Genetic Control of Expression and Splicing in Developing Human Brain Informs Disease Mechanisms.

Tissue-specific regulatory regions harbor substantial genetic risk for disease. Because brain development is a critical epoch for neuropsychiatric disease susceptibility, we characterized the genetic control of the transcriptome in 201 mid-gestational human brains, identifying 7,962 expression quantitative trait loci (eQTL) and 4,635 spliceQTL (sQTL), including several thousand prenatal-specific regulatory regions. We show that significant genetic liability for neuropsychiatric disease lies within prenatal eQTL and sQTL. Integration of eQTL and sQTL with genome-wide association studies (GWAS) via transcriptome-wide association identified dozens of novel candidate risk genes, highlighting shared and stage-specific mechanisms in schizophrenia (SCZ). Gene network analysis revealed that SCZ and autism spectrum disorder (ASD) affect distinct developmental gene co-expression modules. Yet, in each disorder, common and rare genetic variation converges within modules, which in ASD implicates superficial cortical neurons. More broadly, these data, available as a web browser and our analyses, demonstrate the genetic mechanisms by which developmental events have a widespread influence on adult anatomical and behavioral phenotypes.

The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis.

Non-coding regions comprise most of the human genome and harbor a significant fraction of risk alleles for neuropsychiatric diseases, yet their functions remain poorly defined. We created a high-resolution map of non-coding elements involved in human cortical neurogenesis by contrasting chromatin accessibility and gene expression in the germinal zone and cortical plate of the developing cerebral cortex. We link distal regulatory elements (DREs) to their cognate gene(s) together with chromatin interaction data and show that target genes of human-gained enhancers (HGEs) regulate cortical neurogenesis and are enriched in outer radial glia, a cell type linked to human cortical evolution. We experimentally validate the regulatory effects of predicted enhancers for FGFR2 and EOMES. We observe that common genetic variants associated with educational attainment, risk for neuropsychiatric disease, and intracranial volume are enriched within regulatory elements involved in cortical neurogenesis, demonstrating the importance of this early developmental process for adult human cognitive function.

Cas9 gene therapy for Angelman syndrome traps Ube3a-ATS long non-coding RNA.

Angelman syndrome (AS) is a severe neurodevelopmental disorder caused by a mutation or deletion of the maternally inherited UBE3A allele. In neurons, the paternally inherited UBE3A allele is silenced in cis by a long non-coding RNA called UBE3A-ATS. Here, as part of a systematic screen, we found that Cas9 can be used to activate ('unsilence') paternal Ube3a in cultured mouse and human neurons when targeted to Snord115 genes, which are small nucleolar RNAs that are clustered in the 3' region of Ube3a-ATS. A short Cas9 variant and guide RNA that target about 75 Snord115 genes were packaged into an adeno-associated virus and administered to a mouse model of AS during the embryonic and early postnatal stages, when the therapeutic benefit of restoring Ube3a is predicted to be greatest1,2. This early treatment unsilenced paternal Ube3a throughout the brain for at least 17 months and rescued anatomical and behavioural phenotypes in AS mice. Genomic integration of the adeno-associated virus vector into Cas9 target sites caused premature termination of Ube3a-ATS at the vector-derived polyA cassette, or when integrated in the reverse orientation, by transcriptional collision with the vector-derived Cas9 transcript. Our study shows that targeted genomic integration of a gene therapy vector can restore the function of paternally inherited UBE3A throughout life, providing a path towards a disease-modifying treatment for a syndromic neurodevelopmental disorder.

Inference of putative cell-type-specific imprinted regulatory elements and genes during human neuronal differentiation.

Genomic imprinting results in gene expression bias caused by parental chromosome of origin and occurs in genes with important roles during human brain development. However, the cell-type and temporal specificity of imprinting during human neurogenesis is generally unknown. By detecting within-donor allelic biases in chromatin accessibility and gene expression that are unrelated to cross-donor genotype, we inferred imprinting in both primary human neural progenitor cells and their differentiated neuronal progeny from up to 85 donors. We identified 43/20 putatively imprinted regulatory elements (IREs) in neurons/progenitors, and 133/79 putatively imprinted genes in neurons/progenitors. Although 10 IREs and 42 genes were shared between neurons and progenitors, most putative imprinting was only detected within specific cell types. In addition to well-known imprinted genes and their promoters, we inferred novel putative IREs and imprinted genes. Consistent with both DNA methylation-based and H3K27me3-based regulation of imprinted expression, some putative IREs also overlapped with differentially methylated or histone-marked regions. Finally, we identified a progenitor-specific putatively imprinted gene overlapping with copy number variation that is associated with uniparental disomy-like phenotypes. Our results can therefore be useful in interpreting the function of variants identified in future parent-of-origin association studies.

Using neuroimaging genomics to investigate the evolution of human brain structure.

Alterations in brain size and organization represent some of the most distinctive changes in the emergence of our species. Yet, there is limited understanding of how genetic factors contributed to altered neuroanatomy during human evolution. Here, we analyze neuroimaging and genetic data from up to 30,000 people in the UK Biobank and integrate with genomic annotations for different aspects of human evolution, including those based on ancient DNA and comparative genomics. We show that previously reported signals of recent polygenic selection for cortical anatomy are not replicable in a more ancestrally homogeneous sample. We then investigate relationships between evolutionary annotations and common genetic variants shaping cortical surface area and white-matter connectivity for each hemisphere. Our analyses identify single-nucleotide polymorphism heritability enrichment in human-gained regulatory elements that are active in early brain development, affecting surface areas of several parts of the cortex, including left-hemispheric speech-associated regions. We also detect heritability depletion in genomic regions with Neanderthal ancestry for connectivity of the uncinate fasciculus; this is a white-matter tract involved in memory, language, and socioemotional processing with relevance to neuropsychiatric disorders. Finally, we show that common genetic loci associated with left-hemispheric pars triangularis surface area overlap with a human-gained enhancer and affect regulation of ZIC4, a gene implicated in neurogenesis. This work demonstrates how genomic investigations of present-day neuroanatomical variation can help shed light on the complexities of our evolutionary past.

Brain-trait-associated variants impact cell-type-specific gene regulation during neurogenesis.

Interpretation of the function of non-coding risk loci for neuropsychiatric disorders and brain-relevant traits via gene expression and alternative splicing quantitative trait locus (e/sQTL) analyses is generally performed in bulk post-mortem adult tissue. However, genetic risk loci are enriched in regulatory elements active during neocortical differentiation, and regulatory effects of risk variants may be masked by heterogeneity in bulk tissue. Here, we map e/sQTLs, and allele-specific expression in cultured cells representing two major developmental stages, primary human neural progenitors (n = 85) and their sorted neuronal progeny (n = 74), identifying numerous loci not detected in either bulk developing cortical wall or adult cortex. Using colocalization and genetic imputation via transcriptome-wide association, we uncover cell-type-specific regulatory mechanisms underlying risk for brain-relevant traits that are active during neocortical differentiation. Specifically, we identified a progenitor-specific eQTL for CENPW co-localized with common variant associations for cortical surface area and educational attainment.

MRLocus: Identifying causal genes mediating a trait through Bayesian estimation of allelic heterogeneity.

Expression quantitative trait loci (eQTL) studies are used to understand the regulatory function of non-coding genome-wide association study (GWAS) risk loci, but colocalization alone does not demonstrate a causal relationship of gene expression affecting a trait. Evidence for mediation, that perturbation of gene expression in a given tissue or developmental context will induce a change in the downstream GWAS trait, can be provided by two-sample Mendelian Randomization (MR). Here, we introduce a new statistical method, MRLocus, for Bayesian estimation of the gene-to-trait effect from eQTL and GWAS summary data for loci with evidence of allelic heterogeneity, that is, containing multiple causal variants. MRLocus makes use of a colocalization step applied to each nearly-LD-independent eQTL, followed by an MR analysis step across eQTLs. Additionally, our method involves estimation of the extent of allelic heterogeneity through a dispersion parameter, indicating variable mediation effects from each individual eQTL on the downstream trait. Our method is evaluated against other state-of-the-art methods for estimation of the gene-to-trait mediation effect, using an existing simulation framework. In simulation, MRLocus often has the highest accuracy among competing methods, and in each case provides more accurate estimation of uncertainty as assessed through interval coverage. MRLocus is then applied to five candidate causal genes for mediation of particular GWAS traits, where gene-to-trait effects are concordant with those previously reported. We find that MRLocus's estimation of the causal effect across eQTLs within a locus provides useful information for determining how perturbation of gene expression or individual regulatory elements will affect downstream traits. The MRLocus method is implemented as an R package available at https://mikelove.github.io/mrlocus.

Genetic variations within human gained enhancer elements affect human brain sulcal morphology.

The expansion of the cerebral cortex is one of the most distinctive changes in the evolution of the human brain. Cortical expansion and related increases in cortical folding may have contributed to emergence of our capacities for high-order cognitive abilities. Molecular analysis of humans, archaic hominins, and non-human primates has allowed identification of chromosomal regions showing evolutionary changes at different points of our phylogenetic history. In this study, we assessed the contributions of genomic annotations spanning 30 million years to human sulcal morphology measured via MRI in more than 18,000 participants from the UK Biobank. We found that variation within brain-expressed human gained enhancers, regulatory genetic elements that emerged since our last common ancestor with Old World monkeys, explained more trait heritability than expected for the left and right calloso-marginal posterior fissures and the right central sulcus. Intriguingly, these are sulci that have been previously linked to the evolution of locomotion in primates and later on bipedalism in our hominin ancestors.

The statistical fragility of studies on rotator cuff repair with graft augmentation.

BACKGROUND: Clinical decision-making often relies on evidence-based medicine. Our purpose was to determine the fragility index (FI) and fragility quotient (FQ) for studies evaluating rotator cuff repair (RCR) with graft augmentation. A lost to follow-up (LTF) value greater than the FI indicates statistical instability for the reported outcomes and conclusions. METHODS: We performed a systematic review using Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines by searching PubMed, the Cochrane library, and Embase in June 2022 to identify studies of RCR with graft augmentation. Comparative studies with at least 1 statistically analyzed dichotomous outcome were included. Seventeen studies published in seven peer-reviewed journals from 2003 to 2019 were subsequently evaluated. The FI was determined by changing each reported outcome event within 2 × 2 contingency tables until statistical significance or nonsignificance was reversed. The associated FQ was determined by dividing the FI by the sample size. LTF values were also extracted from each included study. RESULTS: The included studies had a total of 1098 patients with 36 dichotomous outcomes. The associated median FI was 4 (interquartile range 2-5), indicating that the reversal of 4 patients' outcomes would have reversed the finding of significant difference. The median FQ was 0.08 (interquartile range 0.04-0.15), indicating that in a sample of 100 patients, reversal of 8 patients' outcomes would reverse statistical significance. The median number of patients LTF was 3 (range 0-25), with 56% of reported outcomes having LTF greater than their respective FI. CONCLUSION: Studies of RCR with graft augmentation lack statistical stability, with few altered outcome events required to reverse statistical significance. Larger comparative studies with better follow-up will strengthen the statistical stability of the evidence for RCR with graft augmentation. For future investigations and reports, we recommend including FI and FQ along with traditional statistical significance analyses to provide better context on the strength of conclusions.

Timing and Duration of Facial Nerve Dysfunction After Mandibular Distraction Osteogenesis for Robin Sequence.

OBJECTIVE: Collect data from craniofacial surgeons to analyze mandibular distraction osteogenesis (MDO) protocols, and facial nerve dysfunction (FND) to characterize this common, but poorly documented complication after MDO in infants with Robin Sequence (RS). DESIGN, SETTING, AND PARTICIPANTS: A 16-question anonymous survey designed through REDCap was digitally distributed to members of the American Cleft Palate-Craniofacial Association and International Society of Craniofacial Surgery (ISCFS). MAIN OUTCOME MEASURE(S): Demographic information, MDO perioperative variables, surgeon experience with FND after MDO for patients with RS, and the timing and duration of FND were analyzed. RESULTS: Eighty-four responses were collected, with 80 included for analysis. Almost two-thirds of respondent surgeons reported FND as a complication of MDO in patients with RS (51, 63.8%); 58.8% (n = 47) transient FND and 5% (n = 4) with permanent facial nerve palsy only. Both transient and permanent FND was documented by 13 (16.3%) respondents. Among respondents, FND was observed immediately following initial device placement/osteotomies in 45.1%, during distraction in 45.1%, during consolidation in 19.6%, and following device removal in 43.1%. Twenty-five of these respondent surgeons reported resolution of FND between 1 and 3 months (53.2%, n = 25). CONCLUSIONS: FND after MDO in patients with RS was noted by most respondents in this survey study. While most surgeons noted temporary FND, one-fifth reported long-term dysfunction. FND was documented most commonly following device placement/osteotomies or during active distraction. Further research should seek to establish risk factors associated with FND and identify surgical and perioperative prevention strategies.

Evaluating brain structure traits as endophenotypes using polygenicity and discoverability.

Human brain structure traits have been hypothesized to be broad endophenotypes for neuropsychiatric disorders, implying that brain structure traits are comparatively "closer to the underlying biology." Genome-wide association studies from large sample sizes allow for the comparison of common variant genetic architectures between traits to test the evidence supporting this claim. Endophenotypes, compared to neuropsychiatric disorders, are hypothesized to have less polygenicity, with greater effect size of each susceptible SNP, requiring smaller sample sizes to discover them. Here, we compare polygenicity and discoverability of brain structure traits, neuropsychiatric disorders, and other traits (91 in total) to directly test this hypothesis. We found reduced polygenicity (FDR = 0.01) and increased discoverability (FDR = 3.68 × 10-9 ) of cortical brain structure traits, as compared to aggregated estimates of multiple neuropsychiatric disorders. We predict that ~8 M individuals will be required to explain the full heritability of cortical surface area by genome-wide significant SNPs, whereas sample sizes over 20 M will be required to explain the full heritability of depression. In conclusion, our findings are consistent with brain structure satisfying the higher power criterion of endophenotypes.

Ten years of enhancing neuro-imaging genetics through meta-analysis: An overview from the ENIGMA Genetics Working Group.

Here we review the motivation for creating the enhancing neuroimaging genetics through meta-analysis (ENIGMA) Consortium and the genetic analyses undertaken by the consortium so far. We discuss the methodological challenges, findings, and future directions of the genetics working group. A major goal of the working group is tackling the reproducibility crisis affecting "candidate gene" and genome-wide association analyses in neuroimaging. To address this, we developed harmonized analytic methods, and support their use in coordinated analyses across sites worldwide, which also makes it possible to understand heterogeneity in results across sites. These efforts have resulted in the identification of hundreds of common genomic loci robustly associated with brain structure. We have found both pleiotropic and specific genetic effects associated with brain structures, as well as genetic correlations with psychiatric and neurological diseases.

Chromosome conformation elucidates regulatory relationships in developing human brain.

Three-dimensional physical interactions within chromosomes dynamically regulate gene expression in a tissue-specific manner. However, the 3D organization of chromosomes during human brain development and its role in regulating gene networks dysregulated in neurodevelopmental disorders, such as autism or schizophrenia, are unknown. Here we generate high-resolution 3D maps of chromatin contacts during human corticogenesis, permitting large-scale annotation of previously uncharacterized regulatory relationships relevant to the evolution of human cognition and disease. Our analyses identify hundreds of genes that physically interact with enhancers gained on the human lineage, many of which are under purifying selection and associated with human cognitive function. We integrate chromatin contacts with non-coding variants identified in schizophrenia genome-wide association studies (GWAS), highlighting multiple candidate schizophrenia risk genes and pathways, including transcription factors involved in neurogenesis, and cholinergic signalling molecules, several of which are supported by independent expression quantitative trait loci and gene expression analyses. Genome editing in human neural progenitors suggests that one of these distal schizophrenia GWAS loci regulates FOXG1 expression, supporting its potential role as a schizophrenia risk gene. This work provides a framework for understanding the effect of non-coding regulatory elements on human brain development and the evolution of cognition, and highlights novel mechanisms underlying neuropsychiatric disorders.

The Evolutionary History of Common Genetic Variants Influencing Human Cortical Surface Area.

Structural brain changes along the lineage leading to modern Homo sapiens contributed to our distinctive cognitive and social abilities. However, the evolutionarily relevant molecular variants impacting key aspects of neuroanatomy are largely unknown. Here, we integrate evolutionary annotations of the genome at diverse timescales with common variant associations from large-scale neuroimaging genetic screens. We find that alleles with evidence of recent positive polygenic selection over the past 2000-3000 years are associated with increased surface area (SA) of the entire cortex, as well as specific regions, including those involved in spoken language and visual processing. Therefore, polygenic selective pressures impact the structure of specific cortical areas even over relatively recent timescales. Moreover, common sequence variation within human gained enhancers active in the prenatal cortex is associated with postnatal global SA. We show that such variation modulates the function of a regulatory element of the developmentally relevant transcription factor HEY2 in human neural progenitor cells and is associated with structural changes in the inferior frontal cortex. These results indicate that non-coding genomic regions active during prenatal cortical development are involved in the evolution of human brain structure and identify novel regulatory elements and genes impacting modern human brain structure.

Administration of Intravenous Dexmedetomidine and Acetaminophen for Improved Postoperative Pain Management in Primary Palatoplasty.

OBJECTIVE: Suboptimal pain management after primary palatoplasty (PP) may lead to complications such as hypoxemia, and increased hospital length of stay. Opioids are the first option for postoperative acute pain control after PP; however, adverse effects include excessive sedation, respiratory depression, and death, among others. Thus, optimizing postoperative pain control using opioid-sparing techniques is critically important. This paper aims to analyze efficacy and safety of combined intravenous (IV), dexmedetomidine, and IV acetaminophen during PP. METHODS: Review of a cohort of patients who underwent PP from April 2009 to July 2018 at a large free-standing children's hospital was performed, comparing patients who received combined IV dexmedetomidine and acetaminophen with those who did not receive either of the 2 medications. Efficacy was measured through opioid and nonopioid analgesic dose and timing, pain scores, duration to oral intake, and length of stay. Safety was measured by 30-day complication rates including readmission for bleeding and need for supplementary oxygen. RESULTS: Total postoperative acetaminophen (P = 0.01) and recovery room fentanyl (P < 0.001) requirements were significantly lower in the study group compared with the control group. Length of stay, oral intake duration, pain scores, total postoperative opioid requirements, and complications rates trended favorably in the study group, though differences did not reach statistical significance. CONCLUSIONS: Intraoperative IV dexmedetomidine and acetaminophen during PP provides safe and effective perioperative pain control, resulting in statistically significant decreased need for postoperative acetaminophen and fentanyl. Larger studies are necessary to determine if other trends identified in this study may be significant.

Administration of Single-Dose Antibiotic Does Not Decrease Oronasal Fistula Rates After Primary Palatoplasty.

OBJECTIVE: Oronasal fistula (ONF) is a known complication after primary palatoplasty (PP). Studies investigating the effect of perioperative antibiotics on fistula rates after PP are limited by inadequate sample size or reliance on self-reporting through national databases. In this study, the authors evaluated the association between single-dose perioperative antibiotics and postoperative fistula rates after PP at a single institution. DESIGN: A retrospective study. PARTICIPANTS: Children younger than 2 years who underwent PP from April 2009 to September 2019 were included. INTERVENTIONS: Patients were divided into 2 categories: Group 1 received a single intraoperative dose of IV antibiotic, while group 2 did not. MAIN OUTCOME MEASURE(S): Outcome measures included ONF formation, length of stay (LOS), and 30-day readmission rates. Multivariable firth logistic regression, quantile regression, and χ2 tests were performed. RESULTS: Of the 424 patients, 215 and 209 patients were in groups 1 and 2, respectively. The overall ONF rate was 1.9% among all patients. Patients in group 1 experienced an ONF rate of 3.3%, while patients in group 2 had an ONF rate of 0.5%. After correcting for confounding variables, the difference in ONF rates was not statistically different (P = .68). Median LOS was 35.7 hours and 35.5 hours (P = .17), while the rate of readmission within 30 days was 4.7% and 2.4% for group 1 and 2, respectively (P = .96). CONCLUSIONS: Administration of a single-dose perioperative antibiotic did not decrease fistula formation after PP, nor did it affect the patient's LOS or 30-day readmission rate.

Safety and Efficacy of Single-Dose Ketorolac for Postoperative Pain Management After Primary Palatoplasty: A Prospective Cohort Study With Historical Controls.

OBJECTIVE: To analyze safety and efficacy of single-dose ketorolac after primary palatoplasty (PP). DESIGN: Consecutive cohort of patients undergoing PP, comparing to historical controls. Setting: A large academic children's hospital. PATIENTS, PARTICIPANTS: A consecutive cohort of 111 patients undergoing PP (study n = 47) compared to historical controls (n = 64). INTERVENTIONS: All patients received intraoperative acetaminophen, dexmedetomidine, and opioids while the study group received an additional single dose of ketorolac (0.5 mg/kg) at the conclusion of PP. MAIN OUTCOME MEASURES: Safety of ketorolac was measured by significant bleeding complications and need for supplementary oxygen. Efficacy was assessed through bleeding, Face Legs Activity Cry Consolability (FLACC) scale, and opioid dose. RESULTS: Length of stay was similar for both groups (control group 38.5 hours [95% CI: 3.6-43.3] versus study group 37.6 hours [95% CI: 31.3-44.0], P = .84). There were no significant differences in all postoperative FLACC scales. The mean dose of opioid rescue medication measured as morphine milligram equivalents did not differ between groups (P = .56). Significant postoperative hemorrhage was not observed. CONCLUSIONS: This is the first prospective study to evaluate the safety and efficacy of single-dose ketorolac after PP. Although lack of standardization between study and historical control groups may have precluded observation of an analgesic benefit, analysis demonstrated a single dose of ketorolac after PP is safe. Further investigations with more patients and different postoperative regimens may clarify the role of ketorolac in improving pain after PP.

Segmentor: a tool for manual refinement of 3D microscopy annotations.

BACKGROUND: Recent advances in tissue clearing techniques, combined with high-speed image acquisition through light sheet microscopy, enable rapid three-dimensional (3D) imaging of biological specimens, such as whole mouse brains, in a matter of hours. Quantitative analysis of such 3D images can help us understand how changes in brain structure lead to differences in behavior or cognition, but distinguishing densely packed features of interest, such as nuclei, from background can be challenging. Recent deep learning-based nuclear segmentation algorithms show great promise for automated segmentation, but require large numbers of accurate manually labeled nuclei as training data. RESULTS: We present Segmentor, an open-source tool for reliable, efficient, and user-friendly manual annotation and refinement of objects (e.g., nuclei) within 3D light sheet microscopy images. Segmentor employs a hybrid 2D-3D approach for visualizing and segmenting objects and contains features for automatic region splitting, designed specifically for streamlining the process of 3D segmentation of nuclei. We show that editing simultaneously in 2D and 3D using Segmentor significantly decreases time spent on manual annotations without affecting accuracy as compared to editing the same set of images with only 2D capabilities. CONCLUSIONS: Segmentor is a tool for increased efficiency of manual annotation and refinement of 3D objects that can be used to train deep learning segmentation algorithms, and is available at https://www.nucleininja.org/ and https://github.com/RENCI/Segmentor .