. Therefore in this study we used RNA sequencing to profile over 70 transcriptomes of CD4+ T cells, a cell type crucial for CD pathogenesis, in both stimulated and resting samples from individuals with CD and unaffected controls. We identified extensive transcriptional changes across all conditions, with the previously established CD gene IFNy the most strongly up-regulated gene (log2 fold change 4.6; Padjusted = 2.40x10-11) in CD4+ T cells from CD patients compared to controls. We show a significant correlation of differentially expressed genes with genetic studies of the disease to date (Padjusted = 0.002), and 21 CD candidate susceptibility genes are differentially expressed under one or more of the conditions used in this study. Pathway analysis revealed significant enrichment of immune related processes. Co-expression network analysis identified several modules of coordinately expressed CD genes. Two modules were particularly highly enriched for differentially expressed genes (P</iframe

The relationship between maternal plasma homocysteine in early pregnancy and birth weight

Background: There is limited evidence that plasma homocysteine (Hcy) is increased in women with adverse pregnancy outcomes, such as low birth weight (LBW). Objective: We examined the relationship between maternal Hcy at the first prenatal visit and birth weight. Study design: In a prospective observational study, women were recruited during their first prenatal visit after sonographic confirmation of gestational age. Along with the standard tests, blood was also taken for the measurement of maternal serum and red blood cell (RBC) folate, vitamin B12, and Hcy. In addition to collecting standard clinical and sociodemographic details, a detailed questionnaire on vitamin supplementation was completed under supervision. Birth outcomes were collected immediately after delivery. Results: Of 498 women recruited, 213 (42.8%) were nulliparous, 97 (19.4%) were obese, 64 (12.9%) selfreported as current smokers, and 489 (98.2%) were taking folic acid (FA) supplements at presentation. The mean (SD) birth weight was 3426.3 g (600.7), 14.0% of infants were small for gestational age, and 7.4% were large for gestational age. Mean (SD) plasma Hcy was 7.1 (2.1) µmol/l. On multiple linear regression, higher plasma Hcy was associated with selfreported smoking (p = .009), relative income poverty (p = .037) and Irish nativity (p = .009). There was no relationship between maternal plasma Hcy and birth weight centile, either overall or when analyzed separately for either smokers (r = 0.0001, p = .98) and nonsmokers (r = −0.007, p = .097). Plasma Hcy was correlated negatively with serum folate, RBC folate, and serum vitamin B12. There was no association between maternal Hcy and the duration of FA supplementation in weeks (r = −0.08, p = .083) or between maternal Hcy and gestational age at phlebotomy (r = −0.54, p = .35). Conclusions: In this well-characterized cohort of women in early pregnancy, there was no correlation between maternal plasma Hcy and birth weight. However, higher Hcy was associated with maternal smoking and social deprivation which may explain the association reported previously between an increased Hcy and LBW. Rationale This study was conducted to investigate the relationship between maternal homocysteine in early pregnancy and infant birth weight. Increased plasma homocysteine in early pregnancy was not associated with a lower birth weight. However, there was a positive correlation between increasing plasma homocysteine and maternal smoking and social disadvantage which are risk factors for lower birth weight. This study highlights the importance of correcting for confounding variables, such as smoking and social disadvantage, when evaluating the relationship maternal nutritional biomarkers and intrauterine fetal development

Comparison At The First Prenatal Visit of the Maternal Dietary Intakes of Smokers With Non-Smokers in a Large Maternity Hospital: A Cross-Sectional Study

Using detailed dietary and supplement questionnaires in early pregnancy, we compared the dietary intakes of micronutrients and macronutrients at the first prenatal visit of women who reported continuing to smoke during pregnancy with the intakes of women who were non-smokers

Economic (gross cost) analysis of systematically implementing a programme of advance care planning in three Irish nursing homes.

Background: Although advance care planning (ACP) and the use of advanced care directives (ACD) and end-of-life care plans are associated with a reduction in inappropriate hospitalisation, there is little evidence supporting the economic benefits of such programmes. We assessed the economic impact (gross savings) of the Let Me Decide (LMD) ACP programme in Ireland, specifically the impact on hospitalisations, bed days and location of resident deaths, before and after systematic implementation of the LMD-ACP combined with a palliative care education programme. Methods: The LMD-ACP was introduced into three long-term care (LTC) facilities in Southern Ireland and outcomes were compared pre and post implementation. In addition, 90 staff were trained in a palliative care educational programme. Economic analysis including probabilistic sensitivity analysis was performed. Results: The uptake of an ACD or end-of-life care post-implementation rose from 25 to 76 %. Post implementation, there were statistically significant decreases in hospitalisation rates from baseline (hospitalisation incidents declined from 27.8 to 14.6 %, z = 3.96, p < 0.001; inpatient hospital days reduced from 0.54 to 0.36 %, z = 8.85, p < 0.001). The percentage of hospital deaths also decreased from 22.9 to 8.4 %, z = 3.22, p = 0.001. However, length of stay (LOS) increased marginally (7–9 days). Economic analysis suggested a cost-reduction related to reduced hospitalisations ranging between €10 and €17.8 million/annum and reduction in ambulance transfers, estimated at €0.4 million/annum if these results were extrapolated nationally. When unit costs and LOS estimates were varied in scenario analyses, the expected cost reduction owing to reduced hospitalisations, ranged from €17.7 to €42.4 million nationally. Conclusions: Implementation of the LMD-ACP (ACD/end-of-life care plans combined with palliative care education) programme resulted in reduced rates of hospitalisation. Despite an increase in LOS, likely reflecting more complex care needs of admitted residents, gross costs were reduced and scenario analysis projected large annual savings if these results were extrapolated to the wider LTC population in Ireland

Bridging the translational gap: what can synaptopathies tell us about autism?

Multiple molecular pathways and cellular processes have been implicated in the neurobiology of autism and other neurodevelopmental conditions. There is a current focus on synaptic gene conditions, or synaptopathies, which refer to clinical conditions associated with rare genetic variants disrupting genes involved in synaptic biology. Synaptopathies are commonly associated with autism and developmental delay and may be associated with a range of other neuropsychiatric outcomes. Altered synaptic biology is suggested by both preclinical and clinical studies in autism based on evidence of differences in early brain structural development and altered glutamatergic and GABAergic neurotransmission potentially perturbing excitatory and inhibitory balance. This review focusses on the NRXN-NLGN-SHANK pathway, which is implicated in the synaptic assembly, trans-synaptic signalling, and synaptic functioning. We provide an overview of the insights from preclinical molecular studies of the pathway. Concentrating on NRXN1 deletion and SHANK3 mutations, we discuss emerging understanding of cellular processes and electrophysiology from induced pluripotent stem cells (iPSC) models derived from individuals with synaptopathies, neuroimaging and behavioural findings in animal models of Nrxn1 and Shank3 synaptic gene conditions, and key findings regarding autism features, brain and behavioural phenotypes from human clinical studies of synaptopathies. The identification of molecular-based biomarkers from preclinical models aims to advance the development of targeted therapeutic treatments. However, it remains challenging to translate preclinical animal models and iPSC studies to interpret human brain development and autism features. We discuss the existing challenges in preclinical and clinical synaptopathy research, and potential solutions to align methodologies across preclinical and clinical research. Bridging the translational gap between preclinical and clinical studies will be necessary to understand biological mechanisms, to identify targeted therapies, and ultimately to progress towards personalised approaches for complex neurodevelopmental conditions such as autism

Policing Matters

This article examines the historical origins of Garda industrial relations [IR] through the lens of the ‘thin blue line’. This concept, which equates the absence of the police with chaos, had significant implications for the IR structure of the nascent force, the manner in which discontent was expressed by Gardaí during various industrial disputes and the nature of political responses to Garda grievances. Although the thin blue line often serves as justification for the curtailment of Garda labour rights, it will be argued that both the Gardaí and the political establishment share a vested interest in its preservation. Paradoxically, until one or both parties relinquish their adherence to this concept, the thin blue line will ensure the continued stagnation of the IR capabilities of the force

A review of the cognitive impact of neurodevelopmental and neuropsychiatric associated copy number variants

Abstract The heritability of intelligence or general cognitive ability is estimated at 41% and 66% in children and adults respectively. Many rare copy number variants are associated with neurodevelopmental and neuropsychiatric conditions (ND-CNV), including schizophrenia and autism spectrum disorders, and may contribute to the observed variability in cognitive ability. Here, we reviewed studies of intelligence quotient or cognitive function in ND-CNV carriers, from both general population and clinical cohorts, to understand the cognitive impact of ND-CNV in both contexts and identify potential genotype-specific cognitive phenotypes. We reviewed aggregate studies of sets ND-CNV broadly linked to neurodevelopmental and neuropsychiatric conditions, and genotype-first studies of a subset of 12 ND-CNV robustly associated with schizophrenia and autism. Cognitive impacts were observed across ND-CNV in both general population and clinical cohorts, with reports of phenotypic heterogeneity. Evidence for ND-CNV-specific impacts were limited by a small number of studies and samples sizes. A comprehensive understanding of the cognitive impact of ND-CNVs would be clinically informative and could identify potential educational needs for ND-CNV carriers. This could improve genetic counselling for families impacted by ND-CNV, and clinical outcomes for those with complex needs