Youth with high callous-unemotional traits (CU) are at risk for early-onset and persistent conduct problems. Research suggests that there may be different developmental pathways to CU ...(genetic/constitutional vs environmental), and that the absence or presence of co-occurring internalizing problems is a key marker. However, it is unclear whether such a distinction is valid. Intermediate phenotypes such as DNA methylation, an epigenetic modification regulating gene expression, may help to clarify etiological pathways. This is the first study to examine prospective inter-relationships between environmental risk (prenatal/postnatal) and DNA methylation (birth, age 7 and 9) in the prediction of CU (age 13), for youth low vs high in internalizing problems. We focused on DNA methylation in the vicinity of the oxytocin receptor (OXTR) gene as it has been previously implicated in CU. Participants were 84 youth with early-onset and persistent conduct problems drawn from the Avon Longitudinal Study of Parents and Children. For youth with low internalizing problems (46%), we found that (i) OXTR methylation at birth associated with higher CU (age 13) as well as decreased experience of victimization during childhood (evocative epigenetic-environment correlation; birth-age 7), (ii) higher prenatal parental risks (maternal psychopathology, criminal behaviors, substance use) associated with higher OXTR methylation at birth and (iii) OXTR methylation levels were more stable across time (birth-age 9). In contrast, for youth with high internalizing problems, CU were associated with prenatal risks of an interpersonal nature (that is, intimate partner violence, family conflict) but not OXTR methylation. Findings support the existence of distinct developmental pathways to CU.
The presence of ribonucleotides in genomic DNA is undesirable given their increased susceptibility to hydrolysis. Ribonuclease (RNase) H enzymes that recognize and process such embedded ...ribonucleotides are present in all domains of life. However, in unicellular organisms such as budding yeast, they are not required for viability or even efficient cellular proliferation, while in humans, RNase H2 hypomorphic mutations cause the neuroinflammatory disorder Aicardi-Goutières syndrome. Here, we report that RNase H2 is an essential enzyme in mice, required for embryonic growth from gastrulation onward. RNase H2 null embryos accumulate large numbers of single (or di-) ribonucleotides embedded in their genomic DNA (>1,000,000 per cell), resulting in genome instability and a p53-dependent DNA-damage response. Our findings establish RNase H2 as a key mammalian genome surveillance enzyme required for ribonucleotide removal and demonstrate that ribonucleotides are the most commonly occurring endogenous nucleotide base lesion in replicating cells.
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► Ribonucleotides are the most common nucleotide base lesion in the mouse genome ► RNase H2 is a key genome surveillance enzyme required for removal of nucleotides ► RNase H2 is essential for mammalian development ► Without RNase H2, cells exhibit genome instability and p53 pathway activation
DNA polymerases can incorporate more than a million ribonucleotides into replicating mouse DNA in each cell, making ribonucleotides the most abundant kind of DNA lesion. RNase H2, which removes this “damage,” has an essential role in genome surveillance and is required for embryonic development.
Human endogenous retroviruses (HERVs) are repetitive elements previously implicated in major psychiatric conditions, but their role in aetiology remains unclear. Here, we perform specialised ...transcriptome-wide association studies that consider HERV expression quantified to precise genomic locations, using RNA sequencing and genetic data from 792 post-mortem brain samples. In Europeans, we identify 1238 HERVs with expression regulated in cis, of which 26 represent expression signals associated with psychiatric disorders, with ten being conditionally independent from neighbouring expression signals. Of these, five are additionally significant in fine-mapping analyses and thus are considered high confidence risk HERVs. These include two HERV expression signatures specific to schizophrenia risk, one shared between schizophrenia and bipolar disorder, and one specific to major depressive disorder. No robust signatures are identified for autism spectrum conditions or attention deficit hyperactivity disorder in Europeans, or for any psychiatric trait in other ancestries, although this is likely a result of relatively limited statistical power. Ultimately, our study highlights extensive HERV expression and regulation in the adult cortex, including in association with psychiatric disorder risk, therefore providing a rationale for exploring neurological HERV expression in complex neuropsychiatric traits.
Despite decades of research on spatial memory, we know surprisingly little about how the brain guides navigation to goals. While some models argue that vectors are represented for navigational ...guidance, other models postulate that the future path is computed. Although the hippocampal formation has been implicated in processing spatial goal information, it remains unclear whether this region processes path- or vector-related information.
We report neuroimaging data collected from subjects navigating London's Soho district; these data reveal that both the path distance and the Euclidean distance to the goal are encoded by the medial temporal lobe during navigation. While activity in the posterior hippocampus was sensitive to the distance along the path, activity in the entorhinal cortex was correlated with the Euclidean distance component of a vector to the goal. During travel periods, posterior hippocampal activity increased as the path to the goal became longer, but at decision points, activity in this region increased as the path to the goal became closer and more direct. Importantly, sensitivity to the distance was abolished in these brain areas when travel was guided by external cues.
The results indicate that the hippocampal formation contains representations of both the Euclidean distance and the path distance to goals during navigation. These findings argue that the hippocampal formation houses a flexible guidance system that changes how it represents distance to the goal depending on the fluctuating demands of navigation.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the worst global health crisis in living memory. The reverse transcription polymerase chain reaction (RT-qPCR) is considered ...the gold standard diagnostic method, but it exhibits limitations in the face of enormous demands. We evaluated a mid-infrared (MIR) data set of 237 saliva samples obtained from symptomatic patients (138 COVID-19 infections diagnosed via RT-qPCR). MIR spectra were evaluated via unsupervised random forest (URF) and classification models. Linear discriminant analysis (LDA) was applied following the genetic algorithm (GA-LDA), successive projection algorithm (SPA-LDA), partial least squares (PLS-DA), and a combination of dimension reduction and variable selection methods by particle swarm optimization (PSO-PLS-DA). Additionally, a consensus class was used. URF models can identify structures even in highly complex data. Individual models performed well, but the consensus class improved the validation performance to 85% accuracy, 93% sensitivity, 83% specificity, and a Matthew’s correlation coefficient value of 0.69, with information at different spectral regions. Therefore, through this unsupervised and supervised framework methodology, it is possible to better highlight the spectral regions associated with positive samples, including lipid (∼1700 cm–1), protein (∼1400 cm–1), and nucleic acid (∼1200–950 cm–1) regions. This methodology presents an important tool for a fast, noninvasive diagnostic technique, reducing costs and allowing for risk reduction strategies.
Schizophrenia is a highly heritable, neuropsychiatric disorder characterized by episodic psychosis and altered cognitive function. Despite success in identifying genetic variants associated with ...schizophrenia, there remains uncertainty about the causal genes involved in disease pathogenesis and how their function is regulated.
We performed a multi-stage epigenome-wide association study, quantifying genome-wide patterns of DNA methylation in a total of 1714 individuals from three independent sample cohorts. We have identified multiple differentially methylated positions and regions consistently associated with schizophrenia across the three cohorts; these effects are independent of important confounders such as smoking. We also show that epigenetic variation at multiple loci across the genome contributes to the polygenic nature of schizophrenia. Finally, we show how DNA methylation quantitative trait loci in combination with Bayesian co-localization analyses can be used to annotate extended genomic regions nominated by studies of schizophrenia, and to identify potential regulatory variation causally involved in disease.
This study represents the first systematic integrated analysis of genetic and epigenetic variation in schizophrenia, introducing a methodological approach that can be used to inform epigenome-wide association study analyses of other complex traits and diseases. We demonstrate the utility of using a polygenic risk score to identify molecular variation associated with etiological variation, and of using DNA methylation quantitative trait loci to refine the functional and regulatory variation associated with schizophrenia risk variants. Finally, we present strong evidence for the co-localization of genetic associations for schizophrenia and differential DNA methylation.
Attention-deficit/hyperactivity disorder (ADHD) is a prevalent developmental disorder, associated with a range of long-term impairments. Variation in DNA methylation, an epigenetic mechanism, is ...implicated in both neurobiological functioning and psychiatric health. However, the potential role of DNA methylation in ADHD symptoms is currently unclear. In this study, we examined data from the Avon Longitudinal Study of Parents and Children (ALSPAC)-specifically the subsample forming the Accessible Resource for Integrated Epigenomics Studies (ARIES)-that includes (1) peripheral measures of DNA methylation (Illumina 450k) at birth (n=817, 49% male) and age 7 (n=892, 50% male) and (2) trajectories of ADHD symptoms (7-15 years). We first employed a genome-wide analysis to test whether DNA methylation at birth associates with later ADHD trajectories; and then followed up at age 7 to investigate the stability of associations across early childhood. We found that DNA methylation at birth differentiated ADHD trajectories across multiple genomic locations, including probes annotated to SKI (involved in neural tube development), ZNF544 (previously implicated in ADHD), ST3GAL3 (linked to intellectual disability) and PEX2 (related to perixosomal processes). None of these probes maintained an association with ADHD trajectories at age 7. Findings lend novel insights into the epigenetic landscape of ADHD symptoms, highlighting the potential importance of DNA methylation variation in genes related to neurodevelopmental and peroxisomal processes that play a key role in the maturation and stability of cortical circuits.
Hyperuricemia in adults is associated with cardiovascular risk factors. However, there is less data regarding this association in children and adolescents. Our purpose was to determine association ...between serum uric acid (SUA) and cardiovascular risk.
A fasting blood sample was collected from 1750 participants aged 6–17 years enrolled in a social project and public schools in Espírito Santo, Brazil. Internal cut-offs were generated to define high SUA (≥90th percentile of SUA concentration for sex and age group). Body mass index percentile (pBMI), body fat percentage (BFP) and muscle mass were determined by bioimpedance. Data are given as mean ± standard deviation. High SUA was associated with overweight/obesity (OR 3.7 CI 95% 2.7–5.0), high waist circumference (WC) (OR 3.9 CI 95% 2.9–5.4), low HDL (OR 2.0 CI 95% 1.5–2.8), high blood pressure (BP) (OR 1.8 CI 95% 1.1–3.2), high BFP (OR 4.1 CI 95% 2.7–6.4), metabolic syndrome (MetS) (OR 3.6 CI 95% 1.8–7.1) and insulin resistance (OR 1.7 CI 95% 1.1–2.7). Individuals in the fourth quartile of SUA, compared to those in the first quartile, showed higher age, pBMI, WC, BFP and muscle mass. Using a reference value of 5.5 mg/dL, the prevalence of hyperuricemia in the sample was 10.3% (CI 95% 8.9–11.7%).
Higher SUA values are associated with higher cardiovascular risk in childhood and adolescence. The main cardiovascular risk factors associated with hyperuricemia were overweight/obesity, high WC, dyslipidemia, high BFP, high BP, insulin resistance and MetS.
•There is lack of information on hyperuricemia and cardiovascular risk in children.•High SUA is associated to higher cardiovascular risk in childhood and adolescence.•The main risk factor associated with hyperuricemia were overweight/obesity.
The first observing run of Advanced LIGO spanned 4 months, from 12 September 2015 to 19 January 2016, during which gravitational waves were directly detected from two binary black hole systems, ...namely GW150914 and GW151226. Confident detection of gravitational waves requires an understanding of instrumental transients and artifacts that can reduce the sensitivity of a search. Studies of the quality of the detector data yield insights into the cause of instrumental artifacts and data quality vetoes specific to a search are produced to mitigate the effects of problematic data. In this paper, the systematic removal of noisy data from analysis time is shown to improve the sensitivity of searches for compact binary coalescences. The output of the PyCBC pipeline, which is a python-based code package used to search for gravitational wave signals from compact binary coalescences, is used as a metric for improvement. GW150914 was a loud enough signal that removing noisy data did not improve its significance. However, the removal of data with excess noise decreased the false alarm rate of GW151226 by more than two orders of magnitude, from 1 in 770 yr to less than 1 in 186 000 yr.
Autism spectrum disorder (ASD) defines a group of common, complex neurodevelopmental disorders. Although the aetiology of ASD has a strong genetic component, there is considerable monozygotic (MZ) ...twin discordance indicating a role for non-genetic factors. Because MZ twins share an identical DNA sequence, disease-discordant MZ twin pairs provide an ideal model for examining the contribution of environmentally driven epigenetic factors in disease. We performed a genome-wide analysis of DNA methylation in a sample of 50 MZ twin pairs (100 individuals) sampled from a representative population cohort that included twins discordant and concordant for ASD, ASD-associated traits and no autistic phenotype. Within-twin and between-group analyses identified numerous differentially methylated regions associated with ASD. In addition, we report significant correlations between DNA methylation and quantitatively measured autistic trait scores across our sample cohort. This study represents the first systematic epigenomic analyses of MZ twins discordant for ASD and implicates a role for altered DNA methylation in autism.
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