Maternal immune activation dysregulation of the fetal brain transcriptome and relevance to the pathophysiology of autism spectrum disorder

OPEN Molecular Psychiatry (2018) 23, 1001–1013 www.nature.com/mp ORIGINAL ARTICLE Maternal immune activation dysregulation of the fetal brain transcriptome and relevance to the pathophysiology of autism spectrum disorder MV Lombardo1,2,5, HM Moon3, J Su3, TD Palmer3, E Courchesne4 and T Pramparo4,5 Maternal immune activation (MIA) via infection during pregnancy is known to increase risk for autism spectrum disorder (ASD). However, it is unclear how MIA disrupts fetal brain gene expression in ways that may explain this increased risk. Here we examine how MIA dysregulates rat fetal brain gene expression (at a time point analogous to the end of the first trimester of human gestation) in ways relevant to ASD-associated pathophysiology. MIA downregulates expression of ASD-associated genes, with the largest enrichments in genes known to harbor rare highly penetrant mutations. MIA also downregulates expression of many genes also known to be persistently downregulated in the ASD cortex later in life and which are canonically known for roles in affecting prenatally late developmental processes at the synapse. Transcriptional and translational programs that are downstream targets of highly ASD-penetrant FMR1 and CHD8 genes are also heavily affected by MIA. MIA strongly upregulates expression of a large number of genes involved in translation initiation, cell cycle, DNA damage and proteolysis processes that affect multiple key neural developmental functions. Upregulation of translation initiation is common to and preserved in gene network structure with the ASD cortical transcriptome throughout life and has downstream impact on cell cycle processes. The cap-dependent translation initiation gene, EIF4E, is one of the most MIA-dysregulated of all ASD-associated genes and targeted network analyses demonstrate prominent MIA-induced transcriptional dysregulation of mTOR and EIF4E-dependent signaling. This dysregulation of translation initiation via alteration of the Tsc2–mTor–Eif4e axis was further validated across MIA rodent models. MIA may confer increased risk for ASD by dysregulating key aspects of fetal brain gene expression that are highly relevant to pathophysiology affecting ASD. Molecular Psychiatry (2018) 23, 1001–1013; doi:10.1038/mp.2017.15; published online 21 March 2017 INTRODUCTION Multiple etiological pathways contribute to increased risk for autism spectrum disorder (ASD). For example, many monogenic syndromes and other rare de novo variants have been identified that have high penetrance for ASD,1–5 with theoretically many others that have yet to be discovered.6 Interestingly, such rare high-confidence mutations tend to be significantly enriched in genes involved in synaptic functions, transcriptional regulation, and chromatin remodeling functions, and/or are downstream targets of the fragile X syndrome protein (FMRP) complex.1,3 In contrast, common variants may also significantly contribute to a large proportion (up to 60%) of genetic liability for ASD,7,8 suggesting that hundreds of genes, individually associated with a small risk, may underlie ASD etiology via a much larger collective effect that acts at the network level either alone or in combination with environmental factors. Supporting this model, evidence from twin studies suggest that while heritability is quite high,9 there is also a substantial environmental component for ASD susceptibility.10 Recent evidence11–20 has also catalyzed the concept that genetic and non-genetic factors and their interaction, may act at very early periods of fetal brain development and potentially alter protein or gene expression regulation leading to shared pathways for complex ASD-related phenotypes. Thus, much can be learned about the biological processes and molecular mechanisms involved in ASD by modeling environmental risk factors and studying their effects on functional genomics during early developmental stages of fetal brain development. One environmental fetal programming21,22 factor known to alter early fetal brain development and increase the risk for ASD is maternal infection during pregnancy.17–19,23–26 The effects of prenatal maternal infection on fetal brain development can be studied with maternal immune activation (MIA) animal models.27–30 MIA can be induced experimentally via immunogens, such as polyinosinic-polycytidylic acid (poly(I:C)) and lipopolysaccharide (LPS). Poly(I:C) attempts to mimic viral-like infections via toll-like receptor 3 (TLR3) signaling, which induces production of type I interferons (IFN-α and IFN-β). In contrast, LPS mimics bacterial-like infections via TLR4 signaling which stimulates downstream production and secretion of TNF-α from innate immune cells (e.g., macrophages).30 Both poly(I:C) and LPS affect maternal cytokine signaling (e.g., interleukin-6) that passes through the placenta to affect fetal brain development31 and blocking key pathways prevents MIA-induced neural and behavioral abnormalities in ASD model systems.32 The consequences of MIA include behavioral deficits of broad relevance to ASD33–35 as 1 Center for Applied Neuroscience, Department of Psychology, University of Cyprus, Nicosia, Cyprus; 2Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK; 3Department of Neurosurgery, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA and 4Department of Neuroscience, University of California, San Diego, San Diego, CA, USA. Correspondence: Dr MV Lombardo or Dr T Pramparo, Neuroscience University of California, San Diego, 8110 La Jolla Shores Drive Suite 201, La Jolla, CA 92093, USA. E-mail: or 5 These two authors contributed equally to this work. Received 19 July 2016; revised 31 December 2016; accepted 9 January 2017; published online 21 March 2017 MIA dysregulation and ASD MV Lombardo et al 1002 well as numerous ASD-relevant influences on the developing brain.36 These influences include upregulation of cell cycle gene expression31 and shortening of cell cycle as seen in ASD,37 overproduction of neurons38 analogous to some cases of ASD,14 increased cortical thickness,38 increased brain size39 as seen in many ASD toddlers,40,41 altered expression of genes involved in neuronal migration,31 cortical layering defects42 including focal patches of disorganized cortex32 analogous to reports in some ASD cases,11 decreased intrinsic excitability of neurons,43 microglia abnormalities and enhanced microglia priming39,44 as seen in ASD,45–47 alteration of GABAergic signaling,48 cerebellar vermis defects49 and defects of prefrontal dendritic morphology.50 Despite the numerous links between MIA and ASD pathology, several key questions remain with regard to how MIA affects the developing fetal brain at genomic and epigenomic levels and how such influence maps onto known genetic risk mechanisms associated with ASD. For example, does MIA exert its influence via genes associated with ASD and if so, which classes o (...truncated)