Autism and the “Pruning” Problem of the Brain

What does “pruning” mean?

The human brain develops extremely quickly after birth. In the first few years of life, far more nerve cell connections (synapses) are formed than are actually needed later.

This overproduction is normal – it enables learning, language development, and social recognition.

From early childhood onward, the brain begins a cleanup process:

What is pruning?

Pruning means thinning out or trimming back synapses.

The brain removes:

• weak or rarely used connections
• incorrectly wired networks
• superfluous “noise signals”
• narrow connections

This process makes the brain:

• faster
• more efficient
• more stable in behavior
• better at filtering stimuli
• more precise in language, motor skills, and social functions

Pruning is therefore a central developmental step, comparable to the fine-tuning of a complex computer network.

What has been repeatedly found in studies on autism?

PubMed studies from the last 10–15 years (including those from Mount Sinai, MIT, and Columbia University) consistently show:

Reduced pruning in certain brain regions

In many autistic individuals, compared to neurotypical individuals, the following were found:

Too many synapses

Regions with excessive connectivity

Reduced pruning of redundant connections

This particularly affects:

• Prefrontal cortex areas (PFC) – important for planning, impulse control, and attention
• Temporal areas – important for language and social perception
• TPJ (Temporo-Parietal Junction) – a central region for social signals and perspective-taking
• Sensory networks – filtering of stimuli
• Partially also the default mode network

What does “too many connections” mean?

At first glance, “more connections” sounds good, but in practice it leads to:

• • Sensory overload (too many signals at once)
  • Inefficient filtering of sounds, movement, and touch

Overloaded social and linguistic networks

Difficulty distinguishing between important and unimportant information

Increased stress and alertness in the brain

As a result, the brain doesn’t work faster, but incredibly harder – often constantly operating at its limit.

Prefrontal areas and network control

The prefrontal cortex (especially F3/F4 areas) normally regulates:

• Attention
• Impulse control
• Correctly interpreting social context
• Flexible behavior control
• With reduced pruning, this network remains overloaded and reacts less efficiently.
• Prefrontal cortex (especially F3/F4 areas) and therefore less efficiently.

What does this mean for autism?

The leading theory therefore describes autism today not as a “defect,” but as a differently organized, less thinned-out network:

• • • too many parallel signals
    • too little filtering
    • too much detail, too little global summarization
    • high load on social and sensory areas

This creates the typical combination of:

• • • • sensory sensitivity
      • rapid overload
      • social insecurity
      • linguistic-associative peculiarities
      • exceptional attention to detail

Many savant skills (music, mathematics, pattern recognition) are also linked to this overconnectivity in research.

The Development of Synapses Throughout Life

The human brain starts with an extremely high number of synapses. At birth, a baby already has around 2,500 synapses per nerve cell. In the first few years of life, this number explodes to over 15,000 synapses per nerve cell – more than twice as many as in an adult. This “flood of synapses” enables the rapid learning of language, movements, social signals, and sensory processing.

From early childhood onward, pruning begins, the process of pruning unused connections. During childhood, and especially during puberty, the number of synapses shrinks to a functional, efficient level. As a result, the brain becomes faster, more focused, and more efficient – ​​less “overcrowded,” more”Goal-oriented.”

In middle adulthood, the number of synapses stabilizes at a significantly lower, but optimally organized level. Therefore, learning in this phase often appears slower, but more structured.

In old age, natural degenerative processes lead to further synapse loss. This makes the brain less flexible, and new learning content is more difficult to consolidate.

Several PubMed studies show an unusual pattern in autistic individuals: The high number of synapses persists in certain brain networks throughout childhood because pruning is less active there. This maintains the “sensory overload”—the brain areas must constantly process significantly more signals. This explains the typical combination of sensory hypersensitivity, rapid overload, but also often exceptional attention to detail and specialized skills in specific areas.

Summary

In autism, the natural “pruning” process—the thinning out of unnecessary neural connections—functions less effectively in certain brain networks. As a result, too many synapses remain, particularly in areas related to language, social perception, and sensory processing. Consequently, the brain is not organized efficiently enough and receives too many simultaneous signals. This leads to sensory overload, increased susceptibility to stress, and social and linguistic peculiarities. This theory is now one of the most stable and repeatedly confirmed findings in autism research.

References

1) Main Reviews on Impaired Pruning in Autism

Tang, G. et al. (2014) Loss of mTOR-dependent macroautophagy causes autistic-like synaptic pruning deficits.  Cell, 156(1–2), 203–217.
→ One of the most cited studies; directly demonstrates: Autism = reduced synaptic pruning in the prefrontal cortex.

Selemon, L.D. (2013) A role for synaptic plasticity in the adolescent development of executive function.  Translational Psychiatry, 3, e238.
→ Review of puberty-specific pruning, explains why developmental abnormalities in this phase primarily affect the prefrontal cortex—relevant for autism.

Zoghbi, H.Y. & Bear, M.F. (2012) Synaptic dysfunction in neurodevelopmental disorders. Science, 337(6093), 1558–1562.
→ Review of synaptic dysfunction; autism is primarily classified as a disorder of synaptic elimination.

Hutsler, J.J. & Zhang, H. (2010) Increased dendritic spine densities on cortical projection neurons in autism spectrum disorders. Brain Research, 1309, 83–94.
→ Histological study in humans: Autistic children have significantly more synapses in the prefrontal cortex.

2) Central mechanism: mTOR, autophagy & lack of pruning

Schafer, D.P. et al. (2012) Microglia sculpt postnatal neural circuits in an activity- and complement-dependent manner. Neuron, 74(4), 691–705.
→ Shows: Pruning occurs via microglia and the complement system.

This series of studies laid the foundation for today’s autism pruning model.

3) Human studies on overconnectivity and multiple synapses

Courchesne, E. & Pierce, K. (2005) Why the frontal cortex in autism might develop abnormally. Journal of Child Psychology and Psychiatry, 46(6), 557–569.
→ Shows early overdevelopment and overconnectivity in prefrontal networks.

Stoner, R. et al. (2014) Patches of disorganization in the neocortex of children with autism. New England Journal of Medicine, 370, 1209–1219.
→ Important human study: lack of structural “clearing” of neuronal layers in the cortex.

Supekar, K. et al. (2013) Brain hyperconnectivity in children with autism and its links to social deficits.  Cell Reports, 5(3), 738–747.
→ Functional human study: hyperconnectivity = less pruning, direct association with social deficits.

4) Review of Reviews

Happé & Frith (2020), Baron-Cohen (2022), Müller (2015) – all reviews on network overload and pruning.

Summary

Together, these studies demonstrate three recurring key findings:

• Autistic individuals have more synapses in certain brain regions.
• Pruning is reduced in childhood and adolescence.
• The prefrontal cortex (PFC), temporal lobes, and thoracic jugular notch (TPJ) are particularly affected.
• This explains sensory overload, inefficient filtering, and social difficulties.
• mTOR overactivity, microglial dysfunction, and autophagy disorders.are the leading mechanisms today