CE: Swati; WCO/270209; Total nos of Pages: 8; WCO 270209 REVIEW CURRENT OPINION The developmental transcriptome of the human brain: implications for neurodevelopmental disorders Andrew T.N. Tebbenkampa,Ã, A. Jeremy Willseyb,c,Ã, Matthew W. Statec, and Nenad Sˇestana Purpose of review Recent characterizations of the transcriptome of the developing human brain by several groups have generated comprehensive datasets on coding and noncoding RNAs that will be instrumental for illuminating the underlying biology of complex neurodevelopmental disorders. This review summarizes recent studies successfully utilizing these data to increase our understanding of the molecular mechanisms of pathogenesis. Recent findings Several approaches have successfully integrated developmental transcriptome data with gene discovery to generate testable hypotheses about when and where in the developing human brain disease-associated genes converge. Specifically, these include the projection neurons in the prefrontal and primary motor– somatosensory cortex during mid-fetal development in autism spectrum disorder and the frontal cortex during fetal development in schizophrenia. Summary Developmental transcriptome data is a key to interpreting disease-associated mutations and transcriptional changes. Novel approaches integrating the spatial and temporal dimensions of these data have increased our understanding of when and where disease occurs. Refinement of spatial and temporal properties and expanding these findings to other neurodevelopmental disorders will provide critical insights for understanding disease biology. Keywords autism spectrum disorder, gene co-expression analysis, genetics, psychiatric and neurologic disorders, schizophrenia, Williams syndrome INTRODUCTION human postmortem tissue have shown that the The human brain is an immensely complex bio- intricate features of human brain development logical system, composed of many functionally and organization are reflected in the organization distinct regions, neural circuits, and cell types. Furthermore, its development is a highly complex aDepartment of Neurobiology and Kavli Institute for Neuroscience, and strictly regulated process that transpires over an bDepartment of Genetics, Yale School of Medicine, New Haven, Con- extended period of time, during which changes necticut, and cDepartment of Psychiatry, University of California, San occur at both the structural and functional levels. Francisco, San Francisco, California, USA This process is exquisitely dependent on the appro- Correspondence to Nenad Sˇ estan, Department of Neurobiology, Yale priate expression of intact gene products (RNA and School of Medicine, 333 Cedar St. C-323C, New Haven, Connecticut 06510, USA. Tel: +1 203 737 2190; fax: +1 203 785 5263; e-mail: protein). Mutations that alter gene expression or [email protected]; Matthew W. State, Department of Psychiatry, function can result in or contribute to neurological University of California, San Francisco, San Francisco, CA 94143, USA. and psychiatric conditions ranging from intellectual Tel: +1 415 476 7730; Fax: +1 415 476 7320; email: matthew.state disability to autism spectrum disorder (ASD) and @ucsf.edu schizophrenia (SCZ). ÃA. Tebbenkamp and J. Willsey contributed equally to this work. Recent advances in high-throughput and Curr Opin Neurol 2014, 27:000–000 genome-wide analyses of the transcriptome using DOI:10.1097/WCO.0000000000000069 1350-7540 ß 2014 Wolters Kluwer Health | Lippincott Williams & Wilkins www.co-neurology.com Copyright © Lippincott Williams & Wilkins. Unauthorized reproduction of this article is prohibited. CE: Swati; WCO/270209; Total nos of Pages: 8; WCO 270209 Developmental disorders avenue to dissect the specific molecular under- KEY POINTS pinnings of this specialization and, importantly, Gene expression patterns in the developing human how it may go awry in neurodevelopmental dis- brain are highly dynamic and reflect the underlying orders. Thus, research into the molecular aspects biological processes. of normal human brain development using post- mortem human tissue has created a critical resource Transcriptome studies of human postmortem tissues from for understanding the cause of a range of complex affected and unaffected donors identify candidate mechanisms for abnormal brain development. and poorly understood disorders. In this review, we interpret recent studies of Genetic mutations perturbing neurodevelopmental differential gene expression in patients with psychi- processes are known to result in psychiatric or atric and neurological disorders against the back- neurological disorders. Recent whole-exome studies drop of these comprehensive developmental human have identified variants in genes displaying a much wider array of functional diversity. brain transcriptomes. We then highlight recent studies in which these transcriptome data are inte- Expression patterns of the diverse genes disrupted in grated with genome-wide gene discovery efforts in complex neurodevelopmental disorders in the a spatially and temporally informed analysis to developing human brain give a fresh perspective on the gain deeper insight into manifestations of these dis- underlying biology. orders. and complexity of its transcriptional architecture AUTISM SPECTRUM DISORDERS [1–9]. In particular, the initial comprehensive With regard to protein-coding genes and complex analyses of the human brain transcriptome have neurodevelopmental disease, genes linked to both revealed the remarkable dynamism of coding and syndromic and idiopathic forms of ASD show varied noncoding transcripts during prenatal and early developmental expression trajectories [10–15,16&]. postnatal development of the human brain [1,3,5] For several of the earliest identified genes associated (www.brainspan.org). Furthermore, they have pro- with idiopathic ASD, such as neurexin1 (NRXN1) and vided critical insights into the trajectories of genes neuroligin 4, X-linked (NLGN4X), their expression associated with specific neurodevelopmental proc- increases during late prenatal development and esses (Fig. 1). These studies have demonstrated cor- peaks just after birth in the cerebral cortex, as would relations between gene expression dynamics and be predicted given their function in synapse devel- the morphological and functional specialization opment [9]. Additional insight were gained by per- of brain regions, and consequently provide an forming gene ontology enrichment analysis on the Birth Adolescence Embryonic Fetal Infancy Childhood Adulthood 100 80 Neocortex Cell proliferation 60 Progenitors and immature neurons 40 Synapse development Dendrite development Myelination 20 Gene expression (% of maximum) (% of expression Gene 0 0–8 PCW 8–38 PCW 0–12 M 1–12 Y 12–20 Y 20 Y > Age (log scale) FIGURE 1. Timeline of major human neurodevelopmental processes based on gene expression trajectories. Expression trajectories of genes associated with major neurodevelopmental processes reflect the occurrence and progression of these processes in the human neocortex. The expression levels and trajectories have been adopted from Kang et al. [5]. These trajectories suggest that the prenatal development is the most dynamic phase of the human brain development. PCW, postconceptional weeks; M, months; Y, years. 2 www.co-neurology.com Volume 27 Number 00 Month 2014 Copyright © Lippincott Williams & Wilkins. Unauthorized reproduction of this article is prohibited. CE: Swati; WCO/270209; Total nos of Pages: 8; WCO 270209 Developmental transcriptome of human brain Tebbenkamp et al. group of genes co-expressed with NRXN1, NLGN4X, mouse NCX, only primate transcripts have gained and other ASD-related genes expressed during a sequence motif for binding to FMRP that enables normal human brain development. This analysis efficient translation in a subset of cortical projec- assesses the gene ontology terms (biological descrip- tion neurons [21]. NOS1 protein levels are dramatic- tors) for each gene in the group and determines ally reduced in postmortem developing human whether there is statistically significant recurrence fragile X NCX, but not in mouse disease models of gene ontology terms among the genes in the (i.e., FMRP-deficient mouse). These findings suggest group, with enrichment indicating shared biology a novel etiological mechanism for intellectual dis- between the genes. Here, gene ontology enrichment ability and ASD via nitric oxide signaling, and analysis identified enrichment of categories such as identify specific cell types and developing neural ‘phosphoprotein,’ ‘synapse,’ and ’neuron projec- circuits affected in fragile X syndrome [21]. In addi- tion’ [5]. However, for other genes associated with tion, this study illustrates why it is important to idiopathic forms of ASD, their expression patterns study species-specific aspects of brain development and cellular localizations are less informative with and how this can lead to a better understanding of respect to their role(s) in normal or abnormal brain neural circuit dysfunctions in human cognitive dis- development. orders. One strategy for addressing the lack of immedi- Viable alternatives to postmortem human brain ately obvious mechanistic insights emerging from tissue analysis may be cell lines and induced pluri- gene discovery efforts is to analyze global changes in potent (iPS) cells derived from patients diagnosed gene expression, comparing primary affected versus with ASD [22]. In one recent example, investigators unaffected brain tissue. The first