Research

Our Science

Everything we experience produces electrical activity in our brain. Brain activity turns on a particular set of genes in each different kind of brain cell that allow us to adapt to and learn from our environment. This neuronal activity-dependent gene expression is essential for healthy brain development, function, and maturation. While the transcriptional and epigenetic effects of neuronal activity have been systematically explored in rodents, very little is known about these adaptive changes in human brain cells.

OSTN expression is induced by sensory experience in the primate cortex.

In human neurons in vitro, and in non-human primates in vivo, the Boulting Laboratory investigates activity-dependent transcriptional and epigenomic dynamics that cannot be studied in other animal model systems. By identifying novel patterns of gene regulation, we demonstrate how these critical gene expression programs have evolved to vary between species. We have uncovered both primate-specific neuronal activity-regulated genes, as well as evolutionarily-conserved genes that have been repurposed in the primate brain. Ongoing experiments explore how the molecular functions these genes impart new adaptive functions to the human brain.

Primate-specific enhancer regulation by MEF2 drives neuronal activity-dependent induction of OSTN.

One example is the gene Osteocrin (OSTN) that encodes a small secreted peptide. Dr. Boulting helped identify OSTN as selectively induced by neuronal activity in human and macaque brain, but not that of mouse or rat. Previous studies showed that the induction of OSTN in primates relies on a series of base-pair changes within an otherwise conserved enhancer sequence. And that OSTN expression dramatically regulates dendritic outgrowth of developing human neurons.

The Boulting lab is now continuing its investigation into the regulatory evolution and function of OSTN, and the transcription factors that control its expression (SATB2 and MEF2C), in order to uncover new aspects of human neuronal gene regulation during brain development and disease.

The human brain is enormous and complex, with an estimated 86 billion neurons, expanded cellular diversity, increased neuronal connectivity, and protracted stages of development compared to other mammals^1–4. These differences are thought to contribute to human-specific characteristics such as refined digital dexterity, symbolic language, and abstract thought². How the evolutionary changes in our brain’s development and adaptive capacity have given rise to human or even primate-specific characteristics remains largely uncharacterized.

The development and maturation of the brain is dependent on neuronal activity in a wide range of animal species⁵. Because human brain structures continue to mature over an extraordinarily long timeline of 20-30 years, it seems we are one of the few animals in which sensory input continuously shapes and refines neural circuit architecture over decades.

The limited availability of primary human brain tissue in which neuronal activity can be manipulated has largely precluded molecular characterization of these responses in humans. The Boulting Laboratory uses human stem cells to generate particular populations of human neurons in order to discover the molecular genetics of human neuronal development, cellular identity, and neuronal activity-dependent gene expression.

Multiomic view of the evolutionarily- divergent promoter of the autism-associated gene DHCR7 in human GABAergic stem cell derived neurons.

2. Sousa AMMM, Meyer KA, Santpere G, Gulden FO & Sestan N Evolution of the Human Nervous System Function, Structure, and Development. Cell 170, 226–247 (2017). [PMC free article] [PubMed] [Google Scholar]

3. Lui JH, Hansen DV & Kriegstein AR Development and Evolution of the Human Neocortex. Cell 146, 18–36 (2011). [PMC free article] [PubMed] [Google Scholar]

4. Petanjek Z et al. Extraordinary neoteny of synaptic spines in the human prefrontal cortex. Proceedings of the National Academy of Sciences 108, 13281–13286 (2011). [PMC free article] [PubMed] [Google Scholar]

5. Hensch TK Critical period regulation. Annual review of neuroscience 27, 549–79 (2004). [PubMed] [Google Scholar]

GABAergic neuronal circuits are implicated in several neurological disorders. In Dr. Boulting’s postdoctoral work, she conducted a comprehensive activity-dependent transcriptional and epigenetic profiling of human induced pluripotent stem cell (hiPSC)-derived GABAergic neurons similar to those of the early developing striatum. This study identified genes whose expression is inducible following membrane depolarization, some of which have specifically evolved in primates, and/or are associated with neurological diseases, including schizophrenia, bipolar disorder, and autism spectrum disorder (ASD).

Human cortical neurons expressing the disease-associated transcription factor protein SATB2 (red nuclei), derived from either human pluripotent stem cells in vitro (above left) , or from primary human brain tissue (above right).

This finding, that depolarization-induced genes of human GABAergic cells are enriched for ASD-association, taken together with the neurological disease heritability enrichment observed in activity-responsive gene regulatory elements, suggests a role for dysregulated calcium-dependent gene expression within developing striatal neurons in ASD etiology.

One of our current research directions focuses on how the primate and human brain activity-dependent transcriptional and epigenetic response may be different from other animals, and how subtle genetic changes can lead to important and disease-relevant differences in human brain cells. We hope this will enable improved fine mapping of neurological disease-associated genome sequence variants within neuronal activity-dependent regulatory elements and lay the foundation for future comparisons between the activity-dependent regulatory landscapes of different human neuronal subtypes.