HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author Nat Neurosci Manuscript Author . Author manuscript; Manuscript Author available in PMC 2019 June 17. Published in final edited form as: Nat Neurosci. 2019 January ; 22(1): 25–36. doi:10.1038/s41593-018-0287-x. Widespread RNA editing dysregulation in brains from autistic individuals Stephen S. Tran1,2, Hyun-Ik Jun2, Jae Hoon Bahn2, Adel Azghadi2, Gokul Ramaswami3, Eric L. Van Nostrand4,5,6, Thai B. Nguyen4,5,6, Yun-Hua E. Hsiao7, Changhoon Lee3, Gabriel A. Pratt4,5,6,8, Verónica Martínez-Cerdeño9, Randi J. Hagerman10, Gene W. Yeo4,5,6,8, Daniel H. Geschwind3,11,12,*, and Xinshu Xiao1,2,13,14,* 1Bioinformatics Interdepartmental Program, UCLA, Los Angeles, California, CA, 90095, USA 2Department of Integrative Biology and Physiology, UCLA, Los Angeles, California, CA, 90095, USA 3Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, California, CA, 90095, USA 4Department of Cellular and Molecular Medicine, UCSD, La Jolla, CA, 92093, USA 5Stem Cell Program, UCSD, La Jolla, CA, 92093, USA 6Institute for Genomic Medicine, UCSD, La Jolla, CA, 92093, USA 7Department of Bioengineering, UCLA, Los Angeles, California, CA, 90095, USA 8Bioinformatics and Systems Biology Graduate Program, UCSD, La Jolla, CA, 92093, USA Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:http://www.nature.com/authors/editorial_policies/license.html#terms *Correspondence: [email protected], [email protected]. Author contributions S.S.T.carried out data analyses, with input from G.R.. H.I.J., J.H.B. and A.A. performed molecular biology experiments. E.L.V.N., T.B.N., G.A.P. and G.W.Y carried out eCLIP experiments and data processing. Y.H.E.H. contributed to data visualization. C.L. carried out ASD RNA-Seq data generation. V.M.C. and R.J.H. provided postmortem Fragile X and control samples. S.S.T, D.H.G. and X.X. designed the study, interpreted the results and wrote the manuscript. Accession Codes Data generated by this study are available at the Gene Expression omnibus with IDs: GSE107895, GSE107867, GSE117776. Competing Interests Statement G.W.Y, is a co-founder of Locana and Eclipse Bioinnovations and member of the scientific advisory boards of Locana, Eclipse Bioinnovations and Aquinnah Pharmaceuticals. E.V.N, is a co-founder and member of the scientific advisory board of Eclipse BioInnovations. The terms of these arrangements have been reviewed and approved by the University of California, San Diego in accordance with its conflict of interest policies. Code availability R code for the analysis of RNA editing of ASD against controls is available as Supplementary Software. It is also available in GitHub (where updates will be released): https://github.com/gxiaolab/RNA_editing_in_ASD.Nat_neuroscience.Tran_et_al Data availability eCLIP-seq data on FMRP and FXR1P from postmortem human brain have been deposited to GEO with accession GSE107895. RNA- seq data of Fragile X patients, carriers, and controls have been deposited to GEO with accession GSE107867 (NeuroBiobank dataset) and GSE117776 (UC Davis FXTAS dataset). Fastq files of RNA-Seq from the idiopathic ASD, dup15q, and control brains were obtained from our previous study9 and are available in the PsychENCODE website (https://www.synapse.org//#!Synapse:syn4921369/ wiki/235539). Fastq files of RNA-seq data from the replicate ASD and control cohort are available on GEO (accession GSE51264 / GSE59288). Tran et al. Page 2 9Department of Pathology and Laboratory Medicine, UC Davis School of Medicine, Sacramento, Author ManuscriptAuthor Manuscript Author Manuscript Author Manuscript Author CA, 95817, USA 10The MIND Institute, Department of Pediatrics, UC Davis School of Medicine, Sacramento, CA, 95817, USA 11Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, UCLA, CA, 90095, USA. 12Department of Human Genetics, David Geffen School of Medicine, UCLA, California 90095, USA. 13Molecular Biology Institute, UCLA, Los Angeles, California, CA, 90095, USA 14Institute for Quantitative and Computational Biology, UCLA, Los Angeles, California, CA, 90095, USA Abstract Transcriptomic analyses of postmortem brains have begun to elucidate the molecular abnormalities in autism spectrum disorder (ASD). However, a crucial pathway involved in synaptic development, RNA editing, has not yet been studied on a genome-wide scale. Here, we profiled global patterns of adenosine-to-inosine (A-to-I) editing in a large cohort of post-mortem ASD brains. We observed a global bias for hypoediting in ASD brains, which was shared across brain regions and involved many synaptic genes. We show that the Fragile X proteins, FMRP and FXR1P, interact with ADAR proteins and modulate A-to-I editing. Furthermore, we observed convergent patterns of RNA editing alterations in ASD and Fragile X syndrome, establishing this as a molecular link between these related diseases. Our findings, which are corroborated across multiple datasets, including dup15q cases associated with intellectual disability, highlight RNA editing dysregulation in ASD and reveal novel mechanisms underlying this disorder. Introduction Autism spectrum disorder (ASD) is characterized by a developmental deficit in social communication accompanied by repetitive and restrictive interests1, with a strong neuropathology implicating glutamatergic2 and serotonergic3 circuits, aberrant structural development in multiple brain regions4, excitatory and inhibitory imbalance5, and abnormal synaptogenesis6. The genetic etiology of ASD remains incompletely understood and shows substantial heterogeneity7. Nevertheless, recent studies, leveraging the increasing availability of postmortem samples, have revealed shared patterns of transcriptome dysregulation affecting neuronal and glial coding and non-coding gene expression8,9, neuronal splicing including microexons10, and microRNA targeting11 across approximately 2/3 of ASD patients. These studies highlight down-regulation of activity-dependent genes in neurons and up-regulation of astrocyte and microglial genes as key points of convergence in ASD pathology. Another major RNA processing mechanism is RNA editing, which refers to the alteration of RNA sequences through insertion, deletion or substitution of nucleotides. Catalyzed by the ADAR family of enzymes, adenosine-to-inosine (A-to-I) editing is the most prevalent type Nat Neurosci. Author manuscript; available in PMC 2019 June 17. Tran et al. Page 3 of RNA editing in humans, affecting the majority of human genes12. As inosines in RNA are Author ManuscriptAuthor Manuscript Author Manuscript Author Manuscript Author recognized as guanosines by cellular machinery, A-to-I editing can alter gene expression in different ways, for example, through amino acid substitutions, modulation of RNA stability, alteration of alternative splicing, and modifications of regulatory RNAs or cis-regulatory motifs12,13. RNA editing plays important roles in neurodevelopment and maintenance of normal neuronal function13. Indeed, a number of A-to-I editing sites alone are imperative in modulating excitatory responses and permeability of ionic channels and other neuronal signaling functions13. Not surprisingly, aberrant RNA editing has been reported in several neurological disorders, such as schizophrenia, bipolar disorder, amyotrophic lateral sclerosis,14 and Alzheimer’s disease.15 In ASD, a previous study analyzed a few known RNA editing sites in synaptic genes and reported altered editing patterns in a small cohort of ASD cerebella16. Yet, it remains unaddressed if global patterns of RNA editing may contribute to the neuropathology of ASD, a question that requires larger patient cohorts and multiple implicated brain regions. In addition, the regulatory mechanisms of aberrant editing in neurological disorders including ASD remain largely unknown. Here we report global patterns of dysregulated RNA editing across the largest cohort of ASD brain samples to date, spanning multiple brain regions. We identified a core set of down-regulated RNA editing sites, enriched in genes of glutamatergic and synaptic pathways and ASD susceptibility genes. Multiple lines of evidence associate a distinct set of these hypoedited sites with Fragile X proteins: FMRP and FXR1P. Through transcriptome- wide protein-RNA binding analyses and detailed molecular assays, we show that FMRP and FXR1P interact with ADAR and modulate A-to-I editing. It is known that mutations in FMRP lead to the Fragile X syndrome, a disease with high comorbidity with ASD7. Indeed, we observed convergent dysregulated patterns of RNA editing in Fragile X and ASD patients, which is consistent with the findings that genes harboring ASD risk mutations are enriched in FMRP targets17,18. Overall, we provide global insights regarding RNA editing in ASD pathogenesis and elucidate a regulatory function of Fragile X proteins in RNA editing that additionally serves as a molecular link between ASD and Fragile X Syndrome. Results RNA editing analysis of ASD postmortem brain samples From 69 unique post-mortem subjects, we obtained rRNA-depleted total RNA-Seq (50 base paired-end, non-strand-specific) from three brain regions implicated in ASD-susceptibility: frontal cortex, temporal cortex, and cerebellum (Supplementary Table 1). In total, there were 29, 30, and 31 ASD samples,