Podcast: What is the problem getting to the bottom of biomarkers and gene x environment interactions

Outcome measures for clinical trials and understanding and determining gene x environment interactions have been two (of many) challenging questions for scientists. In the first study, we explain a new study that looks at the feasibility of three potential biomarkers that have the potential to look at presence of a diagnosis as well as effectiveness of an intervention. In the second half, we describe some new research that shows novel approaches to better understand the presence of an environmental factor with genetic influences, or a new method to describe them in different communities. You can read the studies at the links below and you can listen to the podcast here:




New neurons can be generated in a dish (amazing in itself), and then these neurons studied to examine how they grow, expand, divide and connect. Using this technology, researchers are finding differences in different cell functions in different forms of autism. These differences are in proliferation, which is an increase in the number of cells, as well as the ability of those cells to signal to each other once they are formed. Some autism brains have too many cells, others do not proliferate as quickly as typical developing cells. These things are somewhat dependent on the genetic background which controls head size.

While these different forms of autism all have differences in proliferation, sometimes in different directions, they are all altered, regardless of the genes involved. So, is this one basic biological features that may help identify autism from the earliest points in development? Since they can be studied at any time in life, is this a new biomarker? Much needs to be studied but please listen to this week’s ASF podcast with Dr. Robert Connacher to learn more about the studies going on at Rutgers University to examine this issue.


The amygdala has been shown to be differently sized in autistic people – at first it is too big then it becomes smaller than typically developing people. But how early are these differences seen and does it relate to a diagnosis? The Infant Brain Imaging Study tackled this question in a recent study which compared those who were likely to develop autism at 6 months to those with Fragile X to see if there were differences and if it was specific to autism. Their findings will surprise you and have implications for targeted supports and interventions. Listen to the podcast here.


At this year’s International Society of Autism Research meeting in Austin, TX, there was a variety of themes explored. From early development and milestones, to intervention and supports, to different features like sensory issues, treatment, and how to solve the problem of heterogeneity. It comes down to this: Autism means different things to different people. This is just a small subset of everything that was presented at INSAR 2022 and I hope that if you want to see more, you advocate to have the presentations posted online or even have the program book made available publicly. In the meantime, enjoy the 30 minute summary here.


This year’s Day of Learning was a huge success, with topics ranging from biological sex differences to mobile technologies all the way to the importance and documented value of leisure activities in people on the spectrum. the speakers included a discussion of the IACC, sex differences, the value of prevalence data, mobile technologies, leisure activities, and a recognition of two advocates who made or make a difference in families: Samantha Els and Suzanne Wright. Listen to this week’s podcast here for a quickie, but don’t let it prevent you from watching the longer videos, a link to which can be found below.

2022 Day of Learning presentations in full



Autism spectrum disorder (ASD) is an early-onset developmental disorder characterized by deficits in communication and social interaction and restrictive or repetitive behaviours1,2. Family studies demonstrate that ASD has a substantial genetic basis with contributions both from inherited and de novo variants3,4. It has been estimated that de novo mutations may contribute to 30% of all simplex cases, in which only a single child is affected per family5. Tandem repeats (TRs), defined here as sequences of 1 to 20 base pairs in size repeated consecutively, comprise one of the major sources of de novo mutations in humans6. TR expansions are implicated in dozens of neurological and psychiatric disorders7. Yet, de novo TR mutations have not been characterized on a genome-wide scale, and their contribution to ASD remains unexplored. Here we develop new bioinformatics methods for identifying and prioritizing de novo TR mutations from sequencing data and perform a genome-wide characterization of de novo TR mutations in ASD-affected probands and unaffected siblings. We infer specific mutation events and their precise changes in repeat number, and primarily focus on more prevalent stepwise copy number changes rather than large expansions. Our results demonstrate a significant genome-wide excess of TR mutations in ASD probands. Mutations in probands tend to be larger, enriched in fetal brain regulatory regions, and are predicted to be more evolutionarily deleterious. Overall, our results highlight the importance of considering repeat variants in future studies of de novo mutations.

Despite a growing understanding of the molecular and developmental basis of autism spectrum disorder (ASD), how the neuronal encoding of social information is disrupted in ASD and whether it contributes to abnormal social behavior remains unclear. Here, we disrupted and then restored expression of the ASD-associated gene Shank3 in adult male mice while tracking the encoding dynamics of neurons in the medial prefrontal cortex (mPFC) over weeks. We find that Shank3 disruption led to a reduction of neurons encoding the experience of other mice and an increase in neurons encoding the animal’s own experience. This shift was associated with a loss of ability by neurons to distinguish other from self and, therefore, the inability to encode social agency. Restoration of Shank3 expression in the mPFC reversed this encoding imbalance and increased sociability over 5-8 weeks. These findings reveal a neuronal-encoding process that is necessary for social behavior and that may be disrupted in ASD.

Keywords: Computational biology and bioinformatics; Genetics; Genomics.

Background: Marked sex differences in autism prevalence accentuate the need to understand the role of biological sex-related factors in autism. Efforts to unravel sex differences in the brain organization of autism have, however, been challenged by the limited availability of female data.

Methods: We addressed this gap by using a large sample of males and females with autism and neurotypical (NT) control individuals (ABIDE; Autism: 362 males, 82 females; NT: 409 males, 166 females; 7-18 years). Discovery analyses examined main effects of diagnosis, sex and their interaction across five resting-state fMRI (R-fMRI) metrics (voxel-level Z > 3.1, cluster-level P < 0.01, gaussian random field corrected). Secondary analyses assessed the robustness of the results to different pre-processing approaches and their replicability in two independent samples: the EU-AIMS Longitudinal European Autism Project (LEAP) and the Gender Explorations of Neurogenetics and Development to Advance Autism Research.

Results: Discovery analyses in ABIDE revealed significant main effects of diagnosis and sex across the intrinsic functional connectivity of the posterior cingulate cortex, regional homogeneity and voxel-mirrored homotopic connectivity (VMHC) in several cortical regions, largely converging in the default network midline. Sex-by-diagnosis interactions were confined to the dorsolateral occipital cortex, with reduced VMHC in females with autism. All findings were robust to different pre-processing steps. Replicability in independent samples varied by R-fMRI measures and effects with the targeted sex-by-diagnosis interaction being replicated in the larger of the two replication samples-EU-AIMS LEAP.

Limitations: Given the lack of a priori harmonization among the discovery and replication datasets available to date, sample-related variation remained and may have affected replicability.

Conclusions: Atypical cross-hemispheric interactions are neurobiologically relevant to autism. They likely result from the combination of sex-dependent and sex-independent factors with a differential effect across functional cortical networks. Systematic assessments of the factors contributing to replicability are needed and necessitate coordinated large-scale data collection across studies.

Keywords: Autism spectrum disorder; Replication; Resting-state functional connectivity; Robustness; Sex differences; Voxel-mirrored homotopic connectivity.

Autism spectrum disorders (ASDs) are a group of neurodevelopmental disorders associated with deficits in social communication and restrictive, repetitive patterns of behavior, that affect up to 1 in 54 children. ASDs clearly demonstrate a male bias, occurring ~4 times more frequently in males than females, though the basis for this male predominance is not well-understood. In recent years, ASD risk gene discovery has accelerated, with many whole-exome sequencing studies identifying genes that converge on common pathways, such as neuronal communication and regulation of gene expression. ASD genetics studies have suggested that there may be a “female protective effect,” such that females may have a higher threshold for ASD risk, yet its etiology is not well-understood. Here, we review common biological pathways implicated by ASD genetics studies as well as recent analyses of sex differential processes in ASD using imaging genomics, transcriptomics, and animal models. Additionally, we discuss recent investigations of ASD risk genes that have suggested a potential role for estrogens as modulators of biological pathways in ASD, and highlight relevant molecular and cellular pathways downstream of estrogen signaling as potential avenues for further investigation.

Keywords: animal models; autism spectrum disorder; estrogens; female protective effect; genetics; imaging genomics.

Multimodal exploration of objects during toy play is important for a child’s development and is suggested to be abnormal in children with autism spectrum disorder (ASD) due to either atypical attention or atypical action. However, little is known about how children with ASD coordinate their visual attention and manual actions during toy play. The current study aims to understand if and in what ways children with ASD generate exploratory behaviors to toys in natural, unconstrained contexts by utilizing head-mounted eye tracking to quantify moment-by-moment attention. We found no differences in how 24- to 48-mo children with and without ASD distribute their visual attention, generate manual action, or coordinate their visual and manual behaviors during toy play with a parent. Our findings suggest an intact ability and willingness of children with ASD to explore toys and suggest that context is important when studying child behavior.

A recent theory posits that prediction deficits may underlie the core symptoms in autism spectrum disorder (ASD). However, empirical evidence for this hypothesis is minimal. Using a visual extrapolation task, we tested motion prediction abilities in children and adolescents with and without ASD. We examined the factors known to be important for motion prediction: the central-tendency response bias and smooth pursuit eye movements. In ASD, response biases followed an atypical trajectory that was dominated by early responses. This differed from controls who exhibited response biases that reflected a gradual accumulation of knowledge about stimulus statistics. Moreover, while better smooth pursuit eye movements for the moving object were linked to more accurate motion prediction in controls, in ASD, better smooth pursuit was counterintuitively linked to a more pronounced early response bias. Together, these results demonstrate atypical visual prediction abilities in ASD and offer insights into possible mechanisms underlying the observed differences.

Keywords: Autism; eye movements; perception; prediction; vision.