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1. Multi-ancestry phenome-wide association of complement component 4 variation with psychiatric and brain phenotypes in youth

Author: Leanna M. Hernandez, Minsoo Kim, Pan Zhang, Richard A. I. Bethlehem, Gil Hoftman, Robert Loughnan, Diana Smith, Susan Y. Bookheimer, Chun Chieh Fan, Carrie E. Bearden, Wesley K. Thompson, and Michael J. Gandal
Subjects: Schizophrenia, Psychosis, Neuroimaging, Genetics, Gene expression, Complement, Biology (General), QH301-705.5, QH426-470
Abstract: Abstract Background Increased expression of the complement component 4A (C4A) gene is associated with a greater lifetime risk of schizophrenia. In the brain, C4A is involved in synaptic pruning; yet, it remains unclear the extent to which upregulation of C4A alters brain development or is associated with the risk for psychotic symptoms in childhood. Here, we perform a multi-ancestry phenome-wide association study in 7789 children aged 9–12 years to examine the relationship between genetically regulated expression (GREx) of C4A, childhood brain structure, cognition, and psychiatric symptoms. Results While C4A GREx is not related to childhood psychotic experiences, cognition, or global measures of brain structure, it is associated with a localized reduction in regional surface area (SA) of the entorhinal cortex. Furthermore, we show that reduced entorhinal cortex SA at 9–10 years predicts a greater number and severity of psychosis-like events at 1-year and 2-year follow-up time points. We also demonstrate that the effects of C4A on the entorhinal cortex are independent of genome-wide polygenic risk for schizophrenia. Conclusions Our results suggest neurodevelopmental effects of C4A on childhood medial temporal lobe structure, which may serve as a biomarker for schizophrenia risk prior to symptom onset.
Published: 2023
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2. The molecular genetic landscape of human brain size variation

Author: Jakob Seidlitz, Travis T. Mallard, Jacob W. Vogel, Younga H. Lee, Varun Warrier, Gareth Ball, Oskar Hansson, Leanna M. Hernandez, Ayan S. Mandal, Konrad Wagstyl, Michael V. Lombardo, Eric Courchesne, Joseph T. Glessner, Theodore D. Satterthwaite, Richard A.I. Bethlehem, Joshua D. Bernstock, Shinya Tasaki, Bernard Ng, Chris Gaiteri, Jordan W. Smoller, Tian Ge, Raquel E. Gur, Michael J. Gandal, and Aaron F. Alexander-Bloch
Subjects: CP: Neuroscience, Biology (General), QH301-705.5
Abstract: Summary: Human brain size changes dynamically through early development, peaks in adolescence, and varies up to 2-fold among adults. However, the molecular genetic underpinnings of interindividual variation in brain size remain unknown. Here, we leveraged postmortem brain RNA sequencing and measurements of brain weight (BW) in 2,531 individuals across three independent datasets to identify 928 genome-wide significant associations with BW. Genes associated with higher or lower BW showed distinct neurodevelopmental trajectories and spatial patterns that mapped onto functional and cellular axes of brain organization. Expression of BW genes was predictive of interspecies differences in brain size, and bioinformatic annotation revealed enrichment for neurogenesis and cell-cell communication. Genome-wide, transcriptome-wide, and phenome-wide association analyses linked BW gene sets to neuroimaging measurements of brain size and brain-related clinical traits. Cumulatively, these results represent a major step toward delineating the molecular pathways underlying human brain size variation in health and disease.
Published: 2023
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3. Decoupling Sleep and Brain Size in Childhood: An Investigation of Genetic Covariation in the Adolescent Brain Cognitive Development Study

Author: Leanna M. Hernandez, Minsoo Kim, Cristian Hernandez, Wesley Thompson, Chun Chieh Fan, Adriana Galván, Mirella Dapretto, Susan Y. Bookheimer, Andrew Fuligni, and Michael J. Gandal
Subjects: ADHD, Brain, Childhood, Genetics, Heritability, Insomnia, Psychiatry, RC435-571
Abstract: Background: Childhood sleep problems are common and among the most frequent and impairing comorbidities of childhood psychiatric disorders. In adults, sleep disturbances are heritable and show strong genetic associations with brain morphology; however, little is known about the genetic architecture of childhood sleep and potential etiological links between sleep, brain development, and pediatric-onset psychiatric symptoms. Methods: Using data from the Adolescent Brain Cognitive Development Study (nPhenotype = 4428 for discovery/replication, nGenetics = 4728; age 9–10 years), we assessed phenotypic relationships, heritability, and genetic correlations between childhood sleep disturbances (insomnia, arousal, breathing, somnolence, hyperhidrosis, sleep-wake transitions), brain size (surface area, cortical thickness, volume), and dimensional psychopathology. Results: Sleep disturbances showed widespread positive associations with multiple domains of childhood psychopathology; however, only insomnia showed replicable associations with smaller brain surface area. Among the sleep disturbances assessed, only insomnia showed significant heritability (h2SNP = 0.15, p < .05) and showed substantial genetic correlations with externalizing and attention-deficit/hyperactivity disorder symptomatology (rGs > 0.80, ps < .05). We found no evidence of genetic correlation between childhood insomnia and brain size. Furthermore, polygenic risk scores calculated from genome-wide association studies of adult insomnia and adult brain size did not predict childhood insomnia; instead, polygenic risk scores trained using attention-deficit/hyperactivity disorder genome-wide association studies predicted decreased surface area at baseline as well as insomnia and externalizing symptoms longitudinally. Conclusions: Findings demonstrate a distinct genetic architecture underlying childhood insomnia and brain size and suggest genetic overlap between childhood insomnia and attention-deficit/hyperactivity disorder symptomatology. Additional research is needed to examine how genetic risk manifests in altered developmental trajectories and comorbid sleep/psychiatric symptoms across adolescence.
Published: 2023
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4. Association between resting-state functional brain connectivity and gene expression is altered in autism spectrum disorder

Author: Stefano Berto, Alex H. Treacher, Emre Caglayan, Danni Luo, Jillian R. Haney, Michael J. Gandal, Daniel H. Geschwind, Albert A. Montillo, and Genevieve Konopka
Subjects: Science
Abstract: Gene expression patterns have been associated with functional activity patterns in the brain. Here the authors determine how gene expression patterns in the human brain supports brain phenotypes obtained from resting state fMRI imaging, identifying brain regions and genes relevant to autism.
Published: 2022
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5. Associations between patterns in comorbid diagnostic trajectories of individuals with schizophrenia and etiological factors

Author: Morten Dybdahl Krebs, Gonçalo Espregueira Themudo, Michael Eriksen Benros, Ole Mors, Anders D. Børglum, David Hougaard, Preben Bo Mortensen, Merete Nordentoft, Michael J. Gandal, Chun Chieh Fan, Daniel H. Geschwind, Andrew J. Schork, Thomas Werge, and Wesley K. Thompson
Subjects: Science
Abstract: Schizophrenia is a complex disorder where individuals experience different symptoms and outcomes that can be captured by patterns in other diagnoses. Here the authors use computational approaches to summarize these patterns and suggest they are associated with genetic and environmental exposure.
Published: 2021
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6. Integrative genomics identifies a convergent molecular subtype that links epigenomic with transcriptomic differences in autism

Author: Gokul Ramaswami, Hyejung Won, Michael J. Gandal, Jillian Haney, Jerry C. Wang, Chloe C. Y. Wong, Wenjie Sun, Shyam Prabhakar, Jonathan Mill, and Daniel H. Geschwind
Subjects: Science
Abstract: Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by impaired social interactions with repetitive and restrictive behaviours. Here the authors integrate mRNA expression, miRNA expression, DNA methylation, and histone acetylation datasets from a collection of post mortem brain tissues and identify a convergent molecular subtype of ASD.
Published: 2020
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7. Full-length transcript sequencing of human and mouse cerebral cortex identifies widespread isoform diversity and alternative splicing

Author: Szi Kay Leung, Aaron R. Jeffries, Isabel Castanho, Ben T. Jordan, Karen Moore, Jonathan P. Davies, Emma L. Dempster, Nicholas J. Bray, Paul O’Neill, Elizabeth Tseng, Zeshan Ahmed, David A. Collier, Erin D. Jeffery, Shyam Prabhakar, Leonard Schalkwyk, Connor Jops, Michael J. Gandal, Gloria M. Sheynkman, Eilis Hannon, and Jonathan Mill
Subjects: isoform, transcript, expression, brain, cortex, mouse, human, adult, fetal, long-read sequencing, alternative splicing, Biology (General), QH301-705.5
Abstract: Summary: Alternative splicing is a post-transcriptional regulatory mechanism producing distinct mRNA molecules from a single pre-mRNA with a prominent role in the development and function of the central nervous system. We used long-read isoform sequencing to generate full-length transcript sequences in the human and mouse cortex. We identify novel transcripts not present in existing genome annotations, including transcripts mapping to putative novel (unannotated) genes and fusion transcripts incorporating exons from multiple genes. Global patterns of transcript diversity are similar between human and mouse cortex, although certain genes are characterized by striking differences between species. We also identify developmental changes in alternative splicing, with differential transcript usage between human fetal and adult cortex. Our data confirm the importance of alternative splicing in the cortex, dramatically increasing transcriptional diversity and representing an important mechanism underpinning gene regulation in the brain. We provide transcript-level data for human and mouse cortex as a resource to the scientific community.
Published: 2021
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8. Spatial fine-mapping for gene-by-environment effects identifies risk hot spots for schizophrenia

Author: Chun Chieh Fan, John J. McGrath, Vivek Appadurai, Alfonso Buil, Michael J. Gandal, Andrew J. Schork, Preben Bo Mortensen, Esben Agerbo, Sandy A. Geschwind, Daniel Geschwind, Thomas Werge, Wesley K. Thompson, and Carsten Bøcker Pedersen
Subjects: Science
Abstract: Schizophrenia (SCZ) risk is influenced by genetic and environmental factors. Here, the authors develop a statistical method for analyzing gene-by-environment effects in SCZ risk across Denmark with fine spatial resolution.
Published: 2018
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9. Strong correlation of downregulated genes related to synaptic transmission and mitochondria in post-mortem autism cerebral cortex

Author: Matthew Schwede, Shailender Nagpal, Michael J. Gandal, Neelroop N. Parikshak, Karoly Mirnics, Daniel H. Geschwind, and Eric M. Morrow
Subjects: Autism, Human, Cortex, Post-mortem, Transcriptome, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571
Abstract: Abstract Background Genetic studies in autism have pinpointed a heterogeneous group of loci and genes. Further, environment may be an additional factor conferring susceptibility to autism. Transcriptome studies investigate quantitative differences in gene expression between patient-derived tissues and control. These studies may pinpoint genes relevant to pathophysiology yet circumvent the need to understand genetic architecture or gene-by-environment interactions leading to disease. Methods We conducted alternate gene set enrichment analyses using differentially expressed genes from a previously published RNA-seq study of post-mortem autism cerebral cortex. We used three previously published microarray datasets for validation and one of the microarray datasets for additional differential expression analysis. The RNA-seq study used 26 autism and 33 control brains in differential gene expression analysis, and the largest microarray dataset contained 15 autism and 16 control post-mortem brains. Results While performing a gene set enrichment analysis of genes differentially expressed in the RNA-seq study, we discovered that genes associated with mitochondrial function were downregulated in autism cerebral cortex, as compared to control. These genes were correlated with genes related to synaptic function. We validated these findings across the multiple microarray datasets. We also did separate differential expression and gene set enrichment analyses to confirm the importance of the mitochondrial pathway among downregulated genes in post-mortem autism cerebral cortex. Conclusions We found that genes related to mitochondrial function were differentially expressed in autism cerebral cortex and correlated with genes related to synaptic transmission. Our principal findings replicate across all datasets investigated. Further, these findings may potentially replicate in other diseases, such as in schizophrenia.
Published: 2018
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10. NMDA antagonists recreate signal-to-noise ratio and timing perturbations present in schizophrenia

Author: John A. Saunders, Michael J. Gandal, and Steve J. Siegel
Subjects: Schizophrenia, Electrophysiology, Endophenotype, Animal models, NMDA antagonist, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571
Abstract: Rationale: There is increasing evidence that functional deficits in schizophrenia may be driven by a reduction in the signal-to-noise ratio (SNR) and consistent timing of neural signals. This study examined the extent to which exposure to the NMDA receptor antagonists ketamine and MK801, frequently used pharmacological models of schizophrenia, recreate deficits in electrophysiological markers of disturbed brain circuits that are thought to underlie the illness. Furthermore, this study characterizes the specificity of these differences across the frequency spectrum so as to help identify the nature of selective circuit abnormalities that mediate each oscillatory response as relevant to schizophrenia. Design: Mouse EEG was recorded during exposure to repeated auditory stimuli after injection of either vehicle or drug. The dose–response relationship for each electrophysiological measure was determined for ketamine and MK-801. Time-frequency analyses were performed to assess baseline, total, and evoked power and intertrial coherence (ITC) at low (5–10 Hz) and high (35–80 Hz)-frequencies. Results: High frequency evoked and total power was decreased by MK-801 and ketamine in a dose-dependent fashion. High frequency baseline power was increased by MK-801 and ketamine in a dose-dependent fashion. Similar to evoked power, high frequency inter-trial coherence was dose-dependently decreased by both drugs. Low frequency ITC was only decreased by ketamine. Conclusions: Both ketamine and MK-801 cause alterations in high-frequency baseline (noise), total (signal), and evoked (signal) power resulting in a loss of high frequency SNR that is thought to primarily reflect local circuit activity. These changes indicate an inappropriate increase in baseline activity, which can also be interpreted as non-task related activity. Ketamine induced a loss of intertrial coherence at low frequencies, indicating a loss of consistency in low-frequency circuit mechanisms. As a proportion of baseline power, both drugs had a relative shift from low to high frequencies, reflecting a change in the balance of brain activity from coordination of global regions to a pattern of discoordinated, autonomous local activity. These changes are consistent with a pattern of fragmented regional brain activity seen in schizophrenia.
Published: 2012
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11. MeCP2+/− mouse model of RTT reproduces auditory phenotypes associated with Rett syndrome and replicate select EEG endophenotypes of autism spectrum disorder

Author: Wenlin Liao, Michael J. Gandal, Richard S. Ehrlichman, Steven J. Siegel, and Greg C. Carlson
Subjects: Sensory evoked potential, SEP, Auditory evoked potential, AEP, ERP, MeCP2, Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571
Abstract: Impairments in cortical sensory processing have been demonstrated in Rett syndrome (RTT) and Autism Spectrum Disorders (ASD) and are thought to contribute to high-order phenotypic deficits. However, underlying pathophysiological mechanisms for these abnormalities are unknown. This study investigated auditory sensory processing in a mouse model of RTT with a heterozygous loss of MeCP2 function. Cortical abnormalities in a number of neuropsychiatric disorders, including ASD are reflected in auditory evoked potentials and fields measured by EEG and MEG. One of these abnormalities, increased latency of cortically sourced components, is associated with language and developmental delay in autism. Additionally, gamma-band abnormalities have recently been identified as an endophenotype of idiopathic autism. Both of these cortical abnormalities are potential clinical endpoints for assessing treatment. While ascribing similar mechanisms of idiopathic ASD to Rett syndrome (RTT) has been controversial, we sought to determine if mouse models of RTT replicate these intermediate phenotypes. Mice heterozygous for the null mutations of the gene MeCP2, were implanted for EEG. In response to auditory stimulation, these mice recapitulated specific latency differences as well as select gamma and beta band abnormalities associated with ASD. MeCP2 disruption is the predominant cause of RTT, and reductions in MeCP2 expression predominate in ASD. This work further suggests a common cortical pathophysiology for RTT and ASD, and indicates that the MeCP2+/− model may be useful for preclinical development targeting specific cortical processing abnormalities in RTT with potential relevance to ASD.
Published: 2012
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12. No Increased Detection of Nucleic Acids of CNS-related Viruses in the Brains of Patients with Schizophrenia, Bipolar Disorder, and Autism Spectrum Disorder

Author: Shishi Min, Michael J Gandal, Richard F Kopp, Chunyu Liu, and Chao Chen
Subjects: Psychiatry and Mental health
Abstract: Background and Hypothesis Viral infections are increasingly recognized in the etiology of psychiatric disorders based on epidemiological and serological studies. Few studies have analyzed viruses directly within the brain and no comprehensive investigation of viral infection within diseased brains has been completed. This study aims to determine whether viral infection in brain tissues is a risk factor for 3 major psychiatric disorders, including schizophrenia, bipolar disorder, and autism spectrum disorder. Study Design This study directly evaluated the presence of viral DNA or RNA in 1569 brains of patients and controls using whole-genome sequencing and RNA sequencing data with 4 independent cohorts. The PathSeq tool was used to identify known human viruses in the genome and transcriptome of patients and controls. Study Results A variety of DNA and RNA viruses related to the central nervous system were detected in the brains of patients with major psychiatric disorders, including viruses belonging to Herpesviridae, Polyomaviridae, Retroviridae, Flaviviridae, Parvoviridae, and Adenoviridae. However, no consistent significant differences were found between patients and controls in terms of types and amount of virus detected at both DNA and RNA levels. Conclusions The findings of this study do not suggest an association between viral infection in postmortem brains and major psychiatric disorders.
Published: 2023
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13. White matter microstructure shows sex differences in late childhood: Evidence from 6797 children

Author: Katherine E. Lawrence, Zvart Abaryan, Emily Laltoo, Leanna M. Hernandez, Michael J. Gandal, James T. McCracken, and Paul M. Thompson
Subjects: Neurology, Radiological and Ultrasound Technology, Radiology, Nuclear Medicine and imaging, Neurology (clinical), Anatomy
Abstract: Sex differences in white matter microstructure have been robustly demonstrated in the adult brain using both conventional and advanced diffusion-weighted magnetic resonance imaging approaches. However, sex differences in white matter microstructure prior to adulthood remain poorly understood; previous developmental work focused on conventional microstructure metrics and yielded mixed results. Here, we rigorously characterized sex differences in white matter microstructure among over 6000 children from the Adolescent Brain Cognitive Development study who were between 9 and 10 years old. Microstructure was quantified using both the conventional model-diffusion tensor imaging (DTI)-and an advanced model, restriction spectrum imaging (RSI). DTI metrics included fractional anisotropy (FA) and mean, axial, and radial diffusivity (MD, AD, RD). RSI metrics included normalized isotropic, directional, and total intracellular diffusion (N0, ND, NT). We found significant and replicable sex differences in DTI or RSI microstructure metrics in every white matter region examined across the brain. Sex differences in FA were regionally specific. Across white matter regions, boys exhibited greater MD, AD, and RD than girls, on average. Girls displayed increased N0, ND, and NT compared to boys, on average, suggesting greater cell and neurite density in girls. Together, these robust and replicable findings provide an important foundation for understanding sex differences in health and disease.
Published: 2022
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14. Human Astrocytes Exhibit Tumor Microenvironment-, Age-, and Sex-Related Transcriptomic Signatures

Author: Mitchell C. Krawczyk, Jillian R. Haney, Lin Pan, Christine Caneda, Rana R. Khankan, Samuel D. Reyes, Julia W. Chang, Marco Morselli, Harry V. Vinters, Anthony C. Wang, Inma Cobos, Michael J. Gandal, Marvin Bergsneider, Won Kim, Linda M. Liau, William Yong, Ali Jalali, Benjamin Deneen, Gerald A. Grant, Gary W. Mathern, Aria Fallah, and Ye Zhang
Subjects: Male, Aging, 1.1 Normal biological development and functioning, Medical and Health Sciences, Mice, astrocyte, Underpinning research, Tumor Microenvironment, Genetics, Animals, Humans, sex, 2.1 Biological and endogenous factors, human, Aetiology, Research Articles, Neurology & Neurosurgery, maturation, General Neuroscience, Psychology and Cognitive Sciences, glioblastoma, Neurosciences, Brain Disorders, Astrocytes, Synapses, Neurological, Female, Transcriptome
Abstract: Astrocytes are critical for the development and function of synapses. There are notable species differences between human astrocytes and commonly used animal models. Yet, it is unclear whether astrocytic genes involved in synaptic function are stable or exhibit dynamic changes associated with disease states and age in humans, which is a barrier in understanding human astrocyte biology and its potential involvement in neurologic diseases. To better understand the properties of human astrocytes, we acutely purified astrocytes from the cerebral cortices of over 40 humans across various ages, sexes, and disease states. We performed RNA sequencing to generate transcriptomic profiles of these astrocytes and identified genes associated with these biological variables. We found that human astrocytes in tumor-surrounding regions downregulate genes involved in synaptic function and sensing of signals in the microenvironment, suggesting involvement of peritumor astrocytes in tumor-associated neural circuit dysfunction. In aging, we also found downregulation of synaptic regulators and upregulation of markers of cytokine signaling, while in maturation we identified changes in ionic transport with implications for calcium signaling. In addition, we identified subtle sexual dimorphism in human cortical astrocytes, which has implications for observed sex differences across many neurologic disorders. Overall, genes involved in synaptic function exhibit dynamic changes in the peritumor microenvironment and aging. These data provide powerful new insights into human astrocyte biology in several biologically relevant states that will aid in generating novel testable hypotheses about homeostatic and reactive astrocytes in humans.SIGNIFICANCE STATEMENTAstrocytes are an abundant class of cells playing integral roles at synapses. Astrocyte dysfunction is implicated in a variety of human neurologic diseases. Yet our knowledge of astrocytes is largely based on mouse studies. Direct knowledge of human astrocyte biology remains limited. Here, we present transcriptomic profiles of human cortical astrocytes, and we identified molecular differences associated with age, sex, and disease state. We found that peritumor and aging astrocytes downregulate genes involved in astrocyte–synapse interactions. These data provide necessary insight into human astrocyte biology that will improve our understanding of human disease.
Published: 2022
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15. Multivariate variance components analysis uncovers genetic architecture of brain isoform expression and novel psychiatric disease mechanisms

Author: Minsoo Kim, Daniel D. Vo, Connor T. Jops, Cindy Wen, Ashok Patowary, Arjun Bhattacharya, Chloe X. Yap, Hua Zhou, and Michael J. Gandal
Abstract: Multivariate variance components linear mixed models are fundamental statistical models in quantitative genetics, widely used to quantify SNP-based heritability (h2SNP) and genetic correlation (rg) across complex traits. However, maximum likelihood estimation of multivariate variance components models remains numerically challenging when the number of traits and variance components are both greater than two. To address this critical gap, here we introduce a novel statistical method for fitting multivariate variance components models. This method improves on existing methods by allowing for arbitrary number of traits and/or variance components. We illustrate the utility of our method by characterizing for the first time the genetic architecture of isoform expression in the human brain, modeling up to 23 isoforms jointly across ∼900 individuals within PsychENCODE. We find a significant proportion of isoforms to be under genetic control (17,721 of 93,293 isoforms) with substantial shared genetic effects among local (orcis-) relative to distal (ortrans-) genetic variants (medianrg,cisandrg,trans= 0.31 and 0.06). Importantly, we find that 11.6% of brain-expressed genes (2,900 genes) are heritable only at the isoform-level. Integrating these isoform-specific genetic signals with psychiatric GWAS signals uncovers previously hidden psychiatric disease mechanisms. Specifically, we highlight reduced expression of a specificXRN2isoform as the underlying driver of the strongest GWAS signal for autism spectrum disorder. Overall, our method for fitting multivariate variance components models is flexible, widely applicable, and is implemented in the Julia programming language and available online.
Published: 2022
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16. TGFβ superfamily signaling regulates the state of human stem cell pluripotency and capacity to create well-structured telencephalic organoids

Author: Momoko Watanabe, Jessie E. Buth, Jillian R. Haney, Neda Vishlaghi, Felix Turcios, Lubayna S. Elahi, Wen Gu, Caroline A. Pearson, Arinnae Kurdian, Natella V. Baliaouri, Amanda J. Collier, Osvaldo A. Miranda, Natassia Dunn, Di Chen, Shan Sabri, Luis de la Torre-Ubieta, Amander T. Clark, Kathrin Plath, Heather R. Christofk, Harley I. Kornblum, Michael J. Gandal, and Bennett G. Novitch
Subjects: Telencephalon, Pluripotent Stem Cells, hippocampus, 1.1 Normal biological development and functioning, Clinical Sciences, Regenerative Medicine, Biochemistry, brain organoid, neural development, neural stem cell, Transforming Growth Factor beta, Underpinning research, Genetics, Humans, pluripotent stem cell, Stem Cell Research - Embryonic - Human, choroid plexus, Neurosciences, stem cell heterogeneity, Cell Differentiation, Cell Biology, differentiation, pluripotency, Stem Cell Research, embryonic stem cell, Organoids, neurogenesis, cerebral cortex, Biochemistry and Cell Biology, Developmental Biology, ganglionic eminence
Abstract: Telencephalic organoids generated from human pluripotent stem cells (hPSCs) are a promising system for studying the distinct features of the developing human brain and the underlying causes of many neurological disorders. While organoid technology is steadily advancing, many challenges remain, including potential batch-to-batch and cell-line-to-cell-line variability, and structural inconsistency. Here, we demonstrate that a major contributor to cortical organoid quality is the way hPSCs are maintained prior to differentiation. Optimal results were achieved using particular fibroblast-feeder-supported hPSCs rather than feeder-independent cells, differences that were reflected in their transcriptomic states at the outset. Feeder-supported hPSCs displayed activation of diverse transforming growth factor β (TGFβ) superfamily signaling pathways and increased expression of genes connected to naive pluripotency. We further identified combinations of TGFβ-related growth factors that are necessary and together sufficient to impart broad telencephalic organoid competency to feeder-free hPSCs and enhance the formation of well-structured brain tissues suitable for disease modeling.
Published: 2022

17. The genetics of cortical organisation and development: A study of 2,347 neuroimaging phenotypes

Author: Varun Warrier, Eva-Maria Stauffer, Qin Qin Huang, Emilie M. Wigdor, Eric A.W. Slob, Jakob Seidlitz, Lisa Ronan, Sofie Valk, Travis T. Mallard, Andrew D. Grotzinger, Rafael Romero-Garcia, Simon Baron-Cohen, Daniel H. Geschwind, Madeline Lancaster, Graham K. Murray, Michael J. Gandal, Aaron Alexander-Bloch, Hyejung Won, Hilary C. Martin, Edward T. Bullmore, Richard A.I. Bethlehem, and Apollo - University of Cambridge Repository
Abstract: Our understanding of the genetic architecture of the human cerebral cortex is limited both in terms of the diversity of brain structural phenotypes and the anatomical granularity of their associations with genetic variants. Here, we conducted genome-wide association meta-analysis of 13 structural and diffusion magnetic resonance imaging derived cortical phenotypes, measured globally and at 180 bilaterally averaged regions in 36,843 individuals from the UK Biobank and the ABCD cohorts. These phenotypes include cortical thickness, surface area, grey matter volume, and measures of folding, neurite density, and water diffusion. We identified 4,349 experiment-wide significant loci associated with global and regional phenotypes. Multiple lines of analyses identified four genetic latent structures and causal relationships between surface area and some measures of cortical folding. These latent structures partly relate to different underlying gene expression trajectories during development and are enriched for different cell types. We also identified differential enrichment for neurodevelopmental and constrained genes and demonstrate that common genetic variants associated with surface area and volume specifically are associated with cephalic disorders. Finally, we identified complex inter-phenotype and inter-regional genetic relationships among the 13 phenotypes which reflect developmental differences among them. These analyses help refine the role of common genetic variants in human cortical development and organisation.One sentence summaryGWAS of 2,347 neuroimaging phenotypes shed light on the global and regional genetic organisation of the cortex, underlying cellular and developmental processes, and links to neurodevelopmental and cephalic disorders.
Published: 2022

18. Isoform-level transcriptome-wide association uncovers extensive novel genetic risk mechanisms for neuropsychiatric disorders in the human brain

Author: Arjun Bhattacharya, Connor Jops, Minsoo Kim, Cindy Wen, Daniel D. Vo, Jonatan L. Hervoso, Bogdan Pasaniuc, and Michael J. Gandal
Abstract: Integrative methods, like colocalization and transcriptome-wide association studies (TWAS), identify transcriptomic mechanisms at only a small fraction of trait-associated genetic loci from genome-wide association studies (GWAS). Here, we show that a reliance on reference functional genomics panels of only total gene expression greatly contributes to this reduced discovery. This is particularly relevant for neuropsychiatric traits, as the brain expresses extensive, complex, and unique alternative splicing patterns giving rise to multiple genetically-regulated transcript-isoforms per gene.We introduce isoTWAS, a scalable, multivariate framework to integrate genetics, isoform-level expression, and phenotypic associations in a step-wise testing framework. Multivariate predictive models were trained using isoform-level expression across tissues from the Genotype-Tissue Expression Project and in the developing and adult human brain from PsychENCODE. Across five neuropsychiatric traits, isoTWAS dramatically increased discovery of trait associations within GWAS loci, capturing 92 unique loci compared with 27 using gene-level TWAS. These power gains reflected a ∼2-fold increase in the number of testable genes, an ∼15-35% increase in total gene expression prediction accuracy, and the ability to jointly capture expression and splicing mechanisms. Results from extensive simulations showed no increase in false discovery rate and reinforce isoTWAS’s advantages in prediction and trait mapping power over TWAS, especially when genetic effects on expression vary across isoforms of the same gene. We illustrate multiple biologically-relevant isoTWAS-identified trait associations undetectable by gene-level methods, including isoforms of AKT3, GIGYF2, and KMT5A with schizophrenia risk.The isoTWAS framework addresses an unmet need to consider the transcriptome on the transcript-isoform level to maximize discovery of trait associations, especially for brain-relevant traits.
Published: 2022
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19. GeneticsMakie.jl: A versatile and scalable toolkit for visualizing locus-level genetic and genomic data

Author: Minsoo Kim, Daniel D Vo, Michi E Kumagai, Connor T Jops, and Michael J Gandal
Subjects: Statistics and Probability, Computational Mathematics, Computational Theory and Mathematics, Molecular Biology, Biochemistry, Computer Science Applications
Abstract: Summary With the continued deluge of results from genome-wide association and functional genomic studies, it has become increasingly imperative to quickly combine and visualize different layers of genetic and genomic data within a given locus to facilitate exploratory and integrative data analyses. While several tools have been developed to visualize locus-level genetic results, the limited speed, scalability and flexibility of current approaches remain a significant bottleneck. Here, we present a Julia package for high-performance genetics and genomics-related data visualization that enables fast, simultaneous plotting of hundreds of association results along with multiple relevant genomic annotations. Leveraging the powerful plotting and layout utilities from Makie.jl facilitates the customization and extensibility of every component of a plot, enabling generation of publication-ready figures. Availability and implementation The GeneticsMakie.jl package is open source and distributed under the MIT license via GitHub (https://github.com/mmkim1210/GeneticsMakie.jl). The GitHub repository contains installation instructions as well as examples and documentation for built-in functions. Supplementary information Supplementary data are available at Bioinformatics online.
Published: 2022
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20. Comment on: What genes are differentially expressed in individuals with schizophrenia? A systematic review

Author: Gabriel E. Hoffman, Andrew E. Jaffe, Michael J. Gandal, Leonardo Collado-Torres, Solveig K. Sieberts, Bernie Devlin, Daniel H. Geschwind, Daniel R. Weinberger, and Panos Roussos
Subjects: Cellular and Molecular Neuroscience, Psychiatry and Mental health, Molecular Biology, Article
Published: 2022

21. Integrative genomics identifies a convergent molecular subtype that links epigenomic with transcriptomic differences in autism

Author: Chloe C. Y. Wong, Gokul Ramaswami, Jillian R. Haney, Michael J. Gandal, Jerry C. Wang, Daniel H. Geschwind, Jonathan Mill, Shyam Prabhakar, Wenjie Sun, and Hyejung Won
Subjects: 0301 basic medicine, Epigenomics, Autism Spectrum Disorder, Autism, Messenger, General Physics and Astronomy, Gene regulatory networks, Histones, Transcriptome, 0302 clinical medicine, Neurodevelopmental disorder, 2.1 Biological and endogenous factors, Gene Regulatory Networks, Aetiology, lcsh:Science, Pediatric, 0303 health sciences, Multidisciplinary, Brain, Genomics, Autism spectrum disorders, Mental Health, DNA methylation, Epigenetics, Biotechnology, Intellectual and Developmental Disabilities (IDD), 1.1 Normal biological development and functioning, Science, Computational biology, Biology, behavioral disciplines and activities, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, Underpinning research, mental disorders, Genetics, medicine, Humans, RNA, Messenger, Gene, 030304 developmental biology, Genetic heterogeneity, Human Genome, Neurosciences, General Chemistry, Epigenome, DNA Methylation, medicine.disease, Brain Disorders, MicroRNAs, 030104 developmental biology, Gene Expression Regulation, Expression quantitative trait loci, RNA, lcsh:Q, Gene expression, 030217 neurology & neurosurgery
Abstract: Autism spectrum disorder (ASD) is a phenotypically and genetically heterogeneous neurodevelopmental disorder. Despite this heterogeneity, previous studies have shown patterns of molecular convergence in post-mortem brain tissue from autistic subjects. Here, we integrate genome-wide measures of mRNA expression, miRNA expression, DNA methylation, and histone acetylation from ASD and control brains to identify a convergent molecular subtype of ASD with shared dysregulation across both the epigenome and transcriptome. Focusing on this convergent subtype, we substantially expand the repertoire of differentially expressed genes in ASD and identify a component of upregulated immune processes that are associated with hypomethylation. We utilize eQTL and chromosome conformation datasets to link differentially acetylated regions with their cognate genes and identify an enrichment of ASD genetic risk variants in hyperacetylated noncoding regulatory regions linked to neuronal genes. These findings help elucidate how diverse genetic risk factors converge onto specific molecular processes in ASD., Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by impaired social interactions with repetitive and restrictive behaviours. Here the authors integrate mRNA expression, miRNA expression, DNA methylation, and histone acetylation datasets from a collection of post mortem brain tissues and identify a convergent molecular subtype of ASD.
Published: 2020
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22. Distal gene regulation mediated by non-coding RNAs contributes to germline risk for breast and prostate cancer

Author: Nolan Cole, Paige Lee, Tommer Schwarz, Pan Zhang, Matthew L. Freedman, Alexander Gusev, Sara Lindström, Michael J. Gandal, Bogdan Pasaniuc, and Arjun Bhattacharya
Abstract: Genome-wide association studies (GWAS) have identified numerous genetic loci associated with breast and prostate cancer risk, suggesting that germline genetic dysregulation influences tumorigenesis. However, the biological function underlying many genetic associations is not well-understood. Previous efforts to annotate loci focused on protein-coding genes (pcGenes) largely ignore non-coding RNAs (ncRNAs) which account for most transcriptional output in human cells and can regulate transcription of both pcGenes and other ncRNAs. Though the biological roles of most ncRNAs are not well-defined, many ncRNAs are involved in cancer development. Here, we explore one regulatory hypothesis: ncRNAs as trans-acting mediators of gene expression regulation in non-cancerous and tumor breast and prostate tissue. Using germline genetics as a causal anchor, we categorize distal (>1 Megabase) expression quantitative trait loci (eQTLs) of pcGenes significantly mediated by local-eQTLs of ncRNAs (within 1 Megabase). We find over 300 mediating ncRNAs and show the linked pcGenes are enriched for immunoregulatory and cellular organization pathways. By integrating eQTL and cancer GWAS results through colocalization and genetically-regulated expression analyses, we detect overlapping signals in nine known breast cancer loci and one known prostate cancer locus, and multiple novel genetic associations. Our results suggest a strong transcriptional impact of ncRNAs in breast and prostate tissue with implications for cancer etiology. More broadly, our framework can be systematically applied to functional genomic features to characterize genetic variants distally regulating transcription through trans-mechanisms.SIGNIFICANCEThis study identifies non-coding RNAs that potentially regulate gene expression in trans-pathways and overlap with genetic signals for breast and prostate cancer susceptibility, with implications for interpretation of cancer genome-wide association studies.
Published: 2022
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23. Dissecting the Shared Genetic Architecture of Suicide Attempt, Psychiatric Disorders, and Known Risk Factors

Author: Niamh Mullins, JooEun Kang, Adrian I. Campos, Jonathan R.I. Coleman, Alexis C. Edwards, Hanga Galfalvy, Daniel F. Levey, Adriana Lori, Andrey Shabalin, Anna Starnawska, Mei-Hsin Su, Hunna J. Watson, Mark Adams, Swapnil Awasthi, Michael Gandal, Jonathan D. Hafferty, Akitoyo Hishimoto, Minsoo Kim, Satoshi Okazaki, Ikuo Otsuka, Stephan Ripke, Erin B. Ware, Andrew W. Bergen, Wade H. Berrettini, Martin Bohus, Harry Brandt, Xiao Chang, Wei J. Chen, Hsi-Chung Chen, Steven Crawford, Scott Crow, Emily DiBlasi, Philibert Duriez, Fernando Fernández-Aranda, Manfred M. Fichter, Steven Gallinger, Stephen J. Glatt, Philip Gorwood, Yiran Guo, Hakon Hakonarson, Katherine A. Halmi, Hai-Gwo Hwu, Sonia Jain, Stéphane Jamain, Susana Jiménez-Murcia, Craig Johnson, Allan S. Kaplan, Walter H. Kaye, Pamela K. Keel, James L. Kennedy, Kelly L. Klump, Dong Li, Shih-Cheng Liao, Klaus Lieb, Lisa Lilenfeld, Chih-Min Liu, Pierre J. Magistretti, Christian R. Marshall, James E. Mitchell, Eric T. Monson, Richard M. Myers, Dalila Pinto, Abigail Powers, Nicolas Ramoz, Stefan Roepke, Vsevolod Rozanov, Stephen W. Scherer, Christian Schmahl, Marcus Sokolowski, Michael Strober, Laura M. Thornton, Janet Treasure, Ming T. Tsuang, Stephanie H. Witt, D. Blake Woodside, Zeynep Yilmaz, Lea Zillich, Rolf Adolfsson, Ingrid Agartz, Tracy M. Air, Martin Alda, Lars Alfredsson, Ole A. Andreassen, Adebayo Anjorin, Vivek Appadurai, María Soler Artigas, Sandra Van der Auwera, M. Helena Azevedo, Nicholas Bass, Claiton H.D. Bau, Bernhard T. Baune, Frank Bellivier, Klaus Berger, Joanna M. Biernacka, Tim B. Bigdeli, Elisabeth B. Binder, Michael Boehnke, Marco P. Boks, Rosa Bosch, David L. Braff, Richard Bryant, Monika Budde, Enda M. Byrne, Wiepke Cahn, Miguel Casas, Enrique Castelao, Jorge A. Cervilla, Boris Chaumette, Sven Cichon, Aiden Corvin, Nicholas Craddock, David Craig, Franziska Degenhardt, Srdjan Djurovic, Howard J. Edenberg, Ayman H. Fanous, Jerome C. Foo, Andreas J. Forstner, Mark Frye, Janice M. Fullerton, Justine M. Gatt, Pablo V. Gejman, Ina Giegling, Hans J. Grabe, Melissa J. Green, Eugenio H. Grevet, Maria Grigoroiu-Serbanescu, Blanca Gutierrez, Jose Guzman-Parra, Steven P. Hamilton, Marian L. Hamshere, Annette Hartmann, Joanna Hauser, Stefanie Heilmann-Heimbach, Per Hoffmann, Marcus Ising, Ian Jones, Lisa A. Jones, Lina Jonsson, René S. Kahn, John R. Kelsoe, Kenneth S. Kendler, Stefan Kloiber, Karestan C. Koenen, Manolis Kogevinas, Bettina Konte, Marie-Odile Krebs, Mikael Landén, Jacob Lawrence, Marion Leboyer, Phil H. Lee, Douglas F. Levinson, Calwing Liao, Jolanta Lissowska, Susanne Lucae, Fermin Mayoral, Susan L. McElroy, Patrick McGrath, Peter McGuffin, Andrew McQuillin, Sarah E. Medland, Divya Mehta, Ingrid Melle, Yuri Milaneschi, Philip B. Mitchell, Esther Molina, Gunnar Morken, Preben Bo Mortensen, Bertram Müller-Myhsok, Caroline Nievergelt, Vishwajit Nimgaonkar, Markus M. Nöthen, Michael C. O’Donovan, Roel A. Ophoff, Michael J. Owen, Carlos Pato, Michele T. Pato, Brenda W.J.H. Penninx, Jonathan Pimm, Giorgio Pistis, James B. Potash, Robert A. Power, Martin Preisig, Digby Quested, Josep Antoni Ramos-Quiroga, Andreas Reif, Marta Ribasés, Vanesa Richarte, Marcella Rietschel, Margarita Rivera, Andrea Roberts, Gloria Roberts, Guy A. Rouleau, Diego L. Rovaris, Dan Rujescu, Cristina Sánchez-Mora, Alan R. Sanders, Peter R. Schofield, Thomas G. Schulze, Laura J. Scott, Alessandro Serretti, Jianxin Shi, Stanley I. Shyn, Lea Sirignano, Pamela Sklar, Olav B. Smeland, Jordan W. Smoller, Edmund J.S. Sonuga-Barke, Gianfranco Spalletta, John S. Strauss, Beata Świątkowska, Maciej Trzaskowski, Gustavo Turecki, Laura Vilar-Ribó, John B. Vincent, Henry Völzke, James T.R. Walters, Cynthia Shannon Weickert, Thomas W. Weickert, Myrna M. Weissman, Leanne M. Williams, Naomi R. Wray, Clement C. Zai, Allison E. Ashley-Koch, Jean C. Beckham, Elizabeth R. Hauser, Michael A. Hauser, Nathan A. Kimbrel, Jennifer H. Lindquist, Benjamin McMahon, David W. Oslin, Xuejun Qin, Esben Agerbo, Anders D. Børglum, Gerome Breen, Annette Erlangsen, Tõnu Esko, Joel Gelernter, David M. Hougaard, Ronald C. Kessler, Henry R. Kranzler, Qingqin S. Li, Nicholas G. Martin, Andrew M. McIntosh, Ole Mors, Merete Nordentoft, Catherine M. Olsen, David Porteous, Robert J. Ursano, Danuta Wasserman, Thomas Werge, David C. Whiteman, Cynthia M. Bulik, Hilary Coon, Ditte Demontis, Anna R. Docherty, Po-Hsiu Kuo, Cathryn M. Lewis, J. John Mann, Miguel E. Rentería, Daniel J. Smith, Eli A. Stahl, Murray B. Stein, Fabian Streit, Virginia Willour, Douglas M. Ruderfer, Manuel Mattheisen, Abdel Abdellaoui, Mark J. Adams, Till F.M. Andlauer, Silviu-Alin Bacanu, Marie Bækvad-Hansen, Aartjan T.F. Beekman, Julien Bryois, Henriette N. Buttenschøn, Jonas Bybjerg-Grauholm, Na Cai, Jane Hvarregaard Christensen, Toni-Kim Clarke, Lucía Colodro-Conde, Baptiste Couvy-Duchesne, Nick Craddock, Gregory E. Crawford, Gail Davies, Eske M. Derks, Nese Direk, Conor V. Dolan, Erin C. Dunn, Thalia C. Eley, Valentina Escott-Price, Farnush Farhadi Hassan Kiadeh, Hilary K. Finucane, Josef Frank, Héléna A. Gaspar, Michael Gill, Fernando S. Goes, Scott D. Gordon, Shantel Marie Weinsheimer, Jürgen Wellmann, Gonneke Willemsen, Yang Wu, Hualin S. Xi, Jian Yang, Futao Zhang, Volker Arolt, Dorret I. Boomsma, Udo Dannlowski, E.J.C. de Geus, J. Raymond Depaulo, Enrico Domenici, Katharina Domschke, Jakob Grove, Lynsey S. Hall, Christine Søholm Hansen, Thomas F. Hansen, Stefan Herms, Ian B. Hickie, Georg Homuth, Carsten Horn, Jouke-Jan Hottenga, David M. Howard, Rick Jansen, Eric Jorgenson, James A. Knowles, Isaac S. Kohane, Julia Kraft, Warren W. Kretzschmar, Zoltán Kutalik, Yihan Li, Penelope A. Lind, Donald J. MacIntyre, Dean F. MacKinnon, Robert M. Maier, Wolfgang Maier, Jonathan Marchini, Hamdi Mbarek, Christel M. Middeldorp, Evelin Mihailov, Lili Milani, Francis M. Mondimore, Grant W. Montgomery, Sara Mostafavi, Matthias Nauck, Bernard Ng, Michel G. Nivard, Dale R. Nyholt, Paul F. O’Reilly, Hogni Oskarsson, Caroline Hayward, Andrew C. Heath, Glyn Lewis, Pamela A.F. Madden, Patrik K. Magnusson, Andres Metspalu, Sara A. Paciga, Nancy L. Pedersen, Jodie N. Painter, Carsten Bøcker Pedersen, Marianne Giørtz Pedersen, Roseann E. Peterson, Wouter J. Peyrot, Danielle Posthuma, Jorge A. Quiroz, Per Qvist, John P. Rice, Brien P. Riley, Saira Saeed Mirza, Robert Schoevers, Eva C. Schulte, Ling Shen, Engilbert Sigurdsson, Grant C.B. Sinnamon, Johannes H. Smit, Hreinn Stefansson, Stacy Steinberg, Jana Strohmaier, Katherine E. Tansey, Henning Teismann, Alexander Teumer, Wesley Thompson, Pippa A. Thomson, Thorgeir E. Thorgeirsson, Matthew Traylor, Jens Treutlein, Vassily Trubetskoy, André G. Uitterlinden, Daniel Umbricht, Albert M. van Hemert, Alexander Viktorin, Peter M. Visscher, Yunpeng Wang, Bradley T. Webb, Roy H. Perlis, David J. Porteous, Catherine Schaefer, Kari Stefansson, Henning Tiemeier, Rudolf Uher, Patrick F. Sullivan, Kevin S. O’Connell, Brandon Coombes, Zhen Qiao, Thomas D. Als, Sigrid Børte, Alexander W. Charney, Ole Kristian Drange, Michael J. Gandal, Saskia P. Hagenaars, Masashi Ikeda, Nolan Kamitaki, Kristi Krebs, Georgia Panagiotaropoulou, Brian M. Schilder, Laura G. Sloofman, Bendik S. Winsvold, Hong-Hee Won, Liliya Abramova, Kristina Adorjan, Mariam Al Eissa, Diego Albani, Ney Alliey-Rodriguez, Verneri Antilla, Anastasia Antoniou, Ji Hyun Baek, Michael Bauer, Eva C. Beins, Sarah E. Bergen, Armin Birner, Erlend Bøen, Murielle Brum, Ben M. Brumpton, Nathalie Brunkhorst-Kanaan, William Byerley, Murray Cairns, Miquel Casas, Pablo Cervantes, Cristiana Cruceanu, Alfredo Cuellar-Barboza, Julie Cunningham, David Curtis, Piotr M. Czerski, Anders M. Dale, Nina Dalkner, Friederike S. David, Amanda L. Dobbyn, Athanassios Douzenis, Torbjørn Elvsåshagen, I. Nicol Ferrier, Alessia Fiorentino, Tatiana M. Foroud, Liz Forty, Oleksandr Frei, Nelson B. Freimer, Louise Frisén, Katrin Gade, Julie Garnham, Ian R. Gizer, Katherine Gordon-Smith, Tiffany A. Greenwood, José Guzman-Parra, Kyooseob Ha, Magnus Haraldsson, Martin Hautzinger, Urs Heilbronner, Dennis Hellgren, Peter A. Holmans, Laura Huckins, Jessica S. Johnson, Janos L. Kalman, Yoichiro Kamatani, Sarah Kittel-Schneider, Maria Koromina, Thorsten M. Kranz, Michiaki Kubo, Ralph Kupka, Steven A. Kushner, Catharina Lavebratt, Markus Leber, Heon-Jeong Lee, Shawn E. Levy, Catrin Lewis, Martin Lundberg, Sigurdur H. Magnusson, Adam Maihofer, Dolores Malaspina, Eirini Maratou, Lina Martinsson, Nathaniel W. McGregor, James D. McKay, Helena Medeiros, Vincent Millischer, Jennifer L. Moran, Derek W. Morris, Thomas W. Mühleisen, Niamh O’Brien, Claire O’Donovan, Loes M. Olde Loohuis, Lilijana Oruc, Sergi Papiol, Antonio F. Pardiñas, Amy Perry, Andrea Pfennig, Evgenia Porichi, Towfique Raj, Mark H. Rapaport, J. Raymond DePaulo, Eline J. Regeer, Fabio Rivas, Julian Roth, Panos Roussos, Fanny Senner, Sally Sharp, Paul D. Shilling, Claire Slaney, Janet L. Sobell, Maria Soler Artigas, Anne T. Spijker, Dan J. Stein, Chikashi Terao, Claudio Toma, Paul Tooney, Evangelia-Eirini Tsermpini, Marquis P. Vawter, Helmut Vedder, Simon Xi, Wei Xu, Jessica Mei Kay Yang, Allan H. Young, Hannah Young, Peter P. Zandi, Hang Zhou, null HUNT All-In Psychiatry, Gulja Babadjanova, Lena Backlund, Susanne Bengesser, Douglas H.R. Blackwood, Vaughan J. Carr, Stanley Catts, Dimitris Dikeos, Bruno Etain, Panagiotis Ferentinos, Micha Gawlik, Elliot S. Gershon, Frans Henskens, Jan Hillert, Kyung Sue Hong, Christina M. Hultman, Kristian Hveem, Nakao Iwata, Assen V. Jablensky, George Kirov, Christine Lochner, Carmel Loughland, Carol A. Mathews, Francis J. McMahon, Patricia Michie, Bryan Mowry, Benjamin M. Neale, Caroline M. Nievergelt, Ketil J. Oedegaard, Tomas Olsson, Chris Pantelis, George P. Patrinos, Eva Z. Reininghaus, Takeo Saito, Ulrich Schall, Martin Schalling, Rodney J. Scott, Eystein Stordal, Arne E. Vaaler, Eduard Vieta, Irwin D. Waldman, John-Anker Zwart, John I. Nurnberger, Arianna Di Florio, Roger A.H. Adan, Tetsuya Ando, Harald Aschauer, Jessica H. Baker, Vladimir Bencko, Andreas Birgegård, Joseph M. Boden, Ilka Boehm, Claudette Boni, Vesna Boraska Perica, Katharina Buehren, Roland Burghardt, Laura Carlberg, Matteo Cassina, Maurizio Clementi, Roger D. Cone, Philippe Courtet, James J. Crowley, Unna N. Danner, Oliver S.P. Davis, Martina de Zwaan, George Dedoussis, Daniela Degortes, Janiece E. DeSocio, Danielle M. Dick, Christian Dina, Monika Dmitrzak-Weglarz, Elisa Docampo Martinez, Laramie E. Duncan, Karin Egberts, Morten Mattingsdal, Sara McDevitt, Ingrid Meulenbelt, Nadia Micali, James Mitchell, Karen Mitchell, Palmiero Monteleone, Alessio Maria Monteleone, Melissa A. Munn-Chernoff, Benedetta Nacmias, Marie Navratilova, Ioanna Ntalla, Julie K. O’Toole, Leonid Padyukov, Aarno Palotie, Jacques Pantel, Hana Papezova, Richard Parker, John F. Pearson, Stefan Ehrlich, Geòrgia Escaramís, Thomas Espeseth, Xavier Estivill, Anne Farmer, Angela Favaro, Krista Fischer, James A.B. Floyd, Manuel Föcker, Lenka Foretova, Monica Forzan, Christopher S. Franklin, Giovanni Gambaro, Johanna Giuranna, Paola Giusti-Rodríquez, Fragiskos Gonidakis, Scott Gordon, Monica Gratacos Mayora, Sébastien Guillaume, Ken B. Hanscombe, Konstantinos Hatzikotoulas, Johannes Hebebrand, Sietske G. Helder, Anjali K. Henders, Beate Herpertz-Dahlmann, Wolfgang Herzog, Anke Hinney, L. John Horwood, Christopher Hübel, Liselotte V. Petersen, Kirstin L. Purves, Anu Raevuori, Ted Reichborn-Kjennerud, Valdo Ricca, Samuli Ripatti, Franziska Ritschel, Marion Roberts, Filip Rybakowski, Paolo Santonastaso, André Scherag, Ulrike Schmidt, Nicholas J. Schork, Alexandra Schosser, Jochen Seitz, Lenka Slachtova, P. Eline Slagboom, Margarita C.T. Slof-Op ‘t Landt, Agnieszka Slopien, Nicole Soranzo, Sandro Sorbi, Lorraine Southam, Vidar W. Steen, Laura M. Huckins, James I. Hudson, Hartmut Imgart, Hidetoshi Inoko, Vladimir Janout, Jennifer Jordan, Antonio Julià, Gursharan Kalsi, Deborah Kaminská, Jaakko Kaprio, Leila Karhunen, Andreas Karwautz, Martien J.H. Kas, Martin A. Kennedy, Anna Keski-Rahkonen, Kirsty Kiezebrink, Youl-Ri Kim, Katherine M. Kirk, Lars Klareskog, Gun Peggy S. Knudsen, Janne T. Larsen, Stephanie Le Hellard, Virpi M. Leppä, Paul Lichtenstein, Bochao Danae Lin, Astri Lundervold, Jurjen Luykx, Mario Maj, Katrin Mannik, Sara Marsal, Garret D. Stuber, Jin P. Szatkiewicz, Ioanna Tachmazidou, Elena Tenconi, Alfonso Tortorella, Federica Tozzi, Artemis Tsitsika, Marta Tyszkiewicz-Nwafor, Konstantinos Tziouvas, Annemarie A. van Elburg, Eric F. van Furth, Tracey D. Wade, Gudrun Wagner, Esther Walton, H. Erich Wichmann, Elisabeth Widen, Shuyang Yao, Eleftheria Zeggini, Stephanie Zerwas, Stephan Zipfel, Martin Jungkunz, Lydie Dietl, Cornelia E. Schwarze, Norbert Dahmen, Björn H. Schott, Arian Mobascher, Silvia Crivelli, Michelle F. Dennis, Phillip D. Harvey, Bruce W. Carter, Jennifer E. Huffman, Daniel Jacobson, Ravi Madduri, Maren K. Olsen, John Pestian, J. Michael Gaziano, Sumitra Muralidhar, Rachel Ramoni, Jean Beckham, Kyong-Mi Chang, Christopher J. O’Donnell, Philip S. Tsao, James Breeling, Grant Huang, J.P. Casas Romero, Jennifer Moser, Stacey B. Whitbourne, Jessica V. Brewer, Mihaela Aslan, Todd Connor, Dean P. Argyres, Brady Stephens, Mary T. Brophy, Donald E. Humphries, Luis E. Selva, Nhan Do, Shahpoor Shayan, Kelly Cho, Saiju Pyarajan, Elizabeth Hauser, Yan Sun, Hongyu Zhao, Peter Wilson, Rachel McArdle, Louis Dellitalia, Kristin Mattocks, John Harley, Clement J. Zablocki, Jeffrey Whittle, Frank Jacono, Salvador Gutierrez, Gretchen Gibson, Kimberly Hammer, Laurence Kaminsky, Gerardo Villareal, Scott Kinlay, Junzhe Xu, Mark Hamner, Roy Mathew, Sujata Bhushan, Pran Iruvanti, Michael Godschalk, Zuhair Ballas, Douglas Ivins, Stephen Mastorides, Jonathan Moorman, Saib Gappy, Jon Klein, Nora Ratcliffe, Hermes Florez, Olaoluwa Okusaga, Maureen Murdoch, Peruvemba Sriram, Shing Shing Yeh, Neeraj Tandon, Darshana Jhala, Samuel Aguayo, David Cohen, Satish Sharma, Suthat Liangpunsakul, Kris Ann Oursler, Mary Whooley, Sunil Ahuja, Joseph Constans, Paul Meyer, Jennifer Greco, Michael Rauchman, Richard Servatius, Melinda Gaddy, Agnes Wallbom, Timothy Morgan, Todd Stapley, Scott Sherman, George Ross, Philip Tsao, Patrick Strollo, Edward Boyko, Laurence Meyer, Samir Gupta, Mostaqul Huq, Joseph Fayad, Adriana Hung, Jack Lichy, Robin Hurley, Brooks Robey, Robert Striker, Dietl, Lydie, Schwarze, Cornelia E., Dahmen, Norbert, Schott, Björn H., Nöthen, Markus M., Ripke, Stephan, Mobascher, Arian, Rujescu, Dan, Lieb, Klaus, Roepke, Stefan, Schmahl, Christian, Bohus, Martin, Rietschel, Marcella, Crivelli, Silvia, Dennis, Michelle F., Harvey, Phillip D., Carter, Bruce W., Huffman, Jennifer E., Jacobson, Daniel, Madduri, Ravi, Olsen, Maren K., Pestian, John, Gaziano, J. Michael, Muralidhar, Sumitra, Ramoni, Rachel, Beckham, Jean, Chang, Kyong-Mi, O'Donnell, Christopher J., Tsao, Philip S., Breeling, James, Huang, Grant, Romero, J. P. Casas, Moser, Jennifer, Whitbourne, Stacey B., Brewer, Jessica V., Aslan, Mihaela, Connor, Todd, Argyres, Dean P., Stephens, Brady, Brophy, Mary T., Humphries, Donald E., Selva, Luis E., Do, Nhan, Shayan, Shahpoor, Cho, Kelly, Pyarajan, Saiju, Hauser, Elizabeth, Sun, Yan, Zhao, Hongyu, Wilson, Peter, McArdle, Rachel, Dellitalia, Louis, Mattocks, Kristin, Harley, John, Zablocki, Clement J., Whittle, Jeffrey, Jacono, Frank, Gutierrez, Salvador, Gibson, Gretchen, Hammer, Kimberly, Kaminsky, Laurence, Villareal, Gerardo, Kinlay, Scott, Xu, Junzhe, Hamner, Mark, Mathew, Roy, Bhushan, Sujata, Iruvanti, Pran, Godschalk, Michael, Ballas, Zuhair, Ivins, Douglas, Mastorides, Stephen, Moorman, Jonathan, Gappy, Saib, Klein, Jon, Ratcliffe, Nora, Florez, Hermes, Okusaga, Olaoluwa, Murdoch, Maureen, Sriram, Peruvemba, Yeh, Shing Shing, Tandon, Neeraj, Jhala, Darshana, Aguayo, Samuel, Cohen, David, Sharma, Satish, Liangpunsakul, Suthat, Oursler, Kris Ann, Whooley, Mary, Ahuja, Sunil, Constans, Joseph, Meyer, Paul, Greco, Jennifer, Rauchman, Michael, Servatius, Richard, Gaddy, Melinda, Wallbom, Agnes, Morgan, Timothy, Stapley, Todd, Sherman, Scott, Ross, George, Tsao, Philip, Strollo, Patrick, Boyko, Edward, Meyer, Laurence, Gupta, Samir, Huq, Mostaqul, Fayad, Joseph, Hung, Adriana, Lichy, Jack, Hurley, Robin, Robey, Brooks, Striker, Robert, Wray, Naomi R., Mattheisen, Manuel, Trzaskowski, Maciej, Byrne, Enda M., Abdellaoui, Abdel, Adams, Mark J., Agerbo, Esben, Air, Tracy M., Andlauer, Till F. M., Bacanu, Silviu-Alin, Bækvad-Hansen, Marie, Beekman, Aartjan T. F., Bigdeli, Tim B., Binder, Elisabeth B., Bryois, Julien, Buttenschøn, Henriette N., Bybjerg-Grauholm, Jonas, Cai, Na, Castelao, Enrique, Christensen, Jane Hvarregaard, Clarke, Toni-Kim, Coleman, Jonathan R. I., Colodro-Conde, Lucía, Couvy-Duchesne, Baptiste, Craddock, Nick, Crawford, Gregory E., Davies, Gail, Degenhardt, Franziska, Derks, Eske M., Direk, Nese, Dolan, Conor V., Dunn, Erin C., Eley, Thalia C., Escott-Price, Valentina, Hassan Kiadeh, Farnush Farhadi, Finucane, Hilary K., Foo, Jerome C., Forstner, Andreas J., Frank, Josef, Gaspar, Héléna A., Gill, Michael, Goes, Fernando S., Gordon, Scott D., Weinsheimer, Shantel Marie, Wellmann, Jürgen, Willemsen, Gonneke, Witt, Stephanie H., Wu, Yang, Xi, Hualin S., Yang, Jian, Zhang, Futao, Arolt, Volker, Baune, Bernhard T., Berger, Klaus, Boomsma, Dorret I., Cichon, Sven, Dannlowski, Udo, de Geus, E. J. C., DePaulo, J. Raymond, Domenici, Enrico, Domschke, Katharina, Esko, Tõnu, Grabe, Hans J., Hamilton, Steven P., Grove, Jakob, Hall, Lynsey S., Hansen, Christine Søholm, Hansen, Thomas F., Herms, Stefan, Hickie, Ian B., Hoffmann, Per, Homuth, Georg, Horn, Carsten, Hottenga, Jouke-Jan, Hougaard, David M., Howard, David M., Ising, Marcus, Jansen, Rick, Jones, Ian, Jones, Lisa A., Jorgenson, Eric, Knowles, James A., Kohane, Isaac S., Kraft, Julia, Kretzschmar, Warren W., Kutalik, Zoltán, Li, Yihan, Lind, Penelope A., MacIntyre, Donald J., MacKinnon, Dean F., Maier, Robert M., Maier, Wolfgang, Marchini, Jonathan, Mbarek, Hamdi, McGrath, Patrick, McGuffin, Peter, Medland, Sarah E., Mehta, Divya, Middeldorp, Christel M., Mihailov, Evelin, Milaneschi, Yuri, Milani, Lili, Mondimore, Francis M., Montgomery, Grant W., Mostafavi, Sara, Mullins, Niamh, Nauck, Matthias, Ng, Bernard, Nivard, Michel G., Nyholt, Dale R., O'Reilly, Paul F., Oskarsson, Hogni, Hayward, Caroline, Heath, Andrew C., Kendler, Kenneth S., Kloiber, Stefan, Lewis, Glyn, Li, Qingqin S., Lucae, Susanne, Madden, Pamela A. F., Magnusson, Patrik K., Martin, Nicholas G., McIntosh, Andrew M., Metspalu, Andres, Mors, Ole, Mortensen, Preben Bo, Müller-Myhsok, Bertram, Nordentoft, Merete, O'Donovan, Michael C., Paciga, Sara A., Pedersen, Nancy L., Owen, Michael J., Painter, Jodie N., Pedersen, Carsten Bøcker, Pedersen, Marianne Giørtz, Peterson, Roseann E., Peyrot, Wouter J., Pistis, Giorgio, Posthuma, Danielle, Quiroz, Jorge A., Qvist, Per, Rice, John P., Riley, Brien P., Rivera, Margarita, Mirza, Saira Saeed, Schoevers, Robert, Schulte, Eva C., Shen, Ling, Shi, Jianxin, Shyn, Stanley I., Sigurdsson, Engilbert, Sinnamon, Grant C. B., Smit, Johannes H., Smith, Daniel J., Stefansson, Hreinn, Steinberg, Stacy, Streit, Fabian, Strohmaier, Jana, Tansey, Katherine E., Teismann, Henning, Teumer, Alexander, Thompson, Wesley, Thomson, Pippa A., Thorgeirsson, Thorgeir E., Traylor, Matthew, Treutlein, Jens, Trubetskoy, Vassily, Uitterlinden, André G., Umbricht, Daniel, Van der Auwera, Sandra, van Hemert, Albert M., Viktorin, Alexander, Visscher, Peter M., Wang, Yunpeng, Webb, Bradley T., Penninx, Brenda W. J. 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Maratou E., Martinsson L., McGregor N.W., McKay J.D., Medeiros H., Millischer V., Moran J.L., Morris D.W., Muhleisen T.W., O'Brien N., O'Donovan C., Olde Loohuis L.M., Oruc L., Papiol S., Pardinas A.F., Perry A., Pfennig A., Porichi E., Raj T., Rapaport M.H., Regeer E.J., Rivas F., Roth J., Roussos P., Ruderfer D.M., Senner F., Sharp S., Shilling P.D., Slaney C., Sobell J.L., Artigas M.S., Spijker A.T., Stein D.J., Terao C., Toma C., Tooney P., Tsermpini E.-E., Vawter M.P., Vedder H., Xi S., Xu W., Kay Yang J.M., Young A.H., Young H., Zandi P.P., Zhou H., HUNT All-In Psychiatry, Babadjanova G., Backlund L., Bengesser S., Blackwood D.H.R., Carr V.J., Catts S., Dikeos D., Etain B., Ferentinos P., Gawlik M., Gershon E.S., Henskens F., Hillert J., Hong K.S., Hultman C.M., Hveem K., Iwata N., Jablensky A.V., Kirov G., Lochner C., Loughland C., Mathews C.A., McMahon F.J., Michie P., Mowry B., Neale B.M., Nievergelt C.M., Oedegaard K.J., Olsson T., Pantelis C., Patrinos G.P., Reininghaus 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F., Tsitsika A., Tyszkiewicz-Nwafor M., Tziouvas K., van Elburg A.A., van Furth E.F., Wade T.D., Wagner G., Walton E., Whiteman D.C., Wichmann H.E., Widen E., Yao S., Zeggini E., Zerwas S., Zipfel S., Jungkunz M., Dietl L., Schwarze C.E., Dahmen N., Schott B.H., Mobascher A., Crivelli S., Dennis M.F., Harvey P.D., Carter B.W., Huffman J.E., Jacobson D., Madduri R., Olsen M.K., Pestian J., Gaziano J.M., Muralidhar S., Ramoni R., Beckham J., Chang K.-M., O'Donnell C.J., Tsao P.S., Breeling J., Huang G., Romero J.P.C., Moser J., Whitbourne S.B., Brewer J.V., Aslan M., Connor T., Argyres D.P., Stephens B., Brophy M.T., Humphries D.E., Selva L.E., Do N., Shayan S., Cho K., Pyarajan S., Hauser E., Sun Y., Zhao H., Wilson P., McArdle R., Dellitalia L., Mattocks K., Harley J., Zablocki C.J., Whittle J., Jacono F., Gutierrez S., Gibson G., Hammer K., Kaminsky L., Villareal G., Kinlay S., Xu J., Hamner M., Mathew R., Bhushan S., Iruvanti P., Godschalk M., Ballas Z., Ivins D., Mastorides S., Moorman J., Gappy S., Klein J., Ratcliffe N., Florez H., Okusaga O., Murdoch M., Sriram P., Yeh S.S., Tandon N., Jhala D., Aguayo S., Cohen D., Sharma S., Liangpunsakul S., Oursler K.A., Whooley M., Ahuja S., Constans J., Meyer P., Greco J., Rauchman M., Servatius R., Gaddy M., Wallbom A., Morgan T., Stapley T., Sherman S., Ross G., Tsao P., Strollo P., Boyko E., Meyer L., Gupta S., Huq M., Fayad J., Hung A., Lichy J., Hurley R., Robey B., Striker R., Erlangsen A., Kessler R.C., Porteous D., Ursano R.J., Wasserman D., Coon H., Demontis D., Docherty A.R., Kuo P.-H., Mann J.J., Renteria M.E., Stein M.B., and Willour V.
Subjects: LD SCORE REGRESSION, Genome-wide association study, Suicide, Attempted, 3124 Neurology and psychiatry, 0302 clinical medicine, Risk Factors, Insomnia, Suicide attempt, GWAS, Suïcidi, Depression (differential diagnoses), Cause of death, Psychiatry, 0303 health sciences, Factors de risc en les malalties, Mental Disorders, Genetic Correlation, Genome-wide Association Study, Pleiotropy, Polygenicity, Suicide, Suicide Attempt, DEPRESSION, 3. Good health, Genetic correlation, Genome-Wide Association Study, Humans, Polymorphism, Single Nucleotide, Depressive Disorder, Major, Mental illness, Cohort, SEX, medicine.symptom, Human, medicine.medical_specialty, Risk factors in diseases, BF, Locus (genetics), BEHAVIORS, Psykiatri, EVENTS, 03 medical and health sciences, SDG 3 - Good Health and Well-being, medicine, ddc:610, GENOME-WIDE ASSOCIATION, IDEATION, Socioeconomic status, METAANALYSIS, Biological Psychiatry, 030304 developmental biology, business.industry, Risk Factor, Genetic architecture, THOUGHTS, RC0321, business, Malalties mentals, 030217 neurology & neurosurgery
Abstract: Statistical analyses were carried out on the NL Genetic Cluster Computer (http://www.geneticcluster.org) hosted by SURFsara and the Mount Sinai high performance computing cluster (http://hpc.mssm.edu), which is supported by the Office of Research Infrastructure of the National Institutes of Health (Grant Nos. S10OD018522 and S10OD026880). This work was conducted in part using the resources of the Advanced Computing Center for Research and Education at Vanderbilt University, Nashville, TN. This work was funded by the National Institutes of Health (Grant Nos. R01MH116269 and R01MH121455 [to DMR]), NIGMS of the National Institutes of Health (Grant No. T32GM007347 [to JK]), and the Brain & Behavior Research Foundation (NARSAD Young Investigator Award No. 29551 [to NM])., BACKGROUND: Suicide is a leading cause of death worldwide, and nonfatal suicide attempts, which occur far more frequently, are a major source of disability and social and economic burden. Both have substantial genetic etiology, which is partially shared and partially distinct from that of related psychiatric disorders. METHODS: We conducted a genome-wide association study (GWAS) of 29,782 suicide attempt (SA) cases and 519,961 controls in the International Suicide Genetics Consortium (ISGC). The GWAS of SA was conditioned on psychiatric disorders using GWAS summary statistics via multitrait-based conditional and joint analysis, to remove genetic effects on SA mediated by psychiatric disorders. We investigated the shared and divergent genetic architectures of SA, psychiatric disorders, and other known risk factors. RESULTS: Two loci reached genome-wide significance for SA: the major histocompatibility complex and an intergenic locus on chromosome 7, the latter of which remained associated with SA after conditioning on psychiatric disorders and replicated in an independent cohort from the Million Veteran Program. This locus has been implicated in risk-taking behavior, smoking, and insomnia. SA showed strong genetic correlation with psychiatric disorders, particularly major depression, and also with smoking, pain, risk-taking behavior, sleep disturbances, lower educational attainment, reproductive traits, lower socioeconomic status, and poorer general health. After conditioning on psychiatric disorders, the genetic correlations between SA and psychiatric disorders decreased, whereas those with nonpsychiatric traits remained largely unchanged. CONCLUSIONS: Our results identify a risk locus that contributes more strongly to SA than other phenotypes and suggest a shared underlying biology between SA and known risk factors that is not mediated by psychiatric disorders., Office of Research Infrastructure of the National Institutes of Health S10OD018522 S10OD026880, United States Department of Health & Human Services, National Institutes of Health (NIH) - USA R01MH116269 R01MH121455, NIH National Institute of General Medical Sciences (NIGMS) T32GM007347 NARSAD 29551
Published: 2022
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24. Maternal Immune Activation during Pregnancy Alters Postnatal Brain Growth and Cognitive Development in Nonhuman Primate Offspring

Author: Lucy H. Funk, Ana-Maria Iosif, Jeffrey Bennett, Amy M. Ryan, Richard J. Maddock, Roza M. Vlasova, Douglas J. Rowland, Cynthia M. Schumann, Judy Van de Water, David G. Amaral, Tyler A. Lesh, Martin Styner, Shuai Chen, Cameron S. Carter, Takeshi Murai, Daniel H. Geschwind, Michael J. Gandal, A. Kimberley McAllister, Melissa D. Bauman, and Casey E. Hogrefe
Subjects: Male, endocrine system diseases, Physiology, Reproductive health and childbirth, Medical and Health Sciences, Neurodevelopmental disorder, Pregnancy, Medicine, Pregnancy Complications, Infectious, Sickness behavior, Research Articles, Pediatric, General Neuroscience, Infectious, Brain, Mental Health, Schizophrenia, Prenatal Exposure Delayed Effects, Gestation, Female, MRI, Interferon Inducers, Offspring, Neurogenesis, autism, rhesus monkey, neuroimmunology, Basic Behavioral and Social Science, Immune system, Behavioral and Social Science, Animals, Neurology & Neurosurgery, business.industry, Animal, animal model, Prevention, Psychology and Cognitive Sciences, Neurosciences, Perinatal Period - Conditions Originating in Perinatal Period, medicine.disease, Macaca mulatta, digestive system diseases, Brain Disorders, Pregnancy Complications, schizophrenia, Disease Models, Animal, Neuroimmunology, Poly I-C, Neurodevelopmental Disorders, Disease Models, business
Abstract: Human epidemiological studies implicate exposure to infection during gestation in the etiology of neurodevelopmental disorders. Animal models of maternal immune activation (MIA) have identified the maternal immune response as the critical link between maternal infection and aberrant offspring brain and behavior development. Here we evaluate neurodevelopment of male rhesus monkeys (Macaca mulatta) born to MIA-treated dams (n= 14) injected with a modified form of the viral mimic polyinosinic:polycytidylic acid at the end of the first trimester. Control dams received saline injections at the same gestational time points (n= 10) or were untreated (n= 4). MIA-treated dams exhibited a strong immune response as indexed by transient increases in sickness behavior, temperature, and inflammatory cytokines. Although offspring born to control or MIA-treated dams did not differ on measures of physical growth and early developmental milestones, the MIA-treated animals exhibited subtle changes in cognitive development and deviated from species-typical brain growth trajectories. Longitudinal MRI revealed significant gray matter volume reductions in the prefrontal and frontal cortices of MIA-treated offspring at 6 months that persisted through the final time point at 45 months along with smaller frontal white matter volumes in MIA-treated animals at 36 and 45 months. These findings provide the first evidence of early postnatal changes in brain development in MIA-exposed nonhuman primates and establish a translationally relevant model system to explore the neurodevelopmental trajectory of risk associated with prenatal immune challenge from birth through late adolescence.SIGNIFICANCE STATEMENTWomen exposed to infection during pregnancy have an increased risk of giving birth to a child who will later be diagnosed with a neurodevelopmental disorder. Preclinical maternal immune activation (MIA) models have demonstrated that the effects of maternal infection on fetal brain development are mediated by maternal immune response. Since the majority of MIA models are conducted in rodents, the nonhuman primate provides a unique system to evaluate the MIA hypothesis in a species closely related to humans. Here we report the first longitudinal study conducted in a nonhuman primate MIA model. MIA-exposed offspring demonstrate subtle changes in cognitive development paired with marked reductions in frontal gray and white matter, further supporting the association between prenatal immune challenge and alterations in offspring neurodevelopment.
Published: 2021

25. Polygenic enrichment distinguishes disease associations of individual cells in single-cell RNA-seq data

Author: Soumya Raychaudhuri, Bruce Wang, Alkes L. Price, Kathryn Weinand, Karthik A. Jagadeesh, Saori Sakaue, Bogdan Pasaniuc, Poorvi Rao, Martin J. Zhang, Kangcheng Hou, Michael J. Gandal, Angela Oliveira Pisco, James Zou, Kushal K. Dey, and Aris Taychameekiatchai
Subjects: Cell type, medicine.anatomical_structure, Cell, Gene expression, medicine, RNA-Seq, Genome-wide association study, Disease, Computational biology, Hippocampal formation, Biology, Gene
Abstract: Gene expression at the individual cell-level resolution, as quantified by single-cell RNA-sequencing (scRNA-seq), can provide unique insights into the pathology and cellular origin of diseases and complex traits. Here, we introduce single-cell Disease Relevance Score (scDRS), an approach that links scRNA-seq with polygenic risk of disease at individual cell resolution; scDRS identifies individual cells that show excess expression levels for genes in a disease-specific gene set constructed from GWAS data. We determined via simulations that scDRS is well-calibrated and powerful in identifying individual cells associated to disease. We applied scDRS to GWAS data from 74 diseases and complex traits (average N=341K) in conjunction with 16 scRNA-seq data sets spanning 1.3 million cells from 31 tissues and organs. At the cell type level, scDRS broadly recapitulated known links between classical cell types and disease, and also produced novel biologically plausible findings. At the individual cell level, scDRS identified subpopulations of disease-associated cells that are not captured by existing cell type labels, including subpopulations of CD4+ T cells associated with inflammatory bowel disease, partially characterized by their effector-like states; subpopulations of hippocampal CA1 pyramidal neurons associated with schizophrenia, partially characterized by their spatial location at the proximal part of the hippocampal CA1 region; and subpopulations of hepatocytes associated with triglyceride levels, partially characterized by their higher ploidy levels. At the gene level, we determined that genes whose expression across individual cells was correlated with the scDRS score (thus reflecting co-expression with GWAS disease genes) were strongly enriched for gold-standard drug target and Mendelian disease genes.
Published: 2021
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26. Identification of neural oscillations and epileptiform changes in human brain organoids

Author: Bennett G. Novitch, Momoko Watanabe, Arinnae Kurdian, Jessie E. Buth, Thomas F. Allison, William E. Lowry, Istvan Mody, Kathrin Plath, Jack M. Parent, Peyman Golshani, Osvaldo A. Miranda, Ranmal A. Samarasinghe, Simon Mitchell, Namie N. Fotion, Isabella Ferando, and Michael J. Gandal
Subjects: Methyl-CpG-Binding Protein 2, Neurodegenerative, Transcriptome, 2.1 Biological and endogenous factors, Psychology, Aetiology, Induced pluripotent stem cell, Child, Neurons, Stem Cell Research - Induced Pluripotent Stem Cell - Human, General Neuroscience, Brain, Human brain, Network formation, medicine.anatomical_structure, Child, Preschool, Neurological, Identification (biology), Female, Cognitive Sciences, Single-Cell Analysis, Adult, Neurogenesis, 1.1 Normal biological development and functioning, Induced Pluripotent Stem Cells, Intact brain, Rett syndrome, Neuroimaging, Biology, Underpinning research, Clinical Research, medicine, Organoid, Rett Syndrome, Humans, Calcium Signaling, Benzothiazoles, Preschool, Epilepsy, Neurology & Neurosurgery, Stem Cell Research - Induced Pluripotent Stem Cell, Neurosciences, medicine.disease, Stem Cell Research, Brain Disorders, Good Health and Well Being, Synapses, Nerve Net, Neuroscience, Toluene
Abstract: Brain organoids represent a powerful tool for studying human neurological diseases, particularly those that affect brain growth and structure. However, many diseases manifest with clear evidence of physiological and network abnormality in the absence of anatomical changes, raising the question of whether organoids possess sufficient neural network complexity to model these conditions. Here, we explore the network-level functions of brain organoids using calcium sensor imaging and extracellular recording approaches that together reveal the existence of complex network dynamics reminiscent of intact brain preparations. We demonstrate highly abnormal and epileptiform-like activity in organoids derived from induced pluripotent stem cells from individuals with Rett syndrome, accompanied by transcriptomic differences revealed by single-cell analyses. We also rescue key physiological activities with an unconventional neuroregulatory drug, pifithrin-α. Together, these findings provide an essential foundation for the utilization of brain organoids to study intact and disordered human brain network formation and illustrate their utility in therapeutic discovery.
Published: 2021

27. Postnatal immune activation causes social deficits in a mouse model of tuberous sclerosis: Role of microglia and clinical implications

Author: Tawnie K. Silva, Daniel H. Geschwind, Alcino J. Silva, Miou Zhou, Andrey Rzhetsky, Sunrae Taloma, Stephanie A. White, Miranda Phan, Karen Bach, Isaiah Herrera, Gayle M. Boxx, Michael J. Gandal, Rochelle Mandanas, Ishanu Chattopadhyay, Elizabeth R. Fraley, Manuel F. López-Aranda, and Genhong Cheng
Subjects: medicine.medical_specialty, Social psychology (sociology), animal diseases, Cognitive Neuroscience, Intellectual and Developmental Disabilities (IDD), Autism, Neurogenetics, chemical and pharmacologic phenomena, Diseases and Disorders, Behavioral neuroscience, Basic Behavioral and Social Science, Tuberous sclerosis, Immune system, Rare Diseases, Tuberous Sclerosis, Behavioral and Social Science, medicine, 2.1 Biological and endogenous factors, Aetiology, ComputingMilieux_MISCELLANEOUS, Pediatric, Multidisciplinary, Innate immune system, Microglia, business.industry, Neurosciences, SciAdv r-articles, biochemical phenomena, metabolism, and nutrition, medicine.disease, Brain Disorders, medicine.anatomical_structure, Mental Health, ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, bacteria, Medical genetics, business, Neuroscience, Research Article
Abstract: Description, Postnatal immune activation leads to social deficits in a mouse model of TSC by abnormal interferon production in microglia., There is growing evidence that prenatal immune activation contributes to neuropsychiatric disorders. Here, we show that early postnatal immune activation resulted in profound impairments in social behavior, including in social memory in adult male mice heterozygous for a gene responsible for tuberous sclerosis complex (Tsc2+/−), a genetic disorder with high prevalence of autism. Early postnatal immune activation did not affect either wild-type or female Tsc2+/− mice. We demonstrate that these memory deficits are caused by abnormal mammalian target of rapamycin–dependent interferon signaling and impairments in microglia function. By mining the medical records of more than 3 million children followed from birth, we show that the prevalence of hospitalizations due to infections in males (but not in females) is associated with future development of autism spectrum disorders (ASD). Together, our results suggest the importance of synergistic interactions between strong early postnatal immune activation and mutations associated with ASD.
Published: 2021

28. White matter microstructure shows sex differences in late childhood: Evidence from 6,797 children

Author: Paul M. Thompson, Emily Laltoo, Michael J. Gandal, James T. McCracken, Katherine E. Lawrence, Zvart Abaryan, and Leanna M. Hernandez
Subjects: medicine.medical_specialty, medicine.diagnostic_test, Radial diffusivity, Magnetic resonance imaging, Audiology, Biology, Late childhood, White matter microstructure, White matter, medicine.anatomical_structure, Fractional anisotropy, medicine, Spectrum imaging, Diffusion MRI
Abstract: Sex differences in white matter microstructure have been robustly demonstrated in the adult brain using both conventional and advanced diffusion-weighted magnetic resonance imaging (dMRI) approaches. However, the effect of sex on white matter microstructure prior to adulthood remains poorly understood, with previous developmental work focusing on conventional microstructure metrics and yielding mixed results. Here we thoroughly and rigorously characterized sex differences in white matter microstructure among over 6,000 children from the Adolescent Brain Cognitive Development (ABCD) Study who were between 9 and 10 years old. Microstructure was quantified using both the conventional model - diffusion tensor imaging (DTI) - and an advanced model, restriction spectrum imaging (RSI). DTI metrics included fractional anisotropy (FA) and mean, axial, and radial diffusivity (MD, AD, RD). RSI metrics included normalized isotropic, directional, and total intracellular diffusion (N0, ND, NT). We found significant and replicable sex differences in DTI or RSI microstructure metrics in every white matter region examined across the brain. The impact of sex on FA was regionally specific. Across white matter regions, boys exhibited greater MD, AD, and RD than girls, on average. Girls displayed increased N0, ND, and NT compared to boys, on average, suggesting greater cell and neurite density in girls. Together, these robust and replicable findings provide an important foundation for understanding sex differences in health and disease.
Published: 2021
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29. Mechanisms of Neuronal Alternative Splicing and Strategies for Therapeutic Interventions

Author: Elizabeth A. Heller, Eduardo Javier López Soto, Sika Zheng, Thomas Gonatopoulos-Pournatzis, Michael J. Gandal, and Diou Luo
Subjects: 0301 basic medicine, Gene isoform, Autism Spectrum Disorder, RNA Splicing, Biology, Axonogenesis, Muscular Atrophy, Spinal, 03 medical and health sciences, 0302 clinical medicine, medicine, Animals, Humans, Protein Isoforms, Neurons, Mammalian nervous system, General Neuroscience, Symposium and Mini-Symposium, Alternative splicing, Spinal muscular atrophy, medicine.disease, Phenotype, Chromatin, Alternative Splicing, 030104 developmental biology, RNA splicing, Neuroscience, 030217 neurology & neurosurgery
Abstract: Many cellular and physiological processes are coordinated by regulatory networks that produce a remarkable complexity of transcript isoforms. In the mammalian nervous system, alternative pre-mRNA splicing generates functionally distinct isoforms that play key roles in normal physiology, supporting development, plasticity, complex behaviors, and cognition. Neuronal splicing programs controlled by RNA-binding proteins, are influenced by chromatin modifications and can exhibit neuronal subtype specificity. As highlighted in recent publications, aberrant alternative splicing is a major contributor to disease phenotypes. Therefore, understanding the underlying mechanisms of alternative splicing regulation and identifying functional splicing isoforms with critical phenotypic roles are expected to provide a comprehensive resource for therapeutic development, as illuminated by recent successful interventions of spinal muscular atrophy. Here, we discuss the latest progress in the study of the emerging complexity of alternative splicing mechanisms in neurons, and how these findings inform new therapies to correct and control splicing defects.
Published: 2019
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30. Profiling allele-specific gene expression in brains from individuals with autism spectrum disorder reveals preferential minor allele usage

Author: Eun Yong Kang, Michael J. Gandal, Daniel H. Geschwind, Changhoon Lee, and Eleazar Eskin
Subjects: 0301 basic medicine, genetic structures, Autism Spectrum Disorder, Population, Allelic Imbalance, Biology, behavioral disciplines and activities, Article, 03 medical and health sciences, 0302 clinical medicine, mental disorders, Gene duplication, Psychology, Humans, RNA, Small Nucleolar, Small nucleolar RNA, Allele, education, Alleles, Small Nucleolar, Regulation of gene expression, Genetics, education.field_of_study, Neurology & Neurosurgery, Gene Expression Profiling, General Neuroscience, Neurosciences, Brain, Gene expression profiling, Minor allele frequency, 030104 developmental biology, RNA, Cognitive Sciences, Transcriptome, Neuroscience, 030217 neurology & neurosurgery
Abstract: One fundamental but understudied mechanism of gene regulation in disease is allele-specific expression (ASE), the preferential expression of one allele. We leveraged RNA-sequencing data from human brain to assess ASE in autism spectrum disorder (ASD). When ASE is observed in ASD, the allele with lower population frequency (minor allele) is preferentially more highly expressed than the major allele, opposite to the canonical pattern. Importantly, genes showing ASE in ASD are enriched in those downregulated in ASD postmortem brains and in genes harboring de novo mutations in ASD. Two regions, 14q32 and 15q11, containing all known orphan C/D box small nucleolar RNAs (snoRNAs), are particularly enriched in shifts to higher minor allele expression. We demonstrate that this allele shifting enhances snoRNA-targeted splicing changes in ASD-related target genes in idiopathic ASD and 15q11-q13 duplication syndrome. Together, these results implicate allelic imbalance and dysregulation of orphan C/D box snoRNAs in ASD pathogenesis.
Published: 2019
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31. Shared Molecular Neuropathology Across Major Psychiatric Disorders Parallels Polygenic Overlap

Author: Virpi Leppa, Jillian R. Haney, Vivek Appadurai, Daniel H. Geschwind, Andrew J. Schork, Alfonso Buil, Christopher Hartl, Neelroop N. Parikshak, Gokul Ramaswami, Thomas Werge, Michael J. Gandal, Chunyu Liu, and Kevin P. White
Subjects: Genetics, Brain dysfunction, Influential Publications, Genetic variants, Neuropathology, Biology, Parallels, Genetic architecture, Neuropsychiatric disease
Abstract: (Gandal et al., "Shared molecular neuropathology across major psychiatric disorders parallels polygenic overlap" Science 09 Feb 2018:Vol. 359, Issue 6376, pp. 693-697 (DOI: 10.1126/science.aad6469). Reprinted with permission from AAAS).
Published: 2019
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32. Leveraging eQTLs to identify individual-level tissue of interest for a complex trait

Author: Tommer Schwarz, Michael J. Gandal, Jonathan Flint, Bogdan Pasaniuc, Na Cai, Arunabha Majumdar, Claudia Giambartolomei, and Tanushree Haldar
Subjects: 0301 basic medicine, Multifactorial Inheritance, Heredity, Single Nucleotide Polymorphisms, Adipose tissue, Gene Expression, Biochemistry, Body Mass Index, 0302 clinical medicine, Genotype, Medicine and Health Sciences, Tissue Distribution, Biology (General), 0303 health sciences, education.field_of_study, Ecology, 030305 genetics & heredity, Brain, Biobank, Phenotypes, Phenotype, Computational Theory and Mathematics, Adipose Tissue, Organ Specificity, Modeling and Simulation, Trait, Algorithms, Research Article, QH301-705.5, Population, Quantitative Trait Loci, Computational biology, Quantitative trait locus, Biology, Genetic Predisposition, Polymorphism, Single Nucleotide, Cellular and Molecular Neuroscience, 03 medical and health sciences, Genetic predisposition, Genetics, Humans, Pharmacokinetics, Computer Simulation, Genetic Predisposition to Disease, Obesity, education, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Pharmacology, Quantitative Traits, Models, Genetic, Biology and Life Sciences, Computational Biology, Bayes Theorem, Genetic architecture, 030104 developmental biology, Expression quantitative trait loci, Genetics of Disease, 030217 neurology & neurosurgery, Software
Abstract: Genetic predisposition for complex traits often acts through multiple tissues at different time points during development. As a simple example, the genetic predisposition for obesity could be manifested either through inherited variants that control metabolism through regulation of genes expressed in the brain, or that control fat storage through dysregulation of genes expressed in adipose tissue, or both. Here we describe a statistical approach that leverages tissue-specific expression quantitative trait loci (eQTLs) corresponding to tissue-specific genes to prioritize a relevant tissue underlying the genetic predisposition of a given individual for a complex trait. Unlike existing approaches that prioritize relevant tissues for the trait in the population, our approach probabilistically quantifies the tissue-wise genetic contribution to the trait for a given individual. We hypothesize that for a subgroup of individuals the genetic contribution to the trait can be mediated primarily through a specific tissue. Through simulations using the UK Biobank, we show that our approach can predict the relevant tissue accurately and can cluster individuals according to their tissue-specific genetic architecture. We analyze body mass index (BMI) and waist to hip ratio adjusted for BMI (WHRadjBMI) in the UK Biobank to identify subgroups of individuals whose genetic predisposition act primarily through brain versus adipose tissue, and adipose versus muscle tissue, respectively. Notably, we find that these individuals have specific phenotypic features beyond BMI and WHRadjBMI that distinguish them from random individuals in the data, suggesting biological effects of tissue-specific genetic contribution for these traits., Author summary A significant component of the genetic susceptibility to complex traits is mediated through genetic control of gene expression in one or multiple tissues. Several studies have highlighted the relevance of tissue specific biological mechanisms underlying the pathogenesis of complex traits, and have often identified multiple tissues relevant to a given phenotype in the population. Since existing methods only prioritize tissues for a complex phenotype in the population, it remains an open question whether certain classes of individuals have their genetic predisposition for the phenotype mediated primarily through a specific tissue. We present an efficient statistical approach that integrates tissue-specific eQTLs (i.e., eQTLs for tissue-specific genes) with genetic association data for a complex trait to probabilistically quantify the tissue-wise genetic contribution to the phenotype of each individual in the study. Using simulations we show that the proposed approach accurately infers the simulated tissue of interest for each individual. Integrating expression data from the GTEx consortium, we apply the proposed approach to two obesity related phenotypes in the UK Biobank. Our approach identified subgroups of individuals with their genetic susceptibility to the phenotype mediated in a tissue-specific manner. Interestingly, multiple metabolic traits, neuropsychiatric traits, and other traits were found to be differentially distributed between the tissue-specific groups of individuals and the remaining population, suggesting a biologically meaningful interpretation for these subgroups of individuals. We provide an R-package ‘eGST’ for general use of the method: https://cran.r-project.org/web/packages/eGST/index.html.
Published: 2021

33. 59. ASSOCIATION BETWEEN COMPLEMENT COMPONENT 4 VARIATION AND CHILDHOOD BRAIN AND BEHAVIORAL PHENOTYPES: MULTIETHNIC PHEWAS IN THE ADOLESCENT BRAIN AND COGNITIVE DEVELOPMENT (ABCD) STUDY

Author: Richard A. I. Bethlehem, Gil D. Hoftman, Wesley K. Thompson, Leanna M. Hernandez, Minsoo Kim, and Michael J. Gandal
Subjects: Pharmacology, Genetics, Psychiatry and Mental health, Behavioral phenotypes, Complement component 4, Variation (linguistics), Neurology, Cognitive development, Pharmacology (medical), Neurology (clinical), Biology, Association (psychology), Biological Psychiatry
Published: 2021
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34. Association between resting-state functional brain connectivity and gene expression is altered in autism spectrum disorder

Author: Genevieve Konopka, Jillian R. Haney, Alex Treacher, Albert Montillo, Emre Caglayan, Daniel H. Geschwind, Danni Luo, Michael J. Gandal, and Stefano Berto
Subjects: Cell type, genetic structures, Autism Spectrum Disorder, Brain activity and meditation, Gene Expression, General Physics and Astronomy, Biology, General Biochemistry, Genetics and Molecular Biology, Genetic linkage, Neural Pathways, mental disorders, Gene expression, medicine, Humans, Brain Mapping, Multidisciplinary, Resting state fMRI, Brain, General Chemistry, medicine.disease, Magnetic Resonance Imaging, Visual cortex, medicine.anatomical_structure, Autism spectrum disorder, Neuroscience, Neurotypical
Abstract: Gene expression covaries with brain activity as measured by resting state functional magnetic resonance imaging (MRI). However, it is unclear how genomic differences driven by disease state can affect this relationship. Here, we integrate from the ABIDE I and II imaging cohorts with datasets of gene expression in brains of neurotypical individuals and individuals with autism spectrum disorder (ASD) with regionally matched brain activity measurements from fMRI datasets. We identify genes linked with brain activity whose association is disrupted in ASD. We identified a subset of genes that showed a differential developmental trajectory in individuals with ASD compared with controls. These genes are enriched in voltage-gated ion channels and inhibitory neurons, pointing to excitation-inhibition imbalance in ASD. We further assessed differences at the regional level showing that the primary visual cortex is the most affected region in ASD. Our results link disrupted brain expression patterns of individuals with ASD to brain activity and show developmental, cell type, and regional enrichment of activity linked genes.
Published: 2021
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35. Genome-wide association study of more than 40,000 bipolar disorder cases provides new insights into the underlying biology

Author: James McKay, Frank Bellivier, Mark A. Frye, Bertram Müller-Myhsok, Fermín Mayoral, I. Nicol Ferrier, Marion Leboyer, Fabian Streit, Dan J. Stein, James L. Kennedy, Christine Søholm Hansen, Scott D. Gordon, Beata Świątkowska, Valentina Escott-Price, Michael Bauer, Lina Martinsson, Donald J. MacIntyre, Oleksandr Frei, Daniel J. Smith, Sara A. Paciga, Takeo Saito, Jennifer L. Moran, Verneri Antilla, C Pantelis, Tomas Olsson, Swapnil Awasthi, Lena Backlund, Eirini Maratou, Martin Schalling, John B. Vincent, Niamh Mullins, Sarah E. Bergen, Niamh L. O'Brien, Marco P. Boks, Carsten Bøcker Pedersen, Mikael Landén, Franziska Degenhardt, Hang Zhou, Margarita Rivera, Andrew M. McIntosh, Manuel Mattheisen, Shawn Levy, Roy H. Perlis, John P. Rice, Sigurdur H. Magnusson, Amanda Dobbyn, Michael Conlon O'Donovan, Julien Bryois, Wolfgang Maier, John-Anker Zwart, J. Raymond DePaulo, Martin Alda, Laura G. Sloofman, Friederike Sophie David, James A. Knowles, Aiden Corvin, Thomas G. Schulze, Markus M. Nöthen, Nolan Kamitaki, Nina Dalkner, Brandon J. Coombes, Gustavo Turecki, Allan H. Young, Caroline M. Nievergelt, Patricia T. Michie, Ingrid Agartz, Towfique Raj, Diego Albani, Maria Grigoroiu-Serbanescu, Bernhard T. Baune, Kyooseob Ha, Vincent Millischer, Engilbert Sigurdsson, Eva C. Beins, Nicholas G. Martin, Gulja Babadjanova, Josef Frank, Eva Z. Reininghaus, Patrick F. Sullivan, Ian R. Gizer, Guy A. Rouleau, Carmel M. Loughland, Christine Lochner, Thorsten M. Kranz, Amy Perry, Arne E. Vaaler, Mariam M. Al Eissa, Simon Xi, Claire O'Donovan, Josep Antoni Ramos-Quiroga, Ketil J. Oedegaard, Helmut Vedder, Carol A. Mathews, Panagiotis Ferentinos, Tim B. Bigdeli, Derek W. Morris, Per Hoffmann, Mark Hyman Rapaport, Peter P. Zandi, Michael John Owen, Douglas M. Ruderfer, Anders D. Børglum, Catharina Lavebratt, Thorgeir E. Thorgeirsson, Paul A. Tooney, Michiaki Kubo, Steven A. Kushner, Jan Hillert, Loes M. Olde Loohuis, Anastasia Antoniou, Murielle Brum, Chikashi Terao, Nathaniel W. McGregor, Fabio Rivas, James B. Potash, Kevin S. O’Connell, Susanne Lucae, Brian M. Schilder, Katrin Gade, Stephan Ripke, Kristina Adorjan, Kari Stefansson, Tiffany A. Greenwood, Panos Roussos, Sarah Kittel-Schneider, Steven A. McCarroll, Sergi Papiol, Heon Jeong Lee, Assen Jablensky, Liliya Abramova, Dennis Hellgren, Jonas Bybjerg-Grauholm, Martin Lundberg, Hong-Hee Won, William Byerley, Lars Alfredsson, Joel Gelernter, Andrew McQuillin, Claire Slaney, Marta Ribasés, Stephanie H. Witt, Yoichiro Kamatani, Kyung Sue Hong, Marie Bækvad-Hansen, María Soler Artigas, Julie M. Cunningham, Fanny Senner, Stacy Steinberg, Paul D. Shilling, Nakao Iwata, Eystein Stordal, Armin Birner, Sarah E. Medland, Miquel Casas, Ben Michael Brumpton, Erlend Bøen, Bryan J. Mowry, Jolanta Lissowska, Francis J. McMahon, Howard J. Edenberg, Grant W. Montgomery, John I. Nurnberger, Stéphane Jamain, Claudio Toma, Ney Alliey-Rodriguez, Ole Mors, Micha Gawlik, David Curtis, Catrin Lewis, Evangelia-Eirini Tsermpini, Georgia Panagiotaropoulou, Marcella Rietschel, Jessica Yang, Ian Jones, Eduard Vieta, Ole A. Andreassen, Richard M. Myers, Dimitris Dikeos, Melissa J. Green, Janet L. Sobell, Maria Koromina, Piotr M. Czerski, Lilijana Oruc, Sven Cichon, Udo Dannlowski, Bruno Etain, Monika Budde, Alessia Fiorentino, Naomi R. Wray, Qingqin S. Li, Murray J. Cairns, Jonathan R. I. Coleman, Jose Guzman-Parra, Andreas J. Forstner, Hannah Young, Alfredo B. Cuellar-Barboza, Julian Roth, Torbjørn Elvsåshagen, Zhen Qiao, Thomas Werge, Athanassios Douzenis, Cristiana Cruceanu, Rolf Adolfsson, Peter Holmans, Vaughan J. Carr, Thomas W. Weickert, Masashi Ikeda, Joanna M. Biernacka, Lea Sirignano, Adam X. Maihofer, Ralph W. Kupka, John Strauss, Anders M. Dale, Elliot S. Gershon, Jakob Grove, Arianna Di Florio, Helena Medeiros, Ingrid Melle, Preben Bo Mortensen, Kristi Krebs, Saskia P. Hagenaars, Liz Forty, Stanley V. Catts, David M. Hougaard, Marianne Giørtz Pedersen, Andreas Reif, Toni-Kim Clarke, Anne T. Spijker, Danielle Posthuma, Manolis Kogevinas, Michael Boehnke, Rosa Bosch, Gerome Breen, Benjamin M. Neale, Jessica S. Johnson, Katherine Gordon-Smith, Cristina Sánchez-Mora, Alexander W. Charney, Henry R. Kranzler, Digby Quested, René S. Kahn, Lili Milani, Merete Nordentoft, Nathalie Brunkhorst-Kanaan, Laura M. Huckins, James T.R. Walters, Sigrid Børte, Antonio F. Pardiñas, Kristian Hveem, Julie Garnham, Jacob Lawrence, Vassily Trubetskoy, Rodney J. Scott, Nicholas Bass, Carlos N. Pato, Andrea Pfennig, Wei Xu, Calwing Liao, Nicholas John Craddock, Thomas Damm Als, Christina M. Hultman, Fernando S. Goes, Adebayo Anjorin, Evgenia Porichi, Frans Henskens, Nelson B. Freimer, Janice M. Fullerton, Cathryn M. Lewis, Srdjan Djurovic, Roel A. Ophoff, Phil Lee, Peter McGuffin, Gunnar Morken, George P. Patrinos, Alessandro Serretti, Cynthia Shannon Weickert, Pablo Cervantes, Bendik S. Winsvold, Tatiana Foroud, Tõnu Esko, Ulrich Schall, Michele T. Pato, Ji Hyun Baek, John R. Kelsoe, Olav B. Smeland, Janos Kalman, Eva C. Schulte, Joanna Hauser, Urs Heilbronner, Magnús Haraldsson, Martin Hautzinger, Lea Zillich, Eline J. Regeer, Douglas Blackwood, Laura J. Scott, Jordan W. Smoller, Michael J. Gandal, Marquis P. Vawter, Philip B. Mitchell, Ole Kristian Drange, Peter R. Schofield, Susanne Bengesser, Stefan Herms, George Kirov, Markus Leber, Louise Frisén, Thomas W. Mühleisen, Susan L. McElroy, Irwin D. Waldman, Wade H. Berrettini, Sally I. Sharp, Minsoo Kim, Lisa Jones, Eli A. Stahl, Hreinn Stefansson, Esben Agerbo, Dolores Malaspina, Complex Trait Genetics, Amsterdam Neuroscience - Complex Trait Genetics, Psychiatry, APH - Mental Health, Amsterdam Neuroscience - Mood, Anxiety, Psychosis, Stress & Sleep, Human genetics, Amsterdam Neuroscience - Compulsivity, Impulsivity & Attention, Amsterdam Reproduction & Development (AR&D), APH - Digital Health, Mullins N., Forstner A.J., O'Connell K.S., Coombes B., Coleman J.R.I., Qiao Z., Als T.D., Bigdeli T.B., Borte S., Bryois J., Charney A.W., Drange O.K., Gandal M.J., Hagenaars S.P., Ikeda M., Kamitaki N., Kim M., Krebs K., Panagiotaropoulou G., Schilder B.M., Sloofman L.G., Steinberg S., Trubetskoy V., Winsvold B.S., Won H.-H., Abramova L., Adorjan K., Agerbo E., Al Eissa M., Albani D., Alliey-Rodriguez N., Anjorin A., Antilla V., Antoniou A., Awasthi S., Baek J.H., Baekvad-Hansen M., Bass N., Bauer M., Beins E.C., Bergen S.E., Birner A., Bocker Pedersen C., Boen E., Boks M.P., Bosch R., Brum M., Brumpton B.M., Brunkhorst-Kanaan N., Budde M., Bybjerg-Grauholm J., Byerley W., Cairns M., Casas M., Cervantes P., Clarke T.-K., Cruceanu C., Cuellar-Barboza A., Cunningham J., Curtis D., Czerski P.M., Dale A.M., Dalkner N., David F.S., Degenhardt F., Djurovic S., Dobbyn A.L., Douzenis A., Elvsashagen T., Escott-Price V., Ferrier I.N., Fiorentino A., Foroud T.M., Forty L., Frank J., Frei O., Freimer N.B., Frisen L., Gade K., Garnham J., Gelernter J., Giortz Pedersen M., Gizer I.R., Gordon S.D., Gordon-Smith K., Greenwood T.A., Grove J., Guzman-Parra J., Ha K., Haraldsson M., Hautzinger M., Heilbronner U., Hellgren D., Herms S., Hoffmann P., Holmans P.A., Huckins L., Jamain S., Johnson J.S., Kalman J.L., Kamatani Y., Kennedy J.L., Kittel-Schneider S., Knowles J.A., Kogevinas M., Koromina M., Kranz T.M., Kranzler H.R., Kubo M., Kupka R., Kushner S.A., Lavebratt C., Lawrence J., Leber M., Lee H.-J., Lee P.H., Levy S.E., Lewis C., Liao C., Lucae S., Lundberg M., MacIntyre D.J., Magnusson S.H., Maier W., Maihofer A., Malaspina D., Maratou E., Martinsson L., Mattheisen M., McCarroll S.A., McGregor N.W., McGuffin P., McKay J.D., Medeiros H., Medland S.E., Millischer V., Montgomery G.W., Moran J.L., Morris D.W., Muhleisen T.W., O'Brien N., O'Donovan C., Olde Loohuis L.M., Oruc L., Papiol S., Pardinas A.F., Perry A., Pfennig A., Porichi E., Potash J.B., Quested D., Raj T., Rapaport M.H., DePaulo J.R., Regeer E.J., Rice J.P., Rivas F., Rivera M., Roth J., Roussos P., Ruderfer D.M., Sanchez-Mora C., Schulte E.C., Senner F., Sharp S., Shilling P.D., Sigurdsson E., Sirignano L., Slaney C., Smeland O.B., Smith D.J., Sobell J.L., Soholm Hansen C., Soler Artigas M., Spijker A.T., Stein D.J., Strauss J.S., Swiatkowska B., Terao C., Thorgeirsson T.E., Toma C., Tooney P., Tsermpini E.-E., Vawter M.P., Vedder H., Walters J.T.R., Witt S.H., Xi S., Xu W., Yang J.M.K., Young A.H., Young H., Zandi P.P., Zhou H., Zillich L., Adolfsson R., Agartz I., Alda M., Alfredsson L., Babadjanova G., Backlund L., Baune B.T., Bellivier F., Bengesser S., Berrettini W.H., Blackwood D.H.R., Boehnke M., Borglum A.D., Breen G., Carr V.J., Catts S., Corvin A., Craddock N., Dannlowski U., Dikeos D., Esko T., Etain B., Ferentinos P., Frye M., Fullerton J.M., Gawlik M., Gershon E.S., Goes F.S., Green M.J., Grigoroiu-Serbanescu M., Hauser J., Henskens F., Hillert J., Hong K.S., Hougaard D.M., Hultman C.M., Hveem K., Iwata N., Jablensky A.V., Jones I., Jones L.A., Kahn R.S., Kelsoe J.R., Kirov G., Landen M., Leboyer M., Lewis C.M., Li Q.S., Lissowska J., Lochner C., Loughland C., Martin N.G., Mathews C.A., Mayoral F., McElroy S.L., McIntosh A.M., McMahon F.J., Melle I., Michie P., Milani L., Mitchell P.B., Morken G., Mors O., Mortensen P.B., Mowry B., Muller-Myhsok B., Myers R.M., Neale B.M., Nievergelt C.M., Nordentoft M., Nothen M.M., O'Donovan M.C., Oedegaard K.J., Olsson T., Owen M.J., Paciga S.A., Pantelis C., Pato C., Pato M.T., Patrinos G.P., Perlis R.H., Posthuma D., Ramos-Quiroga J.A., Reif A., Reininghaus E.Z., Ribases M., Rietschel M., Ripke S., Rouleau G.A., Saito T., Schall U., Schalling M., Schofield P.R., Schulze T.G., Scott L.J., Scott R.J., Serretti A., Shannon Weickert C., Smoller J.W., Stefansson H., Stefansson K., Stordal E., Streit F., Sullivan P.F., Turecki G., Vaaler A.E., Vieta E., Vincent J.B., Waldman I.D., Weickert T.W., Werge T., Wray N.R., Zwart J.-A., Biernacka J.M., Nurnberger J.I., Cichon S., Edenberg H.J., Stahl E.A., McQuillin A., Di Florio A., Ophoff R.A., Andreassen O.A., IMRB - 'Neuropsychiatrie translationnelle' [Créteil] (U955 Inserm - UPEC), Institut Mondor de Recherche Biomédicale (IMRB), Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR10-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12), Centre International de Recherche contre le Cancer - International Agency for Research on Cancer (CIRC - IARC), Organisation Mondiale de la Santé / World Health Organization Office (OMS / WHO), Optimisation thérapeutique en Neuropsychopharmacologie (OPTeN (UMR_S_1144 / U1144)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Groupe Hospitalier Saint Louis - Lariboisière - Fernand Widal [Paris], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), and Etain, Bruno
Subjects: Multifactorial Inheritance, Bipolar Disorder, [SDV.MHEP.PSM] Life Sciences [q-bio]/Human health and pathology/Psychiatrics and mental health, Medizin, Genome-wide association study, Major Histocompatibility Complex/genetics, Major Histocompatibility Complex, 0302 clinical medicine, Risk Factors, MESH: Risk Factors, MESH: Bipolar Disorder, Chromosomes, Human, Spectrum disorder, Genetics, 0303 health sciences, Bipolar Disorder/genetics, MESH: Genetic Predisposition to Disease, MESH: Case-Control Studies, Phenotype, Schizophrenia, Synaptic signaling, Case-Control Studie, Human, Quantitative Trait Loci, Biology, MESH: Phenotype, MESH: Chromosomes, Human, Article, 03 medical and health sciences, MESH: Major Histocompatibility Complex, SDG 3 - Good Health and Well-being, ddc:570, medicine, Humans, Genetic Predisposition to Disease, Bipolar disorder, Multifactorial Inheritance/genetics, MESH: Genome, Human, 030304 developmental biology, MESH: Humans, Genome, Human, Risk Factor, Chromosomes, Human/genetics, Mental illness, medicine.disease, MESH: Quantitative Trait Loci, Human genetics, Psychologie, Case-Control Studies, [SDV.MHEP.PSM]Life Sciences [q-bio]/Human health and pathology/Psychiatrics and mental health, MESH: Genome-Wide Association Study, Expression quantitative trait loci, MESH: Multifactorial Inheritance, Quantitative Trait Loci/genetics, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract: International audience; Bipolar disorder is a heritable mental illness with complex etiology. We performed a genome-wide association study of 41,917 bipolar disorder cases and 371,549 controls of European ancestry, which identified 64 associated genomic loci. Bipolar disorder risk alleles were enriched in genes in synaptic signaling pathways and brain-expressed genes, particularly those with high specificity of expression in neurons of the prefrontal cortex and hippocampus. Significant signal enrichment was found in genes encoding targets of antipsychotics, calcium channel blockers, antiepileptics and anesthetics. Integrating expression quantitative trait locus data implicated 15 genes robustly linked to bipolar disorder via gene expression, encoding druggable targets such as HTR6, MCHR1, DCLK3 and FURIN. Analyses of bipolar disorder subtypes indicated high but imperfect genetic correlation between bipolar disorder type I and II and identified additional associated loci. Together, these results advance our understanding of the biological etiology of bipolar disorder, identify novel therapeutic leads and prioritize genes for functional follow-up studies.
Published: 2021
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36. Associations between patterns in comorbid diagnostic trajectories of individuals with schizophrenia and etiological factors

Author: Chun Chieh Fan, Ole Mors, Gonçalo Espregueira Themudo, Daniel H. Geschwind, Andrew J. Schork, Preben Bo Mortensen, Merete Nordentoft, David M. Hougaard, Wesley K. Thompson, Morten Krebs, Michael J. Gandal, Michael E. Benros, Thomas Werge, and Anders D. Børglum
Subjects: Male, Genetics of the nervous system, Longitudinal study, Epidemiology, General Physics and Astronomy, Comorbidity, Nervous System, Comorbidities, Risk Factors, Genetics research, Longitudinal Studies, Prospective Studies, Registries, Family history, Medical diagnosis, Child, Multidisciplinary, Substance Abuse, Serious Mental Illness, Substance abuse, Mental Health, Schizophrenia, language, Female, Patient Safety, Sequence Analysis, Clinical psychology, Adult, Adolescent, Substance-Related Disorders, Science, Article, General Biochemistry, Genetics and Molecular Biology, Danish, Young Adult, Clinical Research, mental disorders, medicine, Humans, business.industry, General Chemistry, medicine.disease, language.human_language, Brain Disorders, Good Health and Well Being, Multivariate Analysis, Etiology, Morbidity, business
Abstract: Schizophrenia is a heterogeneous disorder, exhibiting variability in presentation and outcomes that complicate treatment and recovery. To explore this heterogeneity, we leverage the comprehensive Danish health registries to conduct a prospective, longitudinal study from birth of 5432 individuals who would ultimately be diagnosed with schizophrenia, building individual trajectories that represent sequences of comorbid diagnoses, and describing patterns in the individual-level variability. We show that psychiatric comorbidity is prevalent among individuals with schizophrenia (82%) and multi-morbidity occur more frequently in specific, time-ordered pairs. Three latent factors capture 79% of variation in longitudinal comorbidity and broadly relate to the number of co-occurring diagnoses, the presence of child versus adult comorbidities and substance abuse. Clustering of the factor scores revealed five stable clusters of individuals, associated with specific risk factors and outcomes. The presentation and course of schizophrenia may be associated with heterogeneity in etiological factors including family history of mental disorders., Schizophrenia is a complex disorder where individuals experience different symptoms and outcomes that can be captured by patterns in other diagnoses. Here the authors use computational approaches to summarize these patterns and suggest they are associated with genetic and environmental exposure.
Published: 2021
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37. Transcriptomic Insight Into the Polygenic Mechanisms Underlying Psychiatric Disorders

Author: Michael J. Gandal, Minsoo Kim, Gil D. Hoftman, Luis de la Torre-Ubieta, Bogdan Pasaniuc, Jillian R. Haney, and Leanna M. Hernandez
Subjects: 0301 basic medicine, Multifactorial Inheritance, Autism Spectrum Disorder, Autism, Genome-wide association study, Medical and Health Sciences, 0302 clinical medicine, Coexpression, GWAS, 2.1 Biological and endogenous factors, Aetiology, Psychiatry, Brain, Genomics, Biological Sciences, Serious Mental Illness, Penetrance, Mental Health, Autism spectrum disorder, Neurological, Major depressive disorder, Biotechnology, medicine.medical_specialty, 1.1 Normal biological development and functioning, Biology, Article, 03 medical and health sciences, Underpinning research, medicine, Genetics, Humans, Genetic Predisposition to Disease, Transcriptomics, Biological Psychiatry, Genetic association, Depressive Disorder, Major, Depressive Disorder, Human Genome, Psychology and Cognitive Sciences, Neurosciences, Major, medicine.disease, Brain Disorders, 030104 developmental biology, Good Health and Well Being, Expression quantitative trait loci, Schizophrenia, Transcriptome, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract: Over the past decade, large-scale genetic studies have successfully identified hundreds of genetic variants robustly associated with risk for psychiatric disorders. However, mechanistic insight -- and clinical translation -- continues to lag the pace of risk variant identification, hindered by the sheer number of targets, their predominant non-coding localization, as well as pervasive pleiotropy and incomplete penetrance. Successful next steps require identification of ‘causal’ genetic variants and their proximal biological consequences; placing variants within biologically-defined functional contexts, reflecting specific molecular pathways, cell-types, circuits, and developmental windows; and characterizing the downstream, convergent neurobiological impact of polygenicity within an individual. Here, we discuss opportunities and challenges of high-throughput transcriptomic profiling in human brain, and how transcriptomics can help pinpoint mechanisms underlying genetic risk for psychiatric disorders at a scale necessary to tackle daunting levels of polygenicity. These include transcriptome-wide association studies (TWAS) and related approaches for candidate risk gene prioritization through integration of GWAS with expression quantitative trait loci (eQTL). We outline transcriptomic results informing our understanding of the brain-level molecular pathology of psychiatric disorders, including autism (ASD), bipolar disorder (BD), major depression (MDD), and schizophrenia (SCZ). Finally, we discuss systems-level approaches for integration of distinct genetic, genomic and phenotypic levels, including combining spatially-resolved gene expression and human neuroimaging maps. Results highlight the importance of understanding gene expression (dys)regulation across human brain development as a major contributor to psychiatric disease pathogenesis, from common variants acting as expression quantitative trait loci (eQTL) to rare variants enriched for gene expression regulatory pathways.
Published: 2021

38. Broad transcriptomic dysregulation across the cerebral cortex in ASD

Author: Bogdan Pasaniuc, T. Grant Belgard, Sepideh Parhami, Diego de Alba, Neelroop N. Parikshak, Gil D. Hoftman, Gaurav Kale, Ting Jin, Prashant Emani, Ye Emily Wu, Jillian R. Haney, Nathan Chang, Brie Wamsley, Gokul Ramaswami, Daifeng Wang, Mark Gerstein, Vivek Swarup, George T. Chen, Jing Ou, Michael J. Gandal, Christopher Hartl, and Daniel H. Geschwind
Subjects: Gene isoform, medicine.anatomical_structure, Visual cortex, Cerebral cortex, Synaptic plasticity, medicine, Posterior parietal cortex, Sensory system, Epigenetics, Biology, Neuroscience, Temporal lobe
Abstract: Classically, psychiatric disorders have been considered to lack defining pathology, but recent work has demonstrated consistent disruption at the molecular level, characterized by transcriptomic and epigenetic alterations.1–3 In ASD, upregulation of microglial, astrocyte, and immune signaling genes, downregulation of specific synaptic genes, and attenuation of regional gene expression differences are observed.1,2,4–6 However, whether these changes are limited to the cortical association areas profiled is unknown. Here, we perform RNA-sequencing (RNA-seq) on 725 brain samples spanning 11 distinct cortical areas in 112 ASD cases and neurotypical controls. We identify substantially more genes and isoforms that differentiate ASD from controls than previously observed. These alterations are pervasive and cortex-wide, but vary in magnitude across regions, roughly showing an anterior to posterior gradient, with the strongest signal in visual cortex, followed by parietal cortex and the temporal lobe. We find a notable enrichment of ASD genetic risk variants among cortex-wide downregulated synaptic plasticity genes and upregulated protein folding gene isoforms. Finally, using snRNA-seq, we determine that regional variation in the magnitude of transcriptomic dysregulation reflects changes in cellular proportion and cell-type-specific gene expression, particularly impacting L3/4 excitatory neurons. These results highlight widespread, genetically-driven neuronal dysfunction as a major component of ASD pathology in the cerebral cortex, extending beyond association cortices to involve primary sensory regions.
Published: 2020
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39. Full-length transcript sequencing of human and mouse identifies widespread isoform diversity and alternative splicing in the cerebral cortex

Author: Elizabeth Tseng, P. O‘Neill, Eilis Hannon, Michael J. Gandal, Leonard S. Schalkwyk, Zeshan Ahmed, Aaron R. Jeffries, Shyam Prabhakar, Isabel Castanho, J. Mill, Karen M Moore, Nicholas John Bray, Emma Dempster, Sk. Leung, Jonathan P. Davies, and David A. Collier
Subjects: Gene isoform, Regulation of gene expression, Messenger RNA, Transcription (biology), Alternative splicing, Intron, RNA, Computational biology, Biology, Gene
Abstract: Alternative splicing is a post-transcriptional regulatory mechanism producing multiple distinct mRNA molecules from a single pre-mRNA. Alternative splicing has a prominent role in the central nervous system, impacting neurodevelopment and various neuronal functions as well as being increasingly implicated in brain disorders including autism, schizophrenia and Alzheimer’s disease. Standard short-read RNA-Seq approaches only sequence fragments of the mRNA molecule, making it difficult to accurately characterize the true nature of RNA isoform diversity. In this study, we used long-read isoform sequencing (Iso-Seq) to generate full-length cDNA sequences and map transcript diversity in the human and mouse cerebral cortex. We identify widespread RNA isoform diversity amongst expressed genes in the cortex, including many novel transcripts not present in existing genome annotations. Alternative splicing events were found to make a major contribution to RNA isoform diversity in the cortex, with intron retention being a relatively common event associated with nonsense-mediated decay and reduced transcript expression. Of note, we found evidence for transcription from novel (unannotated genes) and fusion events between neighbouring genes. Although global patterns of RNA isoform diversity were found to be generally similar between human and mouse cortex, we identified some notable exceptions. We also identified striking developmental changes in transcript diversity, with differential transcript usage between human adult and fetal cerebral cortex. Finally, we found evidence for extensive isoform diversity in genes associated with autism, schizophrenia and Alzheimer’s disease. Our data confirm the importance of alternative splicing in the cerebral cortex, dramatically increasing transcriptional diversity and representing an important mechanism underpinning gene regulation in the brain. We provide this transcript level data as a resource to the scientific community.
Published: 2020
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40. Decoupling sleep and brain size in childhood: An investigation of genetic covariation in the ABCD study

Author: Andrew J. Fuligni, Minsoo Kim, Chun Chieh Fan, Wesley Thompson, Susan Y. Bookheimer, Cristian Hernandez, Leanna M. Hernandez, Adriana Galván, Mirella Dapretto, and Michael J. Gandal
Subjects: Sleep disorder, business.industry, Context (language use), Genome-wide association study, medicine.disease, Genetic architecture, Arousal, Insomnia, Medicine, medicine.symptom, business, Somnolence, Clinical psychology, Genetic association
Abstract: BackgroundChildhood sleep problems are common and among the most frequent and impairing comorbidities of childhood psychiatric disorders. However, little is known about the genetic architecture of childhood sleep and potential etiological links between sleep, brain morphology, and pediatric-onset psychiatric symptoms.MethodsUsing data from the Adolescent Brain and Cognitive Development Study (NPhenotype=4,428 for discovery/replication, NGenetics=4,728, age: 9-10), we assessed phenotypic relationships, heritability, and genetic correlation between childhood sleep disturbances (SDs: insomnia, arousal, breathing, somnolence, hyperhidrosis, sleep-wake transitions), brain size (surface area [SA], cortical thickness, volume), and dimensional psychopathology.ResultsSDs showed widespread positive associations with multiple domains of childhood psychopathology; however, only insomnia showed replicable associations with smaller brain SA. Among the SDs assessed, only insomnia showed significant SNP-based heritability (h2SNP=0.15, prG’s>0.80, p’sConclusionsThese findings demonstrate a distinct genetic architecture underlying childhood insomnia and brain size and indicate that childhood insomnia should be considered along the dimensional axis of externalizing traits. Uncovering shared and unique genetic risk across childhood traits may inform our understanding of the developmental origins of comorbid psychiatric disorders.
Published: 2020
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41. Maternal immune activation during pregnancy alters early neurobehavioral development in nonhuman primate offspring

Author: Casey E. Hogrefe, Roza M. Vlasova, Amy M. Ryan, Michael J. Gandal, Judy Van de Water, Takeshi Murai, David G. Amaral, Richard J. Maddock, A. Kimberley McAllister, Douglas J. Rowland, Cameron S. Carter, Ana-Maria Iosif, Cynthia M. Schumann, Melissa D. Bauman, Martin Styner, Jeffrey Bennett, Daniel H. Geschwind, and Tyler A. Lesh
Subjects: Pregnancy, Immune system, business.industry, Offspring, medicine, Gestation, Physiology, Neuropathology, medicine.disease, business, Pathophysiology, Sickness behavior, Proinflammatory cytokine
Abstract: BackgroundHuman epidemiologic studies have implicated exposure to infectious or inflammatory insults during gestation in the etiology of neurodevelopmental disorders. Rodent models of maternal immune activation (MIA) have identified the maternal immune response as the critical link between maternal infection and aberrant brain and behavior development in offspring. The nonhuman primate MIA model provides an opportunity to maximize the translational utility of this model in a species more closely related to humans.MethodsHere we evaluate the effects of MIA on brain and behavioral development in the rhesus monkey (Macaca mulatta). A modified form of the viral mimic, Polyinosinic-polycytidylic acid (PolyIC), was delivered to pregnant rhesus monkeys (n=14) in the late first trimester to stimulate a maternal immune response. Control dams received saline injections at the same gestational time points (n=10) or were untreated (n=4).ResultsMIA-treated dams exhibited a strong immune response as indexed by transient increases in sickness behavior, temperature and inflammatory cytokines. MIA-exposed offspring developed species typical milestones and demonstrate subtle changes in early in social development. However, magnetic resonance imaging demonstrated significant gray matter volume reductions in prefrontal and frontal cortices at 6, 12 and 24 months of age.ConclusionsThese findings provide new insights into the emergence of neuropathology in MIA-exposed primates and have implications for the pathophysiology of human psychiatric disorders associated with maternal gestational infection.
Published: 2020
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42. Brain gene co-expression networks link complement signaling with convergent synaptic pathology in schizophrenia

Author: Jillian R. Haney, Leanna M. Hernandez, Laura Pérez-Cano, Michael J. Gandal, Luis de la Torre-Ubieta, Pan Zhang, Minsoo Kim, Loes M. Olde Loohuis, and Lee-kai Wang
Subjects: 0301 basic medicine, Male, Gene Expression, Pathogenesis, Transcriptome, 0302 clinical medicine, Gene expression, Databases, Genetic, 2.1 Biological and endogenous factors, Psychology, Gene Regulatory Networks, Aetiology, 0303 health sciences, General Neuroscience, Brain, Human brain, Serious Mental Illness, Complement (complexity), Mental Health, medicine.anatomical_structure, Schizophrenia, Neurological, Cognitive Sciences, Female, Biotechnology, Signal Transduction, Biology, Article, Databases, 03 medical and health sciences, Genetic, Genetics, medicine, Humans, Genetic Predisposition to Disease, Gene, 030304 developmental biology, Retrospective Studies, Neurology & Neurosurgery, Human Genome, Neurosciences, C4A, medicine.disease, Brain Disorders, Complement system, 030104 developmental biology, Synapses, Neuroscience, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract: The most significant common variant association for schizophrenia (SCZ) reflects increased expression of the complement component 4A (C4A). Yet, it remains unclear how C4A interacts with other SCZ risk genes and whether the complement system is more broadly implicated in SCZ pathogenesis. Here, we integrate several existing, large-scale genetic and transcriptomic datasets to interrogate the functional role of the complement system and C4A in the human brain. Surprisingly, we find no significant genetic enrichment among known complement system genes for SCZ. Conversely, brain co-expression network analyses using C4A as a seed gene revealed that genes down-regulated when C4A expression increased exhibit strong and specific genetic enrichment for SCZ risk. This convergent genomic signal reflected neuronal, synaptic processes and was sexually dimorphic and most prominent in frontal cortical brain regions. Overall, these results indicate that synaptic pathways—rather than the complement system—are the driving force conferring SCZ risk.
Published: 2020

43. A Robust Method Uncovers Significant Context-Specific Heritability in Diverse Complex Traits

Author: Jonathan Flint, Khiem Van Nguyen, Na Cai, Michael J. Gandal, Andrew Dahl, and Noah Zaitlen
Subjects: Male, Multifactorial Inheritance, Computer science, disease subtypes, heritability, Medical and Health Sciences, genetic heterogeneity, 0302 clinical medicine, Models, False positive paradox, Phenomics, Genetics (clinical), Genetics & Heredity, 0303 health sciences, Mental Disorders, Middle Aged, Biological Sciences, Phenotype, Context specific, Female, Functional genomics, heteroskedasticity, Biotechnology, Mixed model, Genetic Markers, Adult, psychiatric disease, Computational biology, Article, GxE, 03 medical and health sciences, Genetic, Genetics, Animals, Humans, Computer Simulation, 030304 developmental biology, Models, Genetic, fungi, Human Genome, Heritability, Precision medicine, Rats, Range (mathematics), Good Health and Well Being, Sample size determination, Gene-Environment Interaction, Generic health relevance, G-E correlation, linear mixed model, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract: Gene-environment interactions (GxE) can be fundamental in applications ranging from functional genomics to precision medicine and is a conjectured source of substantial heritability. However, unbiased methods to profile GxE genome-wide are nascent and, as we show, cannot accommodate general environment variables, modest sample sizes, heterogeneous noise, and binary traits. To address this gap, we propose a simple, unifying mixed model for gene-environment interaction (GxEMM). In simulations and theory, we show that GxEMM can dramatically improve estimates and eliminate false positives when the assumptions of existing methods fail. We apply GxEMM to a range of human and model organism datasets and find broad evidence of context-specific genetic effects, including GxSex, GxAdversity, and GxDisease interactions across thousands of clinical and molecular phenotypes. Overall, GxEMM is broadly applicable for testing and quantifying polygenic interactions, which can be useful for explaining heritability and invaluable for determining biologically relevant environments.
Published: 2020

44. Synaptic and Gene Regulatory Mechanisms in Schizophrenia, Autism, and 22q11.2 Copy Number Variant-Mediated Risk for Neuropsychiatric Disorders

Author: Giovanni Coppola, Daniel Nachun, Daniel H. Geschwind, Carrie E. Bearden, Jennifer K. Forsyth, Ariana Anderson, and Michael J. Gandal
Subjects: 0301 basic medicine, Autism Spectrum Disorder, Autism, Medical and Health Sciences, 0302 clinical medicine, 2.1 Biological and endogenous factors, Copy-number variation, Aetiology, Regulation of gene expression, Genetics, Pediatric, Psychiatry, biology, RNA-Binding Proteins, Functional genomics, Biological Sciences, Serious Mental Illness, Brain development, Mental Health, Autism spectrum disorder, Biotechnology, DNA Copy Number Variations, DGCR8, Intellectual and Developmental Disabilities (IDD), Locus (genetics), 03 medical and health sciences, mental disorders, medicine, Humans, Autistic Disorder, Gene, Biological Psychiatry, Genetic risk, Prevention, Human Genome, Psychology and Cognitive Sciences, Neurosciences, medicine.disease, Brain Disorders, MicroRNAs, 030104 developmental biology, Good Health and Well Being, biology.protein, Schizophrenia, 22q11.2 copy number variants, 030217 neurology & neurosurgery, Genome-Wide Association Study
Abstract: Background 22q11.2 copy number variants are among the most highly penetrant genetic risk variants for developmental neuropsychiatric disorders such as schizophrenia (SCZ) and autism spectrum disorder (ASD). However, the specific mechanisms through which they confer risk remain unclear. Methods Using a functional genomics approach, we integrated transcriptomic data from the developing human brain, genome-wide association findings for SCZ and ASD, protein interaction data, and gene expression signatures from SCZ and ASD postmortem cortex to 1) organize genes into the developmental cellular and molecular systems within which they operate, 2) identify neurodevelopmental processes associated with polygenic risk for SCZ and ASD across the allelic frequency spectrum, and 3) elucidate pathways and individual genes through which 22q11.2 copy number variants may confer risk for each disorder. Results Polygenic risk for SCZ and ASD converged on partially overlapping neurodevelopmental modules involved in synaptic function and transcriptional regulation, with ASD risk variants additionally enriched for modules involved in neuronal differentiation during fetal development. The 22q11.2 locus formed a large protein network during development that disproportionately affected SCZ-associated and ASD-associated neurodevelopmental modules, including loading highly onto synaptic and gene regulatory pathways. SEPT5, PI4KA, and SNAP29 genes are candidate drivers of 22q11.2 synaptic pathology relevant to SCZ and ASD, and DGCR8 and HIRA are candidate drivers of disease-relevant alterations in gene regulation. Conclusions This approach offers a powerful framework to identify neurodevelopmental processes affected by diverse risk variants for SCZ and ASD and elucidate mechanisms through which highly penetrant, multigene copy number variants contribute to disease risk.
Published: 2020

45. TGFβ superfamily signaling regulates the state of human stem cell pluripotency and competency to create telencephalic organoids

Author: Jessie E. Buth, Osvaldo A. Miranda, Shan Sabri, Amanda J. Collier, Kathrin Plath, Jillian R. Haney, Neda Vishlaghi, Felix Turcios, Amander T. Clark, Heather R. Christofk, Di Chen, Michael J. Gandal, Bennett G. Novitch, Wen Gu, and Momoko Watanabe
Subjects: Transcriptome, medicine.anatomical_structure, Cell, medicine, Organoid, Human brain, Biology, Signal transduction, Stem cell, Induced pluripotent stem cell, Tgfβ superfamily, Cell biology
Abstract: SUMMARYTelencephalic organoids generated from human pluripotent stem cells (hPSCs) are emerging as an effective system to study the distinct features of the developing human brain and the underlying causes of many neurological disorders. While progress in organoid technology has been steadily advancing, many challenges remain including rampant batch-to-batch and cell line-to-cell line variability and irreproducibility. Here, we demonstrate that a major contributor to successful cortical organoid production is the manner in which hPSCs are maintained prior to differentiation. Optimal results were achieved using fibroblast-feeder-supported hPSCs compared to feeder-independent cells, related to differences in their transcriptomic states. Feeder-supported hPSCs display elevated activation of diverse TGFβ superfamily signaling pathways and increased expression of genes associated with naïve pluripotency. We further identify combinations of TGFβ-related growth factors that are necessary and together sufficient to impart broad telencephalic organoid competency to feeder-free hPSCs and enable reproducible formation of brain structures suitable for disease modeling.HIGHLIGHTShPSC maintenance conditions influence outcomes in cortical organoid formationIdentification of an intermediate pluripotency state optimal for cortical organoidsFeeder support involves activation of diverse TGFβ signaling pathwaysThe organoid-promoting effects of feeders can be mimicked by a TGFβ factor mixture
Published: 2019
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46. Full-length transcript sequencing of human and mouse cerebral cortex identifies widespread isoform diversity and alternative splicing

Author: Paul O'Neill, Michael J. Gandal, Aaron R. Jeffries, Szi Kay Leung, Jonathan Mill, Connor Jops, Zeshan Ahmed, Emma Dempster, Nicholas John Bray, Shyam Prabhakar, Karen Moore, Jonathan P. Davies, Elizabeth Tseng, David A. Collier, Gloria M. Sheynkman, Ben T. Jordan, Erin D. Jeffery, Eilis Hannon, Isabel Castanho, and Leonard C. Schalkwyk
Subjects: Resource, Gene isoform, QH301-705.5, Gene Expression, Computational biology, Biology, Genome, General Biochemistry, Genetics and Molecular Biology, Mice, Exon, Cortex (anatomy), RNA Precursors, medicine, Animals, Humans, Protein Isoforms, RNA, Messenger, Biology (General), Gene, Cerebral Cortex, Regulation of gene expression, Messenger RNA, Sequence Analysis, RNA, Gene Expression Profiling, Alternative splicing, Brain, High-Throughput Nucleotide Sequencing, Exons, isoform, transcript, expression, brain, cortex, mouse, human, adult, fetal, long-read sequencing, alternative splicing, Alternative Splicing, medicine.anatomical_structure, RNA Splice Sites, Transcriptome
Abstract: Summary Alternative splicing is a post-transcriptional regulatory mechanism producing distinct mRNA molecules from a single pre-mRNA with a prominent role in the development and function of the central nervous system. We used long-read isoform sequencing to generate full-length transcript sequences in the human and mouse cortex. We identify novel transcripts not present in existing genome annotations, including transcripts mapping to putative novel (unannotated) genes and fusion transcripts incorporating exons from multiple genes. Global patterns of transcript diversity are similar between human and mouse cortex, although certain genes are characterized by striking differences between species. We also identify developmental changes in alternative splicing, with differential transcript usage between human fetal and adult cortex. Our data confirm the importance of alternative splicing in the cortex, dramatically increasing transcriptional diversity and representing an important mechanism underpinning gene regulation in the brain. We provide transcript-level data for human and mouse cortex as a resource to the scientific community., Graphical abstract, Highlights • There is widespread transcript diversity in the cortex and many novel transcripts • Some genes display big differences in isoform number between human and mouse cortex • There is evidence of differential transcript usage between human fetal and adult cortex • There are many novel isoforms of genes associated with human brain disease, Leung et al. use long-read sequencing to annotate RNA isoforms in the human and mouse cortex. They identify novel transcripts and evidence for differential transcript usage between the fetal and adult cortex. Their data confirm the importance of alternative splicing as a mechanism underpinning gene regulation in the brain.
Published: 2021
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47. 31. GENETIC CONTROL OF DECONVOLVED BRAIN CELL-TYPES

Author: Alice Franklin, Chloe X. Yap, Jonathan Mill, Arjun Bhattacharya, Michael J. Gandal, Dorothea Seiler Vellame, and Chongyuan Luo
Subjects: Pharmacology, Psychiatry and Mental health, Neurology, Pharmacology (medical), Neurology (clinical), Biology, Brain Cell, Neuroscience, Biological Psychiatry
Published: 2021
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48. Quantum Computing at the Frontiers of Biological Sciences

Author: Jonathan Warrell, Stamatios N. Sotiropoulos, Michael J. Gandal, Geetha Senthil, Justin T. Baker, Stefan Bekiranov, Jacob M. Taylor, Alán Aspuru-Guzik, Thomas Lehner, Matteo Bastiani, Aram W. Harrow, John D. Murray, Michael J. McConnell, Alan Anticevic, Prashant Emani, Guillermo Sapiro, and Mark Gerstein
Subjects: Big Data, Theoretical computer science, Scale (ratio), Computer science, FOS: Physical sciences, Neuroimaging, Biochemistry, Computing Methodologies, Quantitative Biology - Quantitative Methods, Biological Science Disciplines, Article, 03 medical and health sciences, Genetics, Humans, Quantitative Biology - Genomics, Molecular Biology, Quantum, Biological sciences, Quantitative Methods (q-bio.QM), 030304 developmental biology, Quantum computer, Genomics (q-bio.GN), 0303 health sciences, Quantum Physics, Computers, Cell Biology, Genomics, FOS: Biological sciences, Quantitative Biology - Neurons and Cognition, Quantum Theory, Neurons and Cognition (q-bio.NC), Nervous System Diseases, Quantum Physics (quant-ph), Sequence Analysis, Algorithms, Biotechnology
Abstract: The search for meaningful structure in biological data has relied on cutting-edge advances in computational technology and data science methods. However, challenges arise as we push the limits of scale and complexity in biological problems. Innovation in massively parallel, classical computing hardware and algorithms continues to address many of these challenges, but there is a need to simultaneously consider new paradigms to circumvent current barriers to processing speed. Accordingly, we articulate a view towards quantum computation and quantum information science, where algorithms have demonstrated potential polynomial and exponential computational speedups in certain applications, such as machine learning. The maturation of the field of quantum computing, in hardware and algorithm development, also coincides with the growth of several collaborative efforts to address questions across length and time scales, and scientific disciplines. We use this coincidence to explore the potential for quantum computing to aid in one such endeavor: the merging of insights from genetics, genomics, neuroimaging and behavioral phenotyping. By examining joint opportunities for computational innovation across fields, we highlight the need for a common language between biological data analysis and quantum computing. Ultimately, we consider current and future prospects for the employment of quantum computing algorithms in the biological sciences., 22 pages, 3 figures, Perspective
Published: 2019

49. Identification of neural oscillations and epileptiform changes in human brain organoids

Author: Thomas F. Allison, Jessie E. Buth, Simon Mitchell, Istvan Mody, William E. Lowry, Kathrin Plath, Jack M. Parent, Osvaldo A. Miranda, Arinnae Kurdian, Michael J. Gandal, Isabella Ferando, Ranmal A. Samarasinghe, Peyman Golshani, Namie N. Fotion, Bennett G. Novitch, and Momoko Watanabe
Subjects: 0303 health sciences, Human brain, Biology, Network formation, MECP2, Transcriptome, 03 medical and health sciences, 0302 clinical medicine, medicine.anatomical_structure, Extracellular, Organoid, medicine, Identification (biology), Abnormality, Neuroscience, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract: Brain organoids represent a powerful tool for the study of human neurological diseases, particularly those impacting brain growth and structure. However, many diseases manifest with clear evidence of physiological and network abnormality in the absence of anatomical changes. This raises the question of whether organoids possess sufficient neural network complexity to model these conditions. Here, we explore the network level functions of brain organoids using calcium sensor imaging and extracellular recording approaches that together reveal the existence of complex network behaviors reminiscent of intact brain preparations. We demonstrate highly abnormal and epileptiform-like activity in organoids derived from MECP2 mutant patients compared to isogenic controls accompanied by modest transcriptomic differences revealed by single cell analyses. We also rescue key physiological activities with an unconventional neuromodulatory drug, Pifithrin-α. Together, these findings provide an essential foundation for the utilization of brain organoids to study intact and disordered human brain network formation and illustrate their utility in therapeutic discovery.
Published: 2019
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50. Inherited and De Novo Genetic Risk for Autism Impacts Shared Networks

Author: Jin Xu, Chanpreet Singh, Kelley Paskov, Olivia Leventhal, Jae-Yoon Jung, Christopher Hartl, Damon Polioudakis, Lee-kai Wang, Virpi Leppa, David A. Prober, Michael J. Gandal, Elizabeth K. Ruzzo, Dennis P. Wall, Daniel H. Geschwind, Jennifer K. Lowe, Jackson N Hoekstra, Dorna Kashef-Haghighi, Nate Tyler Stockham, and Laura Pérez-Cano
Subjects: Male, Autism Spectrum Disorder, Inheritance Patterns, Medical and Health Sciences, Machine Learning, 0302 clinical medicine, multiplex families, Risk Factors, Databases, Genetic, genetics, Protein Interaction Maps, Child, Promoter Regions, Genetic, Zebrafish, Genetics, 0303 health sciences, Biological Sciences, Phenotype, Pedigree, machine learning, Autism spectrum disorder, symbols, Female, de novo, autism, Biology, ASD, General Biochemistry, Genetics and Molecular Biology, Article, Nuclear Family, 03 medical and health sciences, symbols.namesake, Interaction network, mental disorders, medicine, Animals, Humans, Genetic Predisposition to Disease, Gene, 030304 developmental biology, Whole Genome Sequencing, Tumor Suppressor Proteins, Promoter, medicine.disease, biology.organism_classification, inherited, Disease Models, Animal, Bonferroni correction, Receptors, Mineralocorticoid, Autism, Guanylate Kinases, 030217 neurology & neurosurgery, Gene Deletion, Developmental Biology
Abstract: We performed a comprehensive assessment of rare inherited variation in autism spectrum disorder (ASD) by analyzing whole-genome sequences of 2,308 individuals from families with multiple affected children. We implicate 69 genes in ASD risk, including 24 passing genome-wide Bonferroni correction and 16 new ASD risk genes, most supported by rare inherited variants, a substantial extension of previous findings. Biological pathways enriched for genes harboring inherited variants represent cytoskeletal organization and ion transport, which are distinct from pathways implicated in previous studies. Nevertheless, the de novo and inherited genes contribute to a common protein-protein interaction network. We also identified structural variants (SVs) affecting non-coding regions, implicating recurrent deletions in the promoters of DLG2 and NR3C2. Loss of nr3c2 function in zebrafish disrupts sleep and social function, overlapping with human ASD-related phenotypes. These data support the utility of studying multiplex families in ASD and are available through the Hartwell Autism Research and Technology portal.
Published: 2019

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