Breaking the Genetic Code of Mental Illness: How Shared Variants Shape Psychiatric Disorders

Psychiatric disorders are among the most challenging medical conditions to understand and treat. They affect millions worldwide, yet their underlying causes remain elusive. Unlike many physical illnesses, which can often be traced to a single gene mutation or environmental factor, psychiatric conditions are highly polygenic (they are influenced by numerous genetic variations acting in concert). Moreover, these disorders frequently co-occur, with individuals diagnosed with one condition often exhibiting symptoms of others. This phenomenon, known as pleiotropy, suggests a shared genetic architecture that underlies multiple psychiatric conditions. However, the precise molecular mechanisms driving this overlap remain largely unknown, presenting a significant challenge for researchers and clinicians alike. The rise of genome-wide association studies (GWAS) has led to the identification of hundreds of genetic variants associated with psychiatric disorders such as schizophrenia, bipolar disorder, major depressive disorder, autism spectrum disorder, attention-deficit/hyperactivity disorder, obsessive-compulsive disorder, Tourette syndrome, and anorexia nervosa. While these studies have been instrumental in pinpointing statistical associations, they do not provide insights into the biological function of these variants. Identifying a genetic risk factor is only the first step—understanding how it influences gene expression, cellular function, and ultimately behavior is far more complex. Many of these risk variants are located in non-coding regions of the genome, which means they do not directly alter protein structure but instead likely function as regulatory elements that influence when and where genes are expressed. This raises critical questions: Which genes are being regulated? How do these variants contribute to disease risk? And why do some variants influence multiple disorders while others appear disorder-specific? Addressing these questions requires functional genomics approaches that go beyond statistical associations. The lack of direct experimental validation for many psychiatric risk variants has left researchers with uncertainty about their biological relevance. Moreover, given that psychiatric disorders arise from disruptions in neurodevelopment and brain circuitry, studying genetic risk factors in the appropriate cellular context—such as neurons—remains an ongoing challenge. Traditional methods of studying gene regulation, such as reporter assays or chromatin immunoprecipitation, have been limited in scale and resolution, preventing a comprehensive analysis of the thousands of variants linked to psychiatric disorders.

To overcome these barriers, new research paper published in Cell Journal and conducted by Dr. Sool Lee, Dr. Jessica McAfee, Dr. Jiseok Lee, Dr. Alejandro Gomez, Dr. Austin Ledford, Dr. Declan Clarke, Hyunggyu Min, Professor Mark Gerstein, Professor Alan Boyle, Professor  Patrick Sullivan, Professor  Adriana Beltran, and Professor Hyejung Won from the University of North Carolina at Chapel Hill and Yale University used a massively parallel reporter assay (MPRA) which is high-throughput experimental technique to allow for the simultaneous testing of thousands of genetic variants to determine their impact on gene expression regulation. By performing MPRA in human neural progenitor cells (HNPs), the researchers identified which genetic variants have functional regulatory activity and to distinguish between those with pleiotropic effects (influencing multiple disorders) and those with disorder-specific effects.  Unlike conventional methods that examine one variant at a time, MPRA allows scientists to test thousands simultaneously, providing a clearer picture of how these variants influence gene expression. To ensure relevance to brain development and psychiatric disorders, the authors introduced these genetic sequences into HNPs, an early-stage cell type that gives rise to neurons. After introducing the DNA sequences containing risk variants, they measured RNA output, a direct readout of whether a particular variant could enhance or suppress gene activity. This experiment revealed that about 9.3% of the tested variants exhibited significant regulatory activity, confirming that a subset of psychiatric risk variants do not merely correlate with disease but likely play a direct role in gene expression changes during brain development. As they analyzed these regulatory variants, an interesting pattern emerged: variants associated with multiple psychiatric disorders (pleiotropic variants) displayed a broader impact on gene regulation than disorder-specific variants. These pleiotropic variants exhibited chromatin accessibility—an indicator of active gene regulation—across multiple cell types in the neuronal lineage, whereas disorder-specific variants had a more restricted impact. This suggested that pleiotropic variants may contribute to psychiatric disease by influencing gene networks that are active in a wide range of developing brain cells, whereas disorder-specific variants may exert their effects in more specialized cell populations. Further analysis revealed that these pleiotropic variants often altered transcription factor binding motifs, the DNA sequences where proteins that regulate gene expression attach. Importantly, the affected transcription factors were highly connected in protein-protein interaction networks, suggesting that they play central roles in gene regulation and may propagate their effects through multiple biological pathways.

To confirm that these genetic variants had real biological effects in living cells, the team turned to CRISPR-based gene perturbation, specifically a high-throughput method known as CROP-seq. By using CRISPR interference (CRISPRi), they selectively disrupted specific variants in human-induced pluripotent stem cell (hiPSC)-derived neurons and then measured which genes were affected. Their first target, rs301804, had been identified through MPRA as an active regulatory variant. When they perturbed this variant, it led to significant downregulation of RERE, a gene involved in neurodevelopment and previously linked to cognitive and psychiatric disorders. This confirmed that rs301804 directly regulates RERE, rather than merely being statistically associated with it. Similarly, another highly pleiotropic variant, rs4513167, was linked to DCC, a gene that guides neuronal growth during brain development. Disrupting this variant caused a drop in DCC expression, reinforcing its functional role. This was a key finding—many GWAS studies assume that the closest gene to a variant is its target, but these experiments demonstrated that variants often regulate genes located far away, necessitating functional testing rather than assumptions. Moreover, the researchers compared mutation intolerance scores of the genes affected by these regulatory variants. Genes associated with pleiotropic variants were significantly more constrained, meaning they are rarely disrupted by mutations in the general population, likely because they are essential for brain development. This contrasted with disorder-specific genes, which showed less evolutionary constraint, suggesting that their functions may be more specialized and dispensable in some contexts. Further, pleiotropic genes were more highly connected in protein protein interaction networks, meaning they interact with many other proteins, reinforcing their role as central regulators of gene function. Furthermore, the researchers also wanted to determine whether pleiotropic variants influenced gene expression at different stages of brain development. By analyzing chromatin accessibility data, they found that these variants were active across a broad range of neuronal subtypes, particularly upper-layer excitatory neurons, which are crucial for brain connectivity. In contrast, disorder-specific variants had more localized effects, often restricted to a single developmental stage or neuronal subtype. This distinction could explain why some psychiatric disorders share genetic risk factors while others have more distinct genetic profiles. To further test the functional relevance of their findings, the team conducted in vivo CRISPR perturbation experiments in mouse brains. They targeted Anp32e, a pleiotropic gene, and Kmt5a, a disorder-specific gene, to compare their downstream effects. When they disrupted Anp32e, it led to widespread changes in neuronal gene expression, affecting multiple cell types and altering networks involved in synaptic function. By contrast, disrupting Kmt5a led to more localized changes, primarily in glial cells, supporting their earlier observations that pleiotropic genes exert broader regulatory influence while disorder-specific genes act more selectively. One of the most compelling aspects of this study was how it linked common genetic variants with rare disease-associated mutations. The authors found that genes affected by common pleiotropic variants overlapped significantly with genes known to carry rare, protein-disrupting mutations in neurodevelopmental disorders like autism and developmental delay. This reinforces the idea that common and rare genetic variation may converge on the same biological pathways, providing multiple routes to psychiatric disease.

In conclusion, the research work of University of North Carolina at Chapel Hill scientists and their collaborators successfully provided direct experimental evidence of how variants function at the molecular level. The use of MPRA combined with CRISPR-based perturbation allowed the researchers to pinpoint which genetic variants influence gene regulation, which genes they control, and how they contribute to multiple psychiatric disorders. This is a crucial step in bridging the gap between genetics and neurobiology, offering a clearer understanding of the molecular underpinnings of mental illnesses. We think an important finding is the realization that pleiotropic genetic variants—those linked to multiple psychiatric disorders—exert their influence across a broader range of neuronal cell types than disorder-specific variants. This suggests that these shared risk factors may disrupt fundamental neurodevelopmental processes that are common across multiple conditions, explaining why psychiatric disorders often co-occur. The discovery that pleiotropic variants target genes with high mutational constraint further emphasizes their biological importance, as these genes appear to be essential for normal brain function. This could inform new drug discovery efforts, as targeting these key regulatory pathways may have therapeutic potential for multiple psychiatric conditions rather than just one. Perhaps most importantly, the findings open the door for precision medicine in psychiatry. If psychiatric disorders share common genetic mechanisms, treatments could be developed that target the underlying biology rather than just the symptoms. For example, drugs that modulate transcription factor networks or chromatin accessibility could have broad therapeutic effects across multiple psychiatric conditions. Additionally, this study provides a framework for identifying which patients might respond best to certain treatments based on their genetic profile, paving the way for more personalized interventions.