Absence of evidence for increase in risk for autism or attention-deficit hyperactivity disorder following antidepressant exposure during pregnancy: a replication study
VM Castro, SW Kong, CC Clements, R Brady, AJ Kaimal, AE Doyle, EB Robinson, SE Churchill, IS Kohane, and RH Perlis. 2016. “Absence of evidence for increase in risk for autism or attention-deficit hyperactivity disorder following antidepressant exposure during pregnancy: a replication study.” Transl Psychiatry, 6, Pp. e708.Abstract
Multiple studies have examined the risk of prenatal antidepressant exposure and risk for autism spectrum disorder (ASD) or attention-deficit hyperactivity disorder (ADHD), with inconsistent results. Precisely estimating such risk, if any, is of great importance in light of the need to balance such risk with the benefit of depression and anxiety treatment. We developed a method to integrate data from multiple New England health systems, matching offspring and maternal health data in electronic health records to characterize diagnoses and medication exposure. Children with ASD or ADHD were matched 1:3 with children without neurodevelopmental disorders. Association between maternal antidepressant exposure and ASD or ADHD liability was examined using logistic regression, adjusting for potential sociodemographic and psychiatric confounding variables. In new cohorts of 1245 ASD cases and 1701 ADHD cases, along with age-, sex- and socioeconomic status matched controls, neither disorder was significantly associated with prenatal antidepressant exposure in crude or adjusted models (adjusted odds ratio 0.90, 95% confidence interval 0.50-1.54 for ASD; 0.97, 95% confidence interval 0.53-1.69 for ADHD). Pre-pregnancy antidepressant exposure significantly increased risk for both disorders. These results suggest that prior reports of association between prenatal antidepressant exposure and neurodevelopmental disease are likely to represent a false-positive finding, which may arise in part through confounding by indication. They further demonstrate the potential to integrate data across electronic health records studies spanning multiple health systems to enable efficient pharmacovigilance investigation.
Advancing drug discovery for neuropsychiatric disorders using patient-specific stem cell models
Stephen J Haggarty, Catarina M Silva, Alan Cross, Nicholas J Brandon, and Roy H Perlis. 2016. “Advancing drug discovery for neuropsychiatric disorders using patient-specific stem cell models.” Mol Cell Neurosci, 73, Pp. 104-15.Abstract
Compelling clinical, social, and economic reasons exist to innovate in the process of drug discovery for neuropsychiatric disorders. The use of patient-specific, induced pluripotent stem cells (iPSCs) now affords the ability to generate neuronal cell-based models that recapitulate key aspects of human disease. In the context of neuropsychiatric disorders, where access to physiologically active and relevant cell types of the central nervous system for research is extremely limiting, iPSC-derived in vitro culture of human neurons and glial cells is transformative. Potential applications relevant to early stage drug discovery, include support of quantitative biochemistry, functional genomics, proteomics, and perhaps most notably, high-throughput and high-content chemical screening. While many phenotypes in human iPSC-derived culture systems may prove adaptable to screening formats, addressing the question of which in vitro phenotypes are ultimately relevant to disease pathophysiology and therefore more likely to yield effective pharmacological agents that are disease-modifying treatments requires careful consideration. Here, we review recent examples of studies of neuropsychiatric disorders using human stem cell models where cellular phenotypes linked to disease and functional assays have been reported. We also highlight technical advances using genome-editing technologies in iPSCs to support drug discovery efforts, including the interpretation of the functional significance of rare genetic variants of unknown significance and for the purpose of creating cell type- and pathway-selective functional reporter assays. Additionally, we evaluate the potential of in vitro stem cell models to investigate early events of disease pathogenesis, in an effort to understand the underlying molecular mechanism, including the basis of selective cell-type vulnerability, and the potential to create new cell-based diagnostics to aid in the classification of patients and subsequent selection for clinical trials. A number of key challenges remain, including the scaling of iPSC models to larger cohorts and integration with rich clinicopathological information and translation of phenotypes. Still, the overall use of iPSC-based human cell models with functional cellular and biochemical assays holds promise for supporting the discovery of next-generation neuropharmacological agents for the treatment and ultimately prevention of a range of severe mental illnesses.
Estimation and testing for multiple regulation of multivariate mixed outcomes
Denis Agniel, Katherine P Liao, and Tianxi Cai. 2016. “Estimation and testing for multiple regulation of multivariate mixed outcomes.” Biometrics, 72, 4, Pp. 1194-1205.Abstract
Considerable interest has recently been focused on studying multiple phenotypes simultaneously in both epidemiological and genomic studies, either to capture the multidimensionality of complex disorders or to understand shared etiology of related disorders. We seek to identify multiple regulators or predictors that are associated with multiple outcomes when these outcomes may be measured on very different scales or composed of a mixture of continuous, binary, and not-fully observed elements. We first propose an estimation technique to put all effects on similar scales, and we induce sparsity on the estimated effects. We provide standard asymptotic results for this estimator and show that resampling can be used to quantify uncertainty in finite samples. We finally provide a multiple testing procedure which can be geared specifically to the types of multiple regulators of interest, and we establish that, under standard regularity conditions, the familywise error rate will approach 0 as sample size diverges. Simulation results indicate that our approach can improve over unregularized methods both in reducing bias in estimation and improving power for testing.
Evolution of Osteocrin as an activity-regulated factor in the primate brain
Bulent Ataman, Gabriella L Boulting, David A Harmin, Marty G Yang, Mollie Baker-Salisbury, Ee-Lynn Yap, Athar N Malik, Kevin Mei, Alex A Rubin, Ivo Spiegel, Ershela Durresi, Nikhil Sharma, Linda S Hu, Mihovil Pletikos, Eric C Griffith, Jennifer N Partlow, Christine R Stevens, Mazhar Adli, Maria Chahrour, Nenad Sestan, Christopher A Walsh, Vladimir K Berezovskii, Margaret S Livingstone, and Michael E Greenberg. 2016. “Evolution of Osteocrin as an activity-regulated factor in the primate brain.” Nature, 539, 7628, Pp. 242-247.Abstract
Sensory stimuli drive the maturation and function of the mammalian nervous system in part through the activation of gene expression networks that regulate synapse development and plasticity. These networks have primarily been studied in mice, and it is not known whether there are species- or clade-specific activity-regulated genes that control features of brain development and function. Here we use transcriptional profiling of human fetal brain cultures to identify an activity-dependent secreted factor, Osteocrin (OSTN), that is induced by membrane depolarization of human but not mouse neurons. We find that OSTN has been repurposed in primates through the evolutionary acquisition of DNA regulatory elements that bind the activity-regulated transcription factor MEF2. In addition, we demonstrate that OSTN is expressed in primate neocortex and restricts activity-dependent dendritic growth in human neurons. These findings suggest that, in response to sensory input, OSTN regulates features of neuronal structure and function that are unique to primates.
Genome-wide Association Studies of Posttraumatic Stress Disorder in 2 Cohorts of US Army Soldiers
Murray B Stein, Chia-Yen Chen, Robert J Ursano, Tianxi Cai, Joel Gelernter, Steven G Heeringa, Sonia Jain, Kevin P Jensen, Adam X Maihofer, Colter Mitchell, Caroline M Nievergelt, Matthew K Nock, Benjamin M Neale, Renato Polimanti, Stephan Ripke, Xiaoying Sun, Michael L Thomas, Qian Wang, Erin B Ware, Susan Borja, Ronald C Kessler, Jordan W Smoller, and Army Study Assess Risk Resilience Servicemembers (STARRS) to and in Collaborators. 2016. “Genome-wide Association Studies of Posttraumatic Stress Disorder in 2 Cohorts of US Army Soldiers.” JAMA Psychiatry, 73, 7, Pp. 695-704.Abstract
IMPORTANCE: Posttraumatic stress disorder (PTSD) is a prevalent, serious public health concern, particularly in the military. The identification of genetic risk factors for PTSD may provide important insights into the biological foundation of vulnerability and comorbidity. OBJECTIVE: To discover genetic loci associated with the lifetime risk for PTSD in 2 cohorts from the Army Study to Assess Risk and Resilience in Servicemembers (Army STARRS). DESIGN, SETTING, AND PARTICIPANTS: Two coordinated genome-wide association studies of mental health in the US military contributed participants. The New Soldier Study (NSS) included 3167 unique participants with PTSD and 4607 trauma-exposed control individuals; the Pre/Post Deployment Study (PPDS) included 947 unique participants with PTSD and 4969 trauma-exposed controls. The NSS data were collected from February 1, 2011, to November 30, 2012; the PDDS data, from January 9 to April 30, 2012. The primary analysis compared lifetime DSM-IV PTSD cases with trauma-exposed controls without lifetime PTSD. Data were analyzed from March 18 to December 27, 2015. MAIN OUTCOMES AND MEASURES: Association analyses for PTSD used logistic regression models within each of 3 ancestral groups (European, African, and Latino American) by study, followed by meta-analysis. Heritability and genetic correlation and pleiotropy with other psychiatric and immune-related disorders were estimated. RESULTS: The NSS population was 80.7% male (6277 of 7774 participants; mean [SD] age, 20.9 [3.3] years); the PPDS population, 94.4% male (5583 of 5916 participants; mean [SD] age, 26.5 [6.0] years). A genome-wide significant locus was found in ANKRD55 on chromosome 5 (rs159572; odds ratio [OR], 1.62; 95% CI, 1.37-1.92; P = 2.34 × 10-8) and persisted after adjustment for cumulative trauma exposure (adjusted OR, 1.64; 95% CI, 1.39-1.95; P = 1.18 × 10-8) in the African American samples from the NSS. A genome-wide significant locus was also found in or near ZNF626 on chromosome 19 (rs11085374; OR, 0.77; 95% CI, 0.70-0.85; P = 4.59 × 10-8) in the European American samples from the NSS. Similar results were not found for either single-nucleotide polymorphism in the corresponding ancestry group from the PPDS sample, in other ancestral groups, or in transancestral meta-analyses. Single-nucleotide polymorphism-based heritability was nonsignificant, and no significant genetic correlations were observed between PTSD and 6 mental disorders or 9 immune-related disorders. Significant evidence of pleiotropy was observed between PTSD and rheumatoid arthritis and, to a lesser extent, psoriasis. CONCLUSIONS AND RELEVANCE: In the largest genome-wide association study of PTSD to date, involving a US military sample, limited evidence of association for specific loci was found. Further efforts are needed to replicate the genome-wide significant association with ANKRD55-associated in prior research with several autoimmune and inflammatory disorders-and to clarify the nature of the genetic overlap observed between PTSD and rheumatoid arthritis and psoriasis.
Genomic mapping and cellular expression of human CPG2 transcripts in the SYNE1 gene
Sven Loebrich, Mette Rathje, Emily Hager, Bulent Ataman, David A Harmin, Michael E Greenberg, and Elly Nedivi. 2016. “Genomic mapping and cellular expression of human CPG2 transcripts in the SYNE1 gene.” Mol Cell Neurosci, 71, Pp. 46-55.Abstract
Bipolar disorder (BD) is a prevalent and severe mood disorder characterized by recurrent episodes of mania and depression. Both genetic and environmental factors have been implicated in BD etiology, but the biological underpinnings remain elusive. Recent genome-wide association studies (GWAS) for identifying genes conferring risk for schizophrenia, BD, and major depression, identified an association between single-nucleotide polymorphisms (SNPs) in the SYNE1 gene and increased risk of BD. SYNE1 has also been identified as a risk locus for multiple other neurological or neuromuscular genetic disorders. The BD associated SNPs map within the gene region homologous to part of rat Syne1 encompassing the brain specific transcripts encoding CPG2, a postsynaptic neuronal protein localized to excitatory synapses and an important regulator of glutamate receptor internalization. Here, we use RNA-seq, ChIP-seq and RACE to map the human SYNE1 transcriptome, focusing on the CPG2 locus. We validate several CPG2 transcripts, including ones not previously annotated in public databases, and identify and clone a full-length CPG2 cDNA expressed in human neocortex, hippocampus and striatum. Using lenti-viral gene knock down/replacement and surface receptor internalization assays, we demonstrate that human CPG2 protein localizes to dendritic spines in rat hippocampal neurons and is functionally equivalent to rat CPG2 in regulating glutamate receptor internalization. This study provides a valuable gene-mapping framework for relating multiple genetic disease loci in SYNE1 with their transcripts, and for evaluating the effects of missense SNPs identified by patient genome sequencing on neuronal function.
Identification of 15 genetic loci associated with risk of major depression in individuals of European descent
Craig L Hyde, Michael W Nagle, Chao Tian, Xing Chen, Sara A Paciga, Jens R Wendland, Joyce Y Tung, David A Hinds, Roy H Perlis, and Ashley R Winslow. 2016. “Identification of 15 genetic loci associated with risk of major depression in individuals of European descent.” Nat Genet, 48, 9, Pp. 1031-6.Abstract
Despite strong evidence supporting the heritability of major depressive disorder (MDD), previous genome-wide studies were unable to identify risk loci among individuals of European descent. We used self-report data from 75,607 individuals reporting clinical diagnosis of depression and 231,747 individuals reporting no history of depression through 23andMe and carried out meta-analysis of these results with published MDD genome-wide association study results. We identified five independent variants from four regions associated with self-report of clinical diagnosis or treatment for depression. Loci with a P value <1.0 × 10(-5) in the meta-analysis were further analyzed in a replication data set (45,773 cases and 106,354 controls) from 23andMe. A total of 17 independent SNPs from 15 regions reached genome-wide significance after joint analysis over all three data sets. Some of these loci were also implicated in genome-wide association studies of related psychiatric traits. These studies provide evidence for large-scale consumer genomic data as a powerful and efficient complement to data collected from traditional means of ascertainment for neuropsychiatric disease genomics.
Integrative analysis of genetic data sets reveals a shared innate immune component in autism spectrum disorder and its co-morbidities
Sumaiya Nazeen, Nathan P Palmer, Bonnie Berger, and Isaac S Kohane. 2016. “Integrative analysis of genetic data sets reveals a shared innate immune component in autism spectrum disorder and its co-morbidities.” Genome Biol, 17, 1, Pp. 228.Abstract
BACKGROUND: Autism spectrum disorder (ASD) is a common neurodevelopmental disorder that tends to co-occur with other diseases, including asthma, inflammatory bowel disease, infections, cerebral palsy, dilated cardiomyopathy, muscular dystrophy, and schizophrenia. However, the molecular basis of this co-occurrence, and whether it is due to a shared component that influences both pathophysiology and environmental triggering of illness, has not been elucidated. To address this, we deploy a three-tiered transcriptomic meta-analysis that functions at the gene, pathway, and disease levels across ASD and its co-morbidities. RESULTS: Our analysis reveals a novel shared innate immune component between ASD and all but three of its co-morbidities that were examined. In particular, we find that the Toll-like receptor signaling and the chemokine signaling pathways, which are key pathways in the innate immune response, have the highest shared statistical significance. Moreover, the disease genes that overlap these two innate immunity pathways can be used to classify the cases of ASD and its co-morbidities vs. controls with at least 70 % accuracy. CONCLUSIONS: This finding suggests that a neuropsychiatric condition and the majority of its non-brain-related co-morbidities share a dysregulated signal that serves as not only a common genetic basis for the diseases but also as a link to environmental triggers. It also raises the possibility that treatment and/or prophylaxis used for disorders of innate immunity may be successfully used for ASD patients with immune-related phenotypes.
Kernel machine testing for risk prediction with stratified case cohort studies
Rebecca Payne, Matey Neykov, Majken Karoline Jensen, and Tianxi Cai. 2016. “Kernel machine testing for risk prediction with stratified case cohort studies.” Biometrics, 72, 2, Pp. 372-81.Abstract
Large assembled cohorts with banked biospecimens offer valuable opportunities to identify novel markers for risk prediction. When the outcome of interest is rare, an effective strategy to conserve limited biological resources while maintaining reasonable statistical power is the case cohort (CCH) sampling design, in which expensive markers are measured on a subset of cases and controls. However, the CCH design introduces significant analytical complexity due to outcome-dependent, finite-population sampling. Current methods for analyzing CCH studies focus primarily on the estimation of simple survival models with linear effects; testing and estimation procedures that can efficiently capture complex non-linear marker effects for CCH data remain elusive. In this article, we propose inverse probability weighted (IPW) variance component type tests for identifying important marker sets through a Cox proportional hazards kernel machine (CoxKM) regression framework previously considered for full cohort studies (Cai et al., 2011). The optimal choice of kernel, while vitally important to attain high power, is typically unknown for a given dataset. Thus, we also develop robust testing procedures that adaptively combine information from multiple kernels. The proposed IPW test statistics have complex null distributions that cannot easily be approximated explicitly. Furthermore, due to the correlation induced by CCH sampling, standard resampling methods such as the bootstrap fail to approximate the distribution correctly. We, therefore, propose a novel perturbation resampling scheme that can effectively recover the induced correlation structure. Results from extensive simulation studies suggest that the proposed IPW CoxKM testing procedures work well in finite samples. The proposed methods are further illustrated by application to a Danish CCH study of Apolipoprotein C-III markers on the risk of coronary heart disease.
Robust risk prediction with biomarkers under two-phase stratified cohort design
Rebecca Payne, Ming Yang, Yingye Zheng, Majken K Jensen, and Tianxi Cai. 2016. “Robust risk prediction with biomarkers under two-phase stratified cohort design.” Biometrics, 72, 4, Pp. 1037-1045.Abstract
Identification of novel biomarkers for risk prediction is important for disease prevention and optimal treatment selection. However, studies aiming to discover which biomarkers are useful for risk prediction often require the use of stored biological samples from large assembled cohorts, and thus the depletion of a finite and precious resource. To make efficient use of such stored samples, two-phase sampling designs are often adopted as resource-efficient sampling strategies, especially when the outcome of interest is rare. Existing methods for analyzing data from two-phase studies focus primarily on single marker analysis or fitting the Cox regression model to combine information from multiple markers. However, the Cox model may not fit the data well. Under model misspecification, the composite score derived from the Cox model may not perform well in predicting the outcome. Under a general two-phase stratified cohort sampling design, we present a novel approach to combining multiple markers to optimize prediction by fitting a flexible nonparametric transformation model. Using inverse probability weighting to account for the outcome-dependent sampling, we propose to estimate the model parameters by maximizing an objective function which can be interpreted as a weighted C-statistic for survival outcomes. Regardless of model adequacy, the proposed procedure yields a sensible composite risk score for prediction. A major obstacle for making inference under two phase studies is due to the correlation induced by the finite population sampling, which prevents standard inference procedures such as the bootstrap from being used for variance estimation. We propose a resampling procedure to derive valid confidence intervals for the model parameters and the C-statistic accuracy measure. We illustrate the new methods with simulation studies and an analysis of a two-phase study of high-density lipoprotein cholesterol (HDL-C) subtypes for predicting the risk of coronary heart disease.