Lineage specific 3D genome structure in the adult human brain and neurodevelopmental changes in the chromatin interactome.

The human brain is a complex organ comprised of distinct cell types, and the contribution of the 3D genome to lineage specific gene expression remains poorly understood. To decipher cell type specific genome architecture, and characterize fine scale changes in the chromatin interactome across neural development, we compared the 3D genome of the human fetal cortical plate to that of neurons and glia isolated from the adult prefrontal cortex. We found that neurons have weaker genome compartmentalization compared to glia, but stronger TADs, which emerge during fetal development. Furthermore, relative to glia, the neuronal genome shifts more strongly towards repressive compartments. Neurons have differential TAD boundaries that are proximal to active promoters involved in neurodevelopmental processes. CRISPRi on CNTNAP2 in hIPSC-derived neurons reveals that transcriptional inactivation correlates with loss of insulation at the differential boundary. Finally, re-wiring of chromatin loops during neural development is associated with transcriptional and functional changes. Importantly, differential loops in the fetal cortex are associated with autism GWAS loci, suggesting a neuropsychiatric disease mechanism affecting the chromatin interactome. Furthermore, neural development involves gaining enhancer-promoter loops that upregulate genes that control synaptic activity. Altogether, our study provides multi-scale insights on the 3D genome in the human brain.

Landscape of Conditional eQTL in Dorsolateral Prefrontal Cortex and Co-localization with Schizophrenia GWAS.

Causal genes and variants within genome-wide association study (GWAS) loci can be identified by integrating GWAS statistics with expression quantitative trait loci (eQTL) and determining which variants underlie both GWAS and eQTL signals. Most analyses, however, consider only the marginal eQTL signal, rather than dissect this signal into multiple conditionally independent signals for each gene. Here we show that analyzing conditional eQTL signatures, which could be important under specific cellular or temporal contexts, leads to improved fine mapping of GWAS associations. Using genotypes and gene expression levels from post-mortem human brain samples (n = 467) reported by the CommonMind Consortium (CMC), we find that conditional eQTL are widespread; 63% of genes with primary eQTL also have conditional eQTL. In addition, genomic features associated with conditional eQTL are consistent with context-specific (e.g., tissue-, cell type-, or developmental time point-specific) regulation of gene expression. Integrating the 2014 Psychiatric Genomics Consortium schizophrenia (SCZ) GWAS and CMC primary and conditional eQTL data reveals 40 loci with strong evidence for co-localization (posterior probability > 0.8), including six loci with co-localization of conditional eQTL. Our co-localization analyses support previously reported genes, identify novel genes associated with schizophrenia risk, and provide specific hypotheses for their functional follow-up.

decorate: differential epigenetic correlation test.

MOTIVATION: Identifying correlated epigenetic features and finding differences in correlation between individuals with disease compared to controls can give novel insight into disease biology. This framework has been successful in analysis of gene expression data, but application to epigenetic data has been limited by the computational cost, lack of scalable software and lack of robust statistical tests. RESULTS: Decorate, differential epigenetic correlation test, identifies correlated epigenetic features and finds clusters of features that are differentially correlated between two or more subsets of the data. The software scales to genome-wide datasets of epigenetic assays on hundreds of individuals. We apply decorate to four large-scale datasets of DNA methylation, ATAC-seq and histone modification ChIP-seq. AVAILABILITY AND IMPLEMENTATION: decorate R package is available from https://github.com/GabrielHoffman/decorate. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Functional interpretation of genetic variants using deep learning predicts impact on chromatin accessibility and histone modification.

Identifying functional variants underlying disease risk and adoption of personalized medicine are currently limited by the challenge of interpreting the functional consequences of genetic variants. Predicting the functional effects of disease-associated protein-coding variants is increasingly routine. Yet, the vast majority of risk variants are non-coding, and predicting the functional consequence and prioritizing variants for functional validation remains a major challenge. Here, we develop a deep learning model to accurately predict locus-specific signals from four epigenetic assays using only DNA sequence as input. Given the predicted epigenetic signal from DNA sequence for the reference and alternative alleles at a given locus, we generate a score of the predicted epigenetic consequences for 438 million variants observed in previous sequencing projects. These impact scores are assay-specific, are predictive of allele-specific transcription factor binding and are enriched for variants associated with gene expression and disease risk. Nucleotide-level functional consequence scores for non-coding variants can refine the mechanism of known functional variants, identify novel risk variants and prioritize downstream experiments.

Comparative efficacy of C-MAC® Miller videolaryngoscope versus McGrath® MAC size "1" videolaryngoscope in neonates and infants undergoing surgical procedures under general anesthesia: A prospective randomized controlled trial.

BACKGROUND: Various anatomical and physiological factors make intubation in infants challenging. C-MAC videolaryngoscope shows better results as compared to the conventional direct laryngoscopy for intubation in infants. McGrath MAC size-1 with a disposable Macintosh type blade has recently been introduced for use in infants and has not been formally evaluated in this population. AIMS: This study aims to evaluate the intubation characteristics of C-MAC Miller and McGrath MAC in neonates and infants with the primary objective to compare the time with the two devices. METHODS: After informed consent from the parents, 140 neonates and infants scheduled for surgical procedures were randomized to undergo intubation with either C-MAC Miller or McGrath MAC after standard general anesthesia. The two devices were compared in terms of total intubation time, Percent of Glottic Opening score, Cormack Lehane grades, time to glottis view, intubation difficulty score, overall success rate, first attempt success rate, and complications. RESULTS: The median glottic view time (6 s [4-9] vs. 6 s [4-9]; p = .40) and intubation time (27 s [25.5-28] vs. 27 s [24.5-29.5]; p = .87) were similar. The mean difference (95% CI) in time to tracheal intubation and time to glottic view was 0.49 s [-3.1 to 2.1] and -1.7 s [-3.8 to 0.47], respectively. However, the Percent of Glottic Opening score, Cormack Lehane grades, and subjective intubation difficulty were significantly better with C-MAC. The first attempt success rates, overall success rates (100% vs. 97.5%), and intubation difficulty scores were comparable. There were two failed intubations with McGrath which were successfully intubated with C-MAC. CONCLUSION: The C-MAC Miller blade showed similar intubation timings, success rates, and intubation difficulty score as compared to McGrath MAC in neonates and infants, though the former provided superior glottic views. Both the videolaryngoscopes may be safely used in infants and neonates for routine intubation scenarios.

Sex differences in brain cell-type specific chromatin accessibility in schizophrenia.

Our understanding of the sex-specific role of the non-coding genome in serious mental illness remains largely incomplete. To address this gap, we explored sex differences in 1,393 chromatin accessibility profiles, derived from neuronal and non-neuronal nuclei of two distinct cortical regions from 234 cases with serious mental illness and 235 controls. We identified sex-specific enhancer-promoter interactions and showed that they regulate genes involved in X-chromosome inactivation (XCI). Examining chromosomal conformation allowed us to identify sex-specific cis- and trans-regulatory domains (CRDs and TRDs). Co-localization of sex-specific TRDs with schizophrenia common risk variants pinpointed male-specific regulatory regions controlling a number of metabolic pathways. Additionally, enhancers from female-specific TRDs were found to regulate two genes known to escape XCI, (XIST and JPX), underlying the importance of TRDs in deciphering sex differences in schizophrenia. Overall, these findings provide extensive characterization of sex differences in the brain epigenome and disease-associated regulomes.

Dynamic alterations in gene co-expression networks and gene-transcript associations characterize co-morbidities in cocaine use disorder.

Background: Individuals with cocaine use disorder (CUD) who attempt abstinence experience craving and relapse, which poses challenges in treatment. Longitudinal studies linking behavioral manifestations in CUD to the blood transcriptome in living individuals are limited. Therefore, we investigated the connection between drug use behaviors during abstinence with blood transcriptomics. Methods: We conducted a comprehensive longitudinal study involving 12 subjects (9 males, 3 females) with CUD and RNA sequencing on blood collected at a drug-free baseline, and 3, 6 & 9 months thereafter. We categorized subjects into 2 responder groups (high-low) based on scores of drug use variables, and 3 responder groups (low-intermediate-high) on days of abstinence. We investigated differential expression and gene-transcript associations across responder groups at each time point. Lastly, we examined genes that are both co-expressed and showed dynamic expression with time. Results: Genes with significant transcript associations between high and. intermediate days of abstinence at 9 months were notably enriched for cannabis use disorder, drinks weekly, and coronary artery disease risk genes. Time-specific gene co-expression analysis prioritized transcripts related to immune processes, cell cycle, RNA-protein synthesis, and second messenger signaling for days of abstinence. Conclusion: We demonstrate that abstinence reflects robust changes in drug use behaviors and the blood transcriptome in CUD. We also highlight the importance of longitudinal studies to capture complex biological processes during abstinence in CUD.

Neuroimmune Mechanisms of Opioid Use Disorder and Recovery: Translatability to Human Studies, and Future Research Directions.

Opioid use disorder (OUD) is a major current cause of morbidity and mortality. Long-term exposure to short-acting opioids (MOP-r agonists such as heroin or fentanyl) results in complex pathophysiological changes to neuroimmune and neuroinflammatory functions, affected in part by peripheral mechanisms (e.g., cytokines in blood), and by neuroendocrine systems such as the hypothalamic-pituitary-adrenal (HPA) stress axis. There are important findings from preclinical models, but their role in the trajectory and outcomes of OUD in humans is not well understood. The goal of this narrative review is to examine available data on immune and inflammatory functions in persons with OUD, and to identify major areas for future research. Peripheral blood biomarker studies revealed a pro-inflammatory state in persons with OUD in withdrawal or early abstinence, consistent with available postmortem brain studies (which show glial activation) and diffusion tensor imaging studies (indicating white matter disruptions), with gradual abstinence-associated recovery. The mechanistic roles of these neuroimmune and neuroinflammatory changes in the trajectory of OUD (including recovery and medication management) cannot be examined practically with postmortem data. Collection of longitudinal data in larger-scale human cohorts would allow examination of these mechanisms associated with OUD stage and progression. Given the heterogeneity in presentation of OUD, a precision medicine approach integrating multi-omic peripheral biomarkers and comprehensive phenotyping, including neuroimaging, can be beneficial in risk stratification, and individually optimized selection of interventions for individuals who will benefit, and assessments under refractory therapy.

The neuronal chromatin landscape in adult schizophrenia brains is linked to early fetal development.

Non-coding variants increase risk of neuropsychiatric disease. However, our understanding of the cell-type specific role of the non-coding genome in disease is incomplete. We performed population scale (N=1,393) chromatin accessibility profiling of neurons and non-neurons from two neocortical brain regions: the anterior cingulate cortex and dorsolateral prefrontal cortex. Across both regions, we observed notable differences in neuronal chromatin accessibility between schizophrenia cases and controls. A per-sample disease pseudotime was positively associated with genetic liability for schizophrenia. Organizing chromatin into cis- and trans-regulatory domains, identified a prominent neuronal trans-regulatory domain (TRD1) active in immature glutamatergic neurons during fetal development. Polygenic risk score analysis using genetic variants within chromatin accessibility of TRD1 successfully predicted susceptibility to schizophrenia in the Million Veteran Program cohort. Overall, we present the most extensive resource to date of chromatin accessibility in the human cortex, yielding insights into the cell-type specific etiology of schizophrenia.

The neuronal chromatin landscape in adult schizophrenia brains is linked to early fetal development.

Non-coding variants increase risk of neuropsychiatric disease. However, our understanding of the cell-type specific role of the non-coding genome in disease is incomplete. We performed population scale (N=1,393) chromatin accessibility profiling of neurons and non-neurons from two neocortical brain regions: the anterior cingulate cortex and dorsolateral prefrontal cortex. Across both regions, we observed notable differences in neuronal chromatin accessibility between schizophrenia cases and controls. A per-sample disease pseudotime was positively associated with genetic liability for schizophrenia. Organizing chromatin into cis- and trans-regulatory domains, identified a prominent neuronal trans-regulatory domain (TRD1) active in immature glutamatergic neurons during fetal development. Polygenic risk score analysis using genetic variants within chromatin accessibility of TRD1 successfully predicted susceptibility to schizophrenia in the Million Veteran Program cohort. Overall, we present the most extensive resource to date of chromatin accessibility in the human cortex, yielding insights into the cell-type specific etiology of schizophrenia.

Anaesthetic Management of 2 Micropreemies with Difficult Airway: Case Report and Review of Literature.

The infants are explicitly vulnerable to develop anaesthesia-related complications, with micropreemies being at the end of the spectrum because of their unique morphological and physiological features. Airway changes in pediatric patients are most exaggerated in these tiny infants and their immature lungs provide a little reserve, and therefore, securing airways can be challenging in this population. Moreover, many devices available for managing difficult airways in adults are not available for use in this miniature version. Videolaryngoscopes are a useful addition to anaesthesiologists' armamentarium but for micropreemies, size of videolaryngoscope can be a limiting factor as no vide- olaryngoscope comes in "00" size. The technique of videolaryngoscope may need to be modified in these patients. Regional anaesthesia can be an invaluable component of their perioperative care to facilitate a smooth recovery. The successful management of these vulnerable neonates requires a multidisciplinary team approach to maintain perioperative homeostasis of their immature organ systems.

The Neuroepigenome: Implications of Chemical and Physical Modifications of Genomic DNA in Schizophrenia.

Schizophrenia is a chronic mental illness with a substantial genetic component. To unfold the complex etiology of schizophrenia, it is important to understand the interplay between genetic and nongenetic factors. Genetic factors involve variation in the DNA sequences of protein-coding genes, which directly contribute to phenotypic traits, and variation in noncoding sequences, which comprise 98% of the genome and contain DNA elements known to play a role in regulating gene expression. The epigenome refers to the chemical modifications on both DNA and the structural proteins that package DNA into the nucleus, which together regulate gene expression in specific cell types, conditions, and developmental stages. The dynamic nature of the epigenome makes it an ideal tool to investigate the relationship between inherited genetic mutations associated with schizophrenia and altered gene regulation throughout the course of brain development. In this review, we focus on the current understanding of the role of epigenetic marks and their three-dimensional nuclear organization in the developmental trajectory of distinct brain cell types to decipher the complex gene regulatory mechanisms that are disrupted in schizophrenia.

Genetics of the human microglia regulome refines Alzheimer's disease risk loci.

Microglia are brain myeloid cells that play a critical role in neuroimmunity and the etiology of Alzheimer's disease (AD), yet our understanding of how the genetic regulatory landscape controls microglial function and contributes to AD is limited. Here, we performed transcriptome and chromatin accessibility profiling in primary human microglia from 150 donors to identify genetically driven variation and cell-specific enhancer-promoter (E-P) interactions. Integrative fine-mapping analysis identified putative regulatory mechanisms for 21 AD risk loci, of which 18 were refined to a single gene, including 3 new candidate risk genes (KCNN4, FIBP and LRRC25). Transcription factor regulatory networks captured AD risk variation and identified SPI1 as a key putative regulator of microglia expression and AD risk. This comprehensive resource capturing variation in the human microglia regulome provides insights into the etiology of neurodegenerative disease.

Population-level variation in enhancer expression identifies disease mechanisms in the human brain.

Identification of risk variants for neuropsychiatric diseases within enhancers underscores the importance of understanding population-level variation in enhancer function in the human brain. Besides regulating tissue-specific and cell-type-specific transcription of target genes, enhancers themselves can be transcribed. By jointly analyzing large-scale cell-type-specific transcriptome and regulome data, we cataloged 30,795 neuronal and 23,265 non-neuronal candidate transcribed enhancers. Examination of the transcriptome in 1,382 brain samples identified robust expression of transcribed enhancers. We explored gene-enhancer coordination and found that enhancer-linked genes are strongly implicated in neuropsychiatric disease. We identified expression quantitative trait loci (eQTLs) for both genes and enhancers and found that enhancer eQTLs mediate a substantial fraction of neuropsychiatric trait heritability. Inclusion of enhancer eQTLs in transcriptome-wide association studies enhanced functional interpretation of disease loci. Overall, our study characterizes the gene-enhancer regulome and genetic mechanisms in the human cortex in both healthy and diseased states.

The three-dimensional landscape of cortical chromatin accessibility in Alzheimer's disease.

To characterize the dysregulation of chromatin accessibility in Alzheimer's disease (AD), we generated 636 ATAC-seq libraries from neuronal and nonneuronal nuclei isolated from the superior temporal gyrus and entorhinal cortex of 153 AD cases and 56 controls. By analyzing a total of ~20 billion read pairs, we expanded the repertoire of known open chromatin regions (OCRs) in the human brain and identified cell-type-specific enhancer-promoter interactions. We show that interindividual variability in OCRs can be leveraged to identify cis-regulatory domains (CRDs) that capture the three-dimensional structure of the genome (3D genome). We identified AD-associated effects on chromatin accessibility, the 3D genome and transcription factor (TF) regulatory networks. For one of the most AD-perturbed TFs, USF2, we validated its regulatory effect on lysosomal genes. Overall, we applied a systematic approach to understanding the role of the 3D genome in AD. We provide all data as an online resource for widespread community-based analysis.

Chromatin domain alterations linked to 3D genome organization in a large cohort of schizophrenia and bipolar disorder brains.

Chromosomal organization, scaling from the 147-base pair (bp) nucleosome to megabase-ranging domains encompassing multiple transcriptional units, including heritability loci for psychiatric traits, remains largely unexplored in the human brain. In this study, we constructed promoter- and enhancer-enriched nucleosomal histone modification landscapes for adult prefrontal cortex from H3-lysine 27 acetylation and H3-lysine 4 trimethylation profiles, generated from 388 controls and 351 individuals diagnosed with schizophrenia (SCZ) or bipolar disorder (BD) (n = 739). We mapped thousands of cis-regulatory domains (CRDs), revealing fine-grained, 104-106-bp chromosomal organization, firmly integrated into Hi-C topologically associating domain stratification by open/repressive chromosomal environments and nuclear topography. Large clusters of hyper-acetylated CRDs were enriched for SCZ heritability, with prominent representation of regulatory sequences governing fetal development and glutamatergic neuron signaling. Therefore, SCZ and BD brains show coordinated dysregulation of risk-associated regulatory sequences assembled into kilobase- to megabase-scaling chromosomal domains.

Better biomolecule thermodynamics from kinetics.

Protein stability is measured by denaturation: When solvent conditions are changed (e.g., temperature, denaturant concentration, or pH) the protein population switches between thermodynamic states. The resulting denaturation curves have baselines. If the baselines are steep, nonlinear, or incomplete, it becomes difficult to characterize protein denaturation. Baselines arise because the chromophore probing denaturation is sensitive to solvent conditions, or because the thermodynamic states evolve structurally when solvent conditions are changed, or because the barriers are very low (downhill folding). Kinetics can largely eliminate such baselines: Relaxation of chromophores, or within thermodynamic states, is much faster than the transition over activation barriers separating states. This separation of time scales disentangles population switching between states (desired signal) from chromophore or population relaxation within states (baselines). We derive simple formulas to extract unfolding thermodynamics from kinetics. The formulas are tested with model data and with a difficult experimental test case: the apparent two-state folder PI3K SH3 domain. Its melting temperature T(m) can be extracted reliably by our "thermodynamics from kinetics approach," even when conventional fitting is unreliable.

Anesthetic management of a patient with congenital diaphragmatic eventration.

Congenital diaphragmatic eventration is uncommon in adults and is caused by paralysis, aplasia or atrophy of the muscular fibers of the diaphragm. It may cause severe dyspnea, orthopnea and hypoxia in adult patients. Most symptomatic patients may be managed efficiently without the need for surgical correction, although any event that leads to an increase in intra-abdominal pressure puts them at the risk of spontaneous diaphragmatic rupture. This case report presents the successful anesthetic management of an adult female with congenital diaphragmatic eventration undergoing diagnostic laparoscopy and hysteroscopy using a total intravenous anesthesia technique. Essential steps to prevent any rise in intrathoracic and intra-abdominal pressures along with care to minimize intragastric volume were taken.

Videolaryngoscopy Bails us out of Difficult Intubation Scenarios in Syndromic Children: A Case Series.

Airway management in children with craniofacial anomalies can be complicated and may require multiple attempts with conventional direct laryngoscopy (DL). Videolaryngoscopes (VLs) have a well-established role in difficult airway management in adults; however, their role remains to be fully elucidated in paediatric age group. There is a relative paucity in the literature regarding the role of VLs in cases of syndromic children, and it is not clear whether they should be used as an initial option or as a rescue device. Herein, we report a series of cases of children with Pierre Robin sequence, Beckwith-Wiedemann syndrome, and Hurler's syndrome wherein VLs proved beneficial after multiple failed DL attempts. Following initial failed attempts to intubate using DL, these children were subsequently intubated using VLs. Therefore, VLs should be used for initial intubation attempts in syndromic children with potential difficult airways.

Multiscale causal networks identify VGF as a key regulator of Alzheimer's disease.

Though discovered over 100 years ago, the molecular foundation of sporadic Alzheimer's disease (AD) remains elusive. To better characterize the complex nature of AD, we constructed multiscale causal networks on a large human AD multi-omics dataset, integrating clinical features of AD, DNA variation, and gene- and protein-expression. These probabilistic causal models enabled detection, prioritization and replication of high-confidence master regulators of AD-associated networks, including the top predicted regulator, VGF. Overexpression of neuropeptide precursor VGF in 5xFAD mice partially rescued beta-amyloid-mediated memory impairment and neuropathology. Molecular validation of network predictions downstream of VGF was also achieved in this AD model, with significant enrichment for homologous genes identified as differentially expressed in 5xFAD brains overexpressing VGF. Our findings support a causal role for VGF in protecting against AD pathogenesis and progression.