Highlights d 102 genes implicated in risk for autism spectrum disorder (ASD genes, FDR % 0.1) d Most are expressed and enriched early in excitatory and inhibitory neuronal lineages d Most affect synapses or regulate other genes; how these roles dovetail is unknown d Some ASD genes alter early development broadly, others appear more specific to ASD

SummaryWe present the largest exome sequencing study of autism spectrum disorder (ASD) to date (n=35,584 total samples, 11,986 with ASD). Using an enhanced Bayesian framework to integrate de novo and case-control rare variation, we identify 102 risk genes at a false discovery rate ≤ 0.1. Of these genes, 49 show higher frequencies of disruptive de novo variants in individuals ascertained for severe neurodevelopmental delay, while 53 show higher frequencies in individuals ascertained for ASD; comparing ASD cases with mutations in these groups reveals phenotypic differences. Expressed early in brain development, most of the risk genes have roles in regulation of gene expression or neuronal communication (i.e., mutations effect neurodevelopmental and neurophysiological changes), and 13 fall within loci recurrently hit by copy number variants. In human cortex single-cell gene expression data, expression of risk genes is enriched in both excitatory and inhibitory neuronal lineages, consistent with multiple paths to an excitatory/inhibitory imbalance underlying ASD.

Highlights d 102 genes implicated in risk for autism spectrum disorder (ASD genes, FDR % 0.1) d Most are expressed and enriched early in excitatory and inhibitory neuronal lineages d Most affect synapses or regulate other genes; how these roles dovetail is unknown d Some ASD genes alter early development broadly, others appear more specific to ASD

Evaluation of expression profile in autism spectrum disorder (ASD) patients is an important approach to understand possible similar functional consequences that may underlie disease pathophysiology regardless of its genetic heterogeneity. Induced pluripotent stem cell (iPSC)-derived neuronal models have been useful to explore this question, but larger cohorts and different ASD endophenotypes still need to be investigated. Moreover, whether changes seen in this in vitro model reflect previous findings in ASD postmortem brains and how consistent they are across the studies remain underexplored questions. We examined the transcriptome of iPSC-derived neuronal cells from a normocephalic ASD cohort composed mostly of high-functioning individuals and from non-ASD individuals. ASD patients presented expression dysregulation of a module of co-expressed genes involved in protein synthesis in neuronal progenitor cells (NPC), and a module of genes related to synapse/neurotransmission and a module related to translation in neurons. Proteomic analysis in NPC revealed potential molecular links between the modules dysregulated in NPC and in neurons. Remarkably, the comparison of our results to a series of transcriptome studies revealed that the module related to synapse has been consistently found as upregulated in iPSC-derived neurons-which has an expression profile more closely related to fetal brain-while downregulated in postmortem brain tissue, indicating a reliable association of this network to the disease and suggesting that its dysregulation might occur in different directions across development in ASD individuals. Therefore, the expression pattern of this network might be used as biomarker for ASD and should be experimentally explored as a therapeutic target.

Computerized neuropsychological tests can be effective and have many benefits. This paper addresses these issues using the computer-based Cambridge Neuropsychological Test Automated Battery (CANTAB) to assess Brazilian children and adults. Preliminary normative data for Brazilian children obtained in a series of CANTAB subtests are presented together with data from adults (controls) and samples of patients with multiple sclerosis and Duchenne muscular dystrophy. The results obtained in children confirmed the normative values reported for American children (Luciana & Nelson, 2002), indicating high applicability of the CANTAB battery for children in the evaluation of visual memory, working memory, planning, and set shifting. For multiple sclerosis patients, CANTAB revealed differences between the control and multiple sclerosis groups for all subtests employed, including visual memory, working memory, spatial memory, decision making, inhibitory control, and sustained attention. In children with Duchenne muscular dystrophy, the CANTAB tests revealed specific detriments in attention and memory. These results of the application of CANTAB in different patient groups indicate that the battery is appropriate for assessing several central nervous system diseases.

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We assessed the neuropsychological test performances of 26 patients (mean age = 41.5 ± 6.1 years; mean years of education = 9.8 ± 1.8; 20 males) diagnosed with chronic occupational mercurialism who were former workers at a fluorescent lamp factory. They had been exposed to elemental mercury for an average of 10.2 ± 3.8 years and had been away from this work for 6 ± 4.7 years. Mean urinary mercury concentrations 1 year after cessation of work were 1.8 ± 0.9 µg/g creatinine. Twenty control subjects matched for age, gender, and education (18 males) were used for comparison. Neuropsychological assessment included attention, inhibitory control, verbal and visual memory, verbal fluency, manual dexterity, visual-spatial function, executive function, and semantic knowledge tests. The Beck Depression Inventory and the State and Trait Inventory were used to assess depression and anxiety symptoms, respectively. The raw score for the group exposed to mercury indicated slower information processing speed, inferior performance in psychomotor speed, verbal spontaneous recall memory, and manual dexterity of the dominant hand and non-dominant hand (P < 0.05). In addition, the patients showed increased depression and anxiety symptoms (P < 0.001). A statistically significant correlation (Pearson) was demonstrable between mean urinary mercury and anxiety trait (r = 0.75, P = 0.03). The neuropsychological performances of the former workers suggest that occupational exposure to elemental mercury has long-term effects on information processing and psychomotor function, with increased depression and anxiety also possibly reflecting the psychosocial context.

Large genomic databases of neurodevelopmental disorders (NDD) are helpful resources of genomic variations in complex and heterogeneous conditions, as Autism Spectrum Disorder (ASD). We evaluated the role of rare copy number variations (CNVs) and exonic de novo variants, in a molecularly unexplored Brazilian cohort of 30 ASD trios (n = 90), by performing a meta‐analysis of our findings in more than 20,000 patients from NDD cohorts. We identified three pathogenic CNVs: two duplications on 1q21 and 17p13, and one deletion on 4q35. CNVs meta‐analysis (n = 8,688 cases and n = 3,591 controls) confirmed 1q21 relevance by identifying duplications in other 16 ASD patients. Exome analysis led the identification of seven de novo variants in ASD genes (SFARI list): three loss‐of‐function pathogenic variants in CUL3, CACNA1H, and SHANK3; one missense pathogenic variant in KCNB1; and three deleterious missense variants in ATP10A, ANKS1B, and DOCK1. From the remaining 12 de novo variants in non‐previous ASD genes, we prioritized PRPF8 and RBM14. Meta‐analysis (n = 13,754 probands; n = 2,299 controls) identified six and two additional patients with validated de novo variants in PRPF8 and RBM14, respectively. By comparing the de novo variants with a previously established mutational rate model, PRPF8 showed nominal significance before multiple test correction (P = 0.039, P‐value adjusted = 0.079, binomial test), suggesting its relevance to ASD. Approximately 60% of our patients presented comorbidities, and the diagnostic yield was estimated in 23% (7/30: three pathogenic CNVs and four pathogenic de novo variants). Our uncharacterized Brazilian cohort with tetra‐hybrid ethnic composition was a valuable resource to validate and identify possible novel candidate loci. Autism Res 2020, 13: 199–206. © 2019 International Society for Autism Research, Wiley Periodicals, Inc. Lay Summary We believed that to study an unexplored autistic population, such as the Brazilian, could help to find novel genes for autism. In order to test this idea, with our limited budget, we compared candidate genes obtained from genomic analyses of 30 children and their parents, with those of more than 20,000 individuals from international studies. Happily, we identified a genetic cause in 23% of our patients and suggest a possible novel candidate gene for autism (PRPF8).