Hidden DNA sequences tied to schizophrenia, bipolar risk

Repeated, human-specific DNA sequences are tied to an increased risk of psychiatric disorders, a Stanford study finds. It might be possible to treat the diseases with existing drugs.

- By Krista Conger

David Kingsley

A series of repeated DNA sequences unique to humans may be linked to the development of schizophrenia and bipolar disorder, according to a new study by researchers at the School of Medicine.

The finding suggests that the rapid evolutionary changes that led to the extraordinary complexity of the human brain may have predisposed our species to psychiatric diseases not found in other animals. It also outlines a possible way to one day identify people at risk for, and ways to intervene in, these disorders.

Although the sequences exist within a small stretch of DNA that has been previously linked to schizophrenia and bipolar disorder, they represent a kind of genomic stutter that is particularly difficult to detect using conventional sequencing methods. As a result, they’ve been effectively hidden from researchers attempting to pinpoint a specific mutation that contributes to risk for the diseases.

“The human genome reference sequence shows only 10 repeats of this 30-nucleotide sequence, but we’ve found that individuals actually have from 100 to 1,000 repeats, and that the sequence itself can vary,” said professor of developmental biology David Kingsley, PhD. “In contrast, chimpanzees and other primates have just one repeat of the sequence, indicating that the region has greatly expanded during human evolution. Some of the sequence variants now found in people are also closely associated with the development of schizophrenia and bipolar disorder.”

Kingsley, who is a Howard Hughes Medical Institute investigator, is the senior author of the research, which was published Aug. 9 in the American Journal of Human Genetics. Graduate student Janet Song and former postdoctoral scholar Craig Lowe, PhD, share lead authorship of the study.

The evolution of our brains

Song and Lowe didn’t start out intending to study psychiatric disorders. Instead, Kingsley and his colleagues have long been interested in identifying regions of the human genome that differ from those of our closest animal relatives such as primates. Studying these regions is a way to trace evolutionary changes that confer some of our uniquely human traits.

But many of these seeming advances, such as walking upright or changing jaws and teeth to accommodate different foods or larger brains come at a cost. New styles of walking and new diets in humans have brought with them a high incidence of bad backs, sore knees and impacted wisdom teeth. Some researchers have wondered whether the rapid evolution of our large, complex brains could also be the reason why humans suffer some psychiatric disorders that don’t appear to afflict members of other species.

It’s a great way for evolution to experiment by ‘tuning’ genes to achieve variable outcomes.

“Human evolution has given us big and active brains and a remarkable cognitive capacity,” Kingsley said. “But a side effect of this could be an increased risk for other, less desirable outcomes.”

About 3 percent of people worldwide suffer from bipolar disease or schizophrenia, which have few effective treatments. Sufferers are at increased risk of suicide, and the disorders are one of the top causes of disability. Although the two diseases are distinct, many previous efforts to identify their genetic causes have implicated genes involved in the transport of calcium into and out of brain cells in response to external signals. These calcium channels are responsible for many critical biological processes, and drugs modulating their function are widely used to treat high blood pressure and cancer.

One calcium channel gene in particular, CACNA1C, has repeatedly been associated with a risk of both schizophrenia and bipolar disorder. But until now, no one has been able to pinpoint any specific disease-associated DNA mutations within the coding region of CACNA1C. Instead, the culprit seemed to lurk within a stretch of 100,000 nucleotides in a noncoding portion of the gene called an intron.

In their quest to identify how the genome sequences of humans and primates vary, Song and Lowe discovered that the human CACNA1C gene contains a sequence that repeats as many as 1,000 times a 30-nucleotide sequence that is found only once in the chimpanzee genome. Large, repeated arrays such as these often form structures that can affect the expression of nearby genes but, because they are unstable when grown in many bacterial strains in the laboratory, they can stymie traditional sequencing methods.

‘Invisible to researchers’

“This massive array was, for the most part, invisible to researchers,” Kingsley said. “It caught our attention because it is located in the region that had been previously linked to schizophrenia and bipolar disease risk. We wondered whether, given all the ‘flavors’ of variation in length and sequences, some combinations of the repeats might confer increased risk to psychiatric disorders by affecting the expression levels of the CACNA1C gene.”

The researchers investigated whether certain sequence combinations in the repeated array correlated with a diagnosis of schizophrenia or bipolar disorder in participants in the 1,000 Genomes Project — an international effort to catalog and understand human genetic variation. They found that although some combinations were strongly linked to the development of schizophrenia or bipolar disorder, others were enriched in patients with protective versions of the gene. When Kingsley and his colleague tested different versions of the arrays for their effects on gene expression in cultured human neural precursor cells, the risk- and protective-associated sequence arrays showed variable abilities to modulate gene expression.

“There’s been a long-standing area of speculation in the literature that this kind of repeated array is likely to both change gene function and generate new variants that will further alter expression levels,” Kingsley said. “It’s a great way for evolution to experiment by ‘tuning’ genes to achieve variable outcomes.”

The researchers’ experiments suggest that those array combinations that appear to protect against the development of schizophrenia and bipolar disorder could increase the expression of CACNA1C. However, different cells and brain regions may react differently to the sequences, and it’s not yet clear precisely how changes in CACNA1C expression affect disease risk. Regardless, the involvement of a calcium channel gene is of interest because drugs targeting these channels are already widely used in humans.

“Better classification of patients based on their repeat arrays in the CACNA1C gene may help identify the particular patient cohorts most likely to respond to existing calcium channel drugs,” Kingsley said. “The best match between patients and drugs is not known right now, but we do hope that genotype-based drug targeting may lead to improved treatments in the future for these devastating diseases.”   

The research was supported by the National Institutes of Health (grant K25DE0253160), the National Science Foundation and the Howard Hughes Medical Institute.

Stanford’s Department of Developmental Biology also supported the work.

About Stanford Medicine

Stanford Medicine is an integrated academic health system comprising the Stanford School of Medicine and adult and pediatric health care delivery systems. Together, they harness the full potential of biomedicine through collaborative research, education and clinical care for patients. For more information, please visit med.stanford.edu.

2023 ISSUE 1

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