Low load for disruptive mutations in autism genes and their biased transmission

We previously computed that genes with de novo (DN) likely gene-disruptive (LGD) mutations in children with autism spectrum disorders (ASD) have high vulnerability: disruptive mutations in many of these genes, the vulnerable autism genes, will have a high likelihood of resulting in ASD. Because individuals with ASD have lower fecundity, such mutations in autism genes would be under strong negative selection pressure. An immediate prediction is that these genes will have a lower LGD load than typical genes in the human gene pool. We confirm this hypothesis in an explicit test by measuring the load of disruptive mutations in whole-exome sequence databases from two cohorts. We use information about mutational load to show that lower and higher intelligence quotients (IQ) affected individuals can be distinguished by the mutational load in their respective gene targets, as well as to help prioritize gene targets by their likelihood of being autism genes. Moreover, we demonstrate that transmission of rare disruptions in genes with a lower LGD load occurs more often to affected offspring; we show transmission originates most often from the mother, and transmission of such variants is seen more often in offspring with lower IQ. A surprising proportion of transmission of these rare events comes from genes expressed in the embryonic brain that show sharply reduced expression shortly after birth

Neurodevelopmental disorders: From genetics to functional pathways

Neurodevelopmental disorders (NDDs) are a class of disorders affecting brain development and function and are characterized by wide genetic and clinical variability. In this review, we discuss the multiple factors that influence the clinical presentation of NDDs, with particular attention to gene vulnerability, mutational load, and the two-hit model. Despite the complex architecture of mutational events associated with NDDs, the various proteins involved appear to converge on common pathways, such as synaptic plasticity/function, chromatin remodelers and the mammalian target of rapamycin (mTOR) pathway. A thorough understanding of the mechanisms behind these pathways will hopefully lead to the identification of candidates that could be targeted for treatment approaches

Intracellular Pathways Associated with the Etiology of Autism

This chapter explores the relationship between the genes and proteins of the Akt and MAPK pathways and autism. This chapter presents the biology of these two pathways, their genes and cascading proteins, and then, it looks at the research that has connected these molecules to autism. Finally, it imparts current and future therapeutic modalities that might exploit abnormalities in these genes and proteins, change them and ultimately alter aberrant autistic behaviors

Rare variants in the genetic background modulate cognitive and developmental phenotypes in individuals carrying disease-associated variants.

To assess the contribution of rare variants in the genetic background toward variability of neurodevelopmental phenotypes in individuals with rare copy-number variants (CNVs) and gene-disruptive variants. We analyzed quantitative clinical information, exome sequencing, and microarray data from 757 probands and 233 parents and siblings who carry disease-associated variants. The number of rare likely deleterious variants in functionally intolerant genes ("other hits") correlated with expression of neurodevelopmental phenotypes in probands with 16p12.1 deletion (n=23, p=0.004) and in autism probands carrying gene-disruptive variants (n=184, p=0.03) compared with their carrier family members. Probands with 16p12.1 deletion and a strong family history presented more severe clinical features (p=0.04) and higher burden of other hits compared with those with mild/no family history (p=0.001). The number of other hits also correlated with severity of cognitive impairment in probands carrying pathogenic CNVs (n=53) or de novo pathogenic variants in disease genes (n=290), and negatively correlated with head size among 80 probands with 16p11.2 deletion. These co-occurring hits involved known disease-associated genes such as SETD5, AUTS2, and NRXN1, and were enriched for cellular and developmental processes. Accurate genetic diagnosis of complex disorders will require complete evaluation of the genetic background even after a candidate disease-associated variant is identified

Strain differences in behaviour and immunity in aged mice: Relevance to autism.

The BTBR mouse model has been shown to be associated with deficits social interaction and a pronounced engagement in repetitive behaviours. Autism spectrum disorder (ASD) is the most prevalent neurodevelopmental condition globally. Despite its ubiquity, most research into the disorder remains focused on childhood, with studies in adulthood and old age relatively rare. To this end, we explored the differences in behaviour and immune function in an aged BTBR T + Itpr3tf/J mouse model of the disease compared to a similarly aged C57bl/6 control. We show that while many of the alterations in behaviour that are observed in young animals are maintained (repetitive behaviours, antidepressant-sensitive behaviours, social deficits & cognition) there are more nuanced effects in terms of anxiety in older animals of the BTBR strain compared to C57bl/6 controls. Furthermore, BTBR animals also exhibit an activated T-cell system. As such, these results represent confirmation that ASD-associated behavioural deficits are maintained in ageing, and that that there may be need for differential interventional approaches to counter these impairments, potentially through targeting the immune system

Developmental gene expression differences between humans and mammalian models

Identifying the molecular programs underlying human organ development and how they differ from model species is key for understanding human health and disease. Developmental gene expression profiles provide a window into the genes underlying organ development and a direct means to compare them across species. We use a transcriptomic resource covering the development of seven organs to characterize the temporal profiles of human genes associated with distinct disease classes and to determine, for each human gene, the similarity of its spatiotemporal expression with its orthologs in rhesus macaque, mouse, rat, and rabbit. We find clear associations between spatiotemporal profiles and the phenotypic manifestations of diseases. We also find that half of human genes differ from their mouse orthologs in their temporal trajectories in at least one of the organs. These include more than 200 genes associated with brain, heart, and liver disease for which mouse models should undergo extra scrutiny

Rethinking the fast-slow continuum of individual differences

The idea that individual differences in behavior and physiology can be partly understood by linking them to a fast-slow continuum of life history strategies has become popular in the evolutionary behavioral sciences. I refer to this approach as the “fast-slow paradigm” of individual differences. The paradigm has generated a substantial amount of research, but has also come increasingly under scrutiny for theoretical, empirical, and methodological reasons. I start by reviewing the basic empirical facts about the fast-slow continuum across species and the main theoretical accounts of its existence. I then discuss the move from the level of species and populations to that of individuals, and the theoretical and empirical complications that follow. I argue that the fast-slow continuum can be a productive heuristic for individual differences; however, the field needs to update its theoretical assumptions, rethink some methodological practices, and explore new approaches and ideas in light of the specific features of the human ecology

Essential Genes And Their Role In Autism Spectrum Disorder

Essential genes (EGs) play central roles in fundamental cellular processes and are required for the survival of an organism. EGs are enriched for human disease genes and are under strong purifying selection. This intolerance to deleterious mutations, commonly observed haploinsufficiency and the importance of EGs in pre- and postnatal development suggests a possible cumulative effect of deleterious variants in EGs on complex neurodevelopmental disorders. Autism spectrum disorder (ASD) is a heterogeneous, highly heritable neurodevelopmental syndrome characterized by impaired social interaction, communication and repetitive behavior. More and more genetic evidence points to a polygenic model of ASD and it is estimated that hundreds of genes contribute to ASD. The central question addressed in this dissertation is whether genes with a strong effect on survival and fitness (i.e. EGs) play a specific role in ASD risk. I compiled a comprehensive catalog of 3,915 mammalian EGs by combining human orthologs of lethal genes in knockout mice and genes responsible for cell-based essentiality. With an updated set of EGs, I characterized the genetic and functional properties of EGs and demonstrated the association between EGs and human diseases. Next I provided evidence for a stronger contribution of EGs to ASD risk, compared to non-essential genes (NEGs). By examining the exonic de novo and inherited variants from 1,781 ASD quartet families, I demonstrated a significantly higher burden of damaging mutations in EGs in ASD probands compared to their non-ASD siblings. Analysis of EGs in the developing brain identified clusters of co-expressed EGs implicated in ASD, among which I proposed a priority list of 29 EGs with potential ASD risk as targets for future functional and behavioral studies. Finally, I developed the essentiality burden score (EBS), which captures the burden of rare mutations in EGs as a novel polygenic predictor of individual ASD risk and a useful addition to the current tools for understanding the polygenic architecture of ASD. Overall, I show that large-scale studies of gene function in model organisms and human cell lines provide a powerful approach for prioritization of genes and pathogenic variants identified by sequencing studies of complex human disease

Identification of novel intracellular mechanisms in developmental spine pruning through Ankyrin B.

Dendritic spines are the predominant site of glutamatergic inputs throughout the brain. Regulation of spines is therefore critical for refining cortical networks. This research sought to define mechanisms for determining spine fate during developmental synapse remodeling. The central hypothesis is that NrCAM requires intracellular interactions within the spine to promote Semaphorin3F receptor clustering and spine retraction, through binding to the actin adaptor AnkB and microtubule binding protein DCLK1. I have delineated intracellular binding partners of NrCAM in synapse-enriched cellular fractions. I made a mutation in NrCAM that disrupts binding to AnkB and DCLK1 and perturbs Sema3F holoreceptor functioning. I demonstrated that chemical disruption of microtubules affects spine morphology and response to Sema3F. Finally, I have shown in vivo mutations affecting AnkB result in altered spine densities. The findings provide insight toward understanding the molecular mechanisms of dendritic spine remodeling and the pathology of neurodevelopmental disorders involving dendritic spine anomalies