Alleviating SYNGAP1 haploinsufficiency in disease models by redirecting alternative splicing

Research from UChicago shows how reduced SYNGAP1 expression can be restored through genetic knockouts and the application of synthetic splice-switching oligonucleotides in models of human diseases.

The genetic process of coding for functional proteins is plastic during splicing, the process during which some segments of genetic material, called introns, are removed while assembling messenger RNAs. Introns can be removed from a single RNA strand in different ways to modify the blueprint and the resulting protein, with the consequences of different functions in the cell. Changes in splicing patterns allow organisms to adapt as they grow and respond to their environments and redirecting splicing has been increasingly used to treat human diseases.

A new study by researchers from the University of Chicago shows that redirecting alternative splicing can upregulate SYNGAP1 expression and alleviate neurodevelopmental deficits in mouse models of human diseases. The SYNGAP1 protein is critical for the plasticity of signal transmission between neuron synapses, and De novo loss-of-function SYNGAP1 mutations are among the leading causes of intellectual disability and autism.  So-called haploinsufficient mutations to this gene cause one copy to become inactive, while the remaining normal copy can’t produce enough protein, disrupting neuronal functions.

In the new study, the researchers show that an alternatively spliced version of Syngap1 in mice triggers mRNA decay that attenuates its expression in normal neural development. However, they show that reversing this naturally occurring process in mice upregulated Syngap1 expression and alleviated haploinsufficient phenotypes in compound heterozygous mouse models.

“SYNGAP1 is such an important molecule and the unproductive splicing event is intriguing,” said Xiaochang Zhang, PhD, Assistant Professor of Human Genetics and the Neuroscience Institute and senior author of the study, published March 13 in Neuron. “We are particularly interested in the regulatory mechanism and function of the SYNGAP1 alternative splicing event in vivo, and to what extent it can be used as a way to upregulate protein expression.”

The researchers also demonstrate how a bit of synthetic genetic material called splice-switching oligonucleotides, or SSOs, can redirect the alternative splicing process and upregulate SYNGAP1 expression in human neurons. Since the same alternative splicing events are conserved in the human SYNGAP1 gene, in addition to the mouse models, the researchers used human neurons derived from induced pluripotent stem cells. In this model, the SSOs also suppressed mRNA decay and upregulated SYNGAP1 expression. This further suggests that averting the alternate splicing event, either through genetic knockouts or SSOs, can upregulate SYNGAP1 expression, suggesting a potential future pathway to treatments.

The study, led by Runwei Yang, PhD and Xinran Feng, from Zhang’s lab, was a collaboration among multiple UChicago teams. Christian Hansel, PhD, Professor of Neurobiology, and Alfredo Garcia, PhD, Assistant Professor of Medicine, both contributed significant neurophysiology studies to this work on top of Zhang’s molecular and genetic analyses.

Garcia, who studies neurodevelopment in the context of conditions ranging from opioid overdose to epilepsy and sleep apnea, said the research opens a new avenue for understanding the origins of cognitive dysfunction. “This study is a nice example of strong collaboration within the university, bringing in two different areas of expertise, both on the neurophysiology and the genetics,” he said.

The study, “Upregulation of SYNGAP1 expression in mice and human neurons by redirecting alternative splicing,” was supported by the Neuroscience Institute, the Quad Undergraduate Research Scholarship, the DENDRITES Leadership Alliance Program, the National Institute of Neurological Disorders and Stroke, the National Center for Advancing Translational Sciences, the National Institute of General Medical Sciences, and the National Institute of Mental Health. Additional authors include Alejandra Arias-Cavieres, Robin M. Mitchell, Ashleigh Polo, Kaining Hu, Rong Zhong, Cai Qi, Rachel S. Zhang, Nathaniel Westneat, Cristabel A. Portillo, and Marcelo A. Nobrega from the University of Chicago.

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