What the eyes may reveal about the epigenetics of early autism development

Autism is a highly heritable and complex neurodevelopmental condition, but it cannot be reliably diagnosed until around two years of age when behavioural characteristics such as differences in social interaction, repetitive behaviours, specialised interests and sensory sensitivities become more evident. By this stage, however, many foundational aspects of brain development have already occurred.

Identifying early biological differences may, therefore, help us better understand autism-related developmental pathways and inform how best to implement supportive strategies that could significantly improve the wellbeing of individuals, especially for those experiencing sensory difficulties, from an earlier point in life.

This is where intermediate phenotypes become particularly useful. These are measurable biological traits that emerge early in development and are associated with later behavioural characteristics. Studying them allows researchers to investigate autism-related biology before behavioural features are fully expressed. One promising candidate intermediate phenotype is the PLR.

Why the pupillary light reflex matters

The PLR is governed by a well-characterised neural circuit and is primarily controlled by the parasympathetic branch of the autonomic nervous system. Because this pathway involves both brainstem and higher-order brain regions, the PLR is a non-invasive indicator of autonomic and brain function in infancy.

Previous studies have shown that PLR responses differ in infants with a family history of autism. These infants often show faster or larger pupil constrictions compared to infants without a family history. Differences in PLR timing (latency) and magnitude (amplitude) have therefore been proposed as early markers of neurodivergence.

Importantly, atypical PLR responses are not specific to autism. Altered PLR has also been reported in other neurological conditions, including dementia, highlighting the PLR as a broader indicator of brain and autonomic function across the lifespan.

Looking beneath the reflex: epigenetics

While the PLR is controlled by a relatively simple neural pathway, the biological mechanisms underlying individual differences in this response are likely complex. One important contributor is epigenetics—chemical changes that turn genes “on” and “off”, influencing gene expression without altering the DNA sequence itself.

A key epigenetic mechanism is DNA methylation, which helps regulate when and how genes are switched on or off during development. DNA methylation is influenced by both genetic background and environmental factors, making it particularly relevant to neurodevelopmental conditions such as autism.

There is now strong evidence that epigenetic processes play a key role in autism. Our research group at the Institute of Psychiatry, Psychology & Neuroscience, and others, have identified epigenetic differences associated with autism across multiple levels of analysis, including post-mortem brain tissue, peripheral blood and buccal cell samples, and early development.

This collection of work has revealed detectable epigenomic patterns linked to autism, DNA methylation differences in autistic individuals and their unaffected co-twins, and early epigenetic variation associated with developmental trajectories in infants with a family history of autism. Together, these findings suggest that epigenetic mechanisms may help bridge genetic predisposition and downstream neurodevelopmental outcomes.

In our latest study, published last week in Nature Scientific Reports, we examined whether variation in peripheral DNA methylation—measured from easily accessible bodily tissues like buccal (cheek) cells, rather than directly from the brain or other inaccessible organs—was associated with differences in PLR development. We focused on a cohort of male infants with a high number of participants with a family history of autism, and assessed DNA methylation at 9 months of age in relation to PLR latency and amplitude measured at 9, 14 and 24 months.

What we found

Using a method called epigenome-wide association analyses which allows us to analyse epigenetic variations across the whole human genome, we identified several robust associations between DNA methylation and PLR characteristics. Most notably, four sites where DNA methylation takes place were strongly associated with PLR latency (the timing of the reflex), particularly between 14 and 24 months—a critical window of neurodevelopment that coincides with PLR maturation previously linked to later autism outcomes.

Associations with PLR amplitude (the size of the reflex) were less consistent. Although we identified several suggestive methylation sites, these findings were harder to interpret, likely reflecting the influence of broader emotional and attentional processes that rely on a broader range of brain networks.

Several of the methylation sites that were linked with PLR were located within genes that have been shown to be involved in neurodevelopment, including NR4A2 and HNRNPU, providing further biological relevance.

Why this is important

What makes this work particularly novel is the link between peripheral epigenetic markers (measured from cheek cells) and a non-invasive physiological indicator of brain function (PLR). Detecting atypical PLR development via DNA methylation measured outside the brain suggests that accessible biological samples can provide meaningful insight into early neurodevelopmental processes.

By connecting easily detectable molecular DNA methylation with an early autonomic and sensory response, this research helps bridge the gap between epigenetics and observable neurodevelopmental function, strengthening the case for the PLR as an informative intermediate phenotype in autism research.

This knowledge could help inform early detection strategies and, ultimately, lead to more effective interventions that are tailored to an individual’s neurodevelopmental and wellbeing needs.

Looking ahead

These findings add to growing evidence that early autonomic and sensory markers, like the PLR, can offer valuable insight into neurodevelopmental trajectories. Larger studies will be needed to replicate these results and explore how epigenetic variation relates to other early developmental traits.

As we continue to study the complex interactions between genes, epigenetics and early development, research like ours helps lay the groundwork for understanding how early biological differences emerge.

While this work is not about prediction or diagnosis, it contributes to a growing foundation of research that may, over time, inform earlier and more personalised approaches to supporting wellbeing. By improving our understanding of neurodevelopmental diversity from infancy, we move closer to a more inclusive and supportive future for neurodivergent individuals.