NEW YORK – An international research team led by investigators at the Broad Institute and Northwestern University Feinberg School of Medicine has linked an extremely rare neurodevelopmental disorder to a gene that encodes a long noncoding RNA.
The new disorder, they found, is caused by the deletion of one copy of the CHASERR, or CHD2 adjacent, suppressive regulatory RNA, gene. CHASERR encodes a lncRNA that typically controls expression of the CHD2 gene.
This represents the first time a human disease has been determined to be caused by the loss of one copy of a lncRNA gene, which doesn't make proteins and instead regulates gene activity. Based on these findings, reported in the New England Journal of Medicine on Thursday, a Broad-led team plans to look more closely at noncoding genomic regions in other patients with unsolved rare diseases.
"Identifying CHASERR opens the possibility that there are additional genes in the noncoding genome that are causing specific syndromes," said Vijay Ganesh, a neurologist at Brigham and Women's Hospital and co-first author on the paper. "It opens up a new class of genes that should be investigated in identifying the cause of undiagnosed rare disease."
The findings also lay the groundwork for developing new treatments based on CHASERR, though researchers will have to be cautious about targeting a so-called "Goldilocks" gene.
The NEJM paper, years in the making, began with outreach from the parents of Emma Broadbent, an 8-year-old girl with a severe neurodevelopmental disorder that caused delays in brain development that have left her nonverbal, unable to walk, and requiring a feeding tube. Her parents were seeking answers to understand what was causing her condition.
The Broadbents connected with the Broad's Rare Genomes Project, which provides genome sequencing to patients with rare and undiagnosed diseases that are suspected to be genetic, after struggling to get an accurate diagnosis for their daughter's condition. Here, researchers ultimately identified the CHASERR deletion.
They determined that the deletion of the lncRNA gene resulted in an overproduction of CHD2 protein and, in turn, caused Emma's disorder. Interestingly, an underproduction of CHD2 protein has previously been linked with other neurodevelopmental disorders, such as autism and epilepsy.
"These findings indicate that CHD2 has bidirectional dosage sensitivity in human disease," Ganesh and colleagues wrote in the paper. "We recommend that other lncRNA-encoding genes be evaluated, particularly those upstream of genes associated with Mendelian disorders."
Since discovering Emma's CHASERR deletion, researchers have identified two other patients in France, unrelated to one another, with similar mutations.
The discovery of this condition caused by CHASERR haploinsufficiency highlights why it's critical to examine the 99 percent of the human genome involving noncoding genes, according to Gemma Carvill, an assistant professor of neurology, pharmacology, and pediatrics at the Northwestern University Feinberg School of Medicine and a co-senior author on the paper.
The Broadbents contacted Carvill, who has studied CHD2's link to autism and epilepsy, and other CHD2 researchers after learning about Emma's CHASERR deletion.
"There are thousands of long noncoding RNAs in the genome, and we really don't have a good feel for which ones are functional or which ones matter in the context of disease," Carvill said. "We have a strong suspicion that many rare diseases, like Emma's case, are likely to be genetic, but they're not … in the 1 percent of the genome that codes for proteins."
Her lab will continue to study how CHASERR regulates CHD2 expression, as well as the role of noncoding genes in other neurodevelopmental disorders.
Carvill and colleagues believe that patients with related neurological disorders, such as epilepsy, could potentially be treated with gene-targeting therapies. Using noncoding regions such as CHASERR to influence expression of nearby genes could be one approach for treating these disorders, and CHASERR could represent a target for RNA-based therapeutics aiming to control the amount of CHD2 protein that's produced. One of the approaches Carvill's lab is investigating involves developing an antisense oligonucleotide to target CHASERR.
However, since too much and too little of the CHD2 protein can disrupt brain development, potential drug developers will have to be cautious. "This 'Goldilocks problem' will need to be addressed, potentially through preclinical models of partial inhibition of CHASERR or CHD2 or both to ameliorate haploinsufficiency of either gene," researchers wrote in the paper.
The study authors also stressed the importance of examining noncoding genes — which aren't included in standard clinical genetic testing — when working to diagnose unsolved rare genetic disorders, with CHASERR haploinsufficiency serving as an example of what that can look like.
However, it can be difficult to identify disease-causing genes in the noncoding region of the genome, noted Ganesh, who is a senior postdoctoral fellow in the lab of Anne O'Donnell-Luria, codirector of the Broad Center for Mendelian Genomics and co-senior author on the paper.
In fact, there was a convergence of events needed to enable this research team to do so, he said.
The Broadbents spearheaded the effort to look more deeply into their daughter's genome, after they began to doubt an initial determination that Emma's condition was caused by a variant in the CHD2 gene known to cause epilepsy, Ganesh said. The family noticed that their daughter had more severe physical and mental disabilities, but less severe seizures, than other children.
The family drove this research effort forward and asked important questions, which is reflected in the fact that Emma's father, Brian Broadbent, is also a coauthor on the NEJM paper. Now, the Broadbents are advocating for additional research into CHASERR, including how the gene works and how it might be leveraged in new treatments. Brian Broadbent is a co-president of the Coalition to Cure CHD2, a group of parents and other experts who are raising money for research into treatments for CHD2-related conditions. Carvill leads the group's scientific advisory board.
But even once a mutation is detected in a noncoding region of the genome, it's challenging to determine what that gene does and whether it's causing the disease in question.
Establishing that mechanism requires collaboration with basic scientists. In this case, the discovery that CHASERR regulates CHD2 had been reported previously by paper coauthor Igor Ulitsky, a lncRNA researcher at the Weizmann Institute of Science in Israel, who had published the finding based on mouse studies in a preprint.
It also helped that CHASERR was adjacent to the CHD2 gene and that that gene was known to cause disorders with similar features to the condition they were seeking to diagnose. And, researchers were able to identify the two other patients with this condition through Matchmaker Exchange, a research network focused on rare genetic diseases.
Altogether, this work has pointed to a broader category of genes that potentially can drive disease and may be amenable targets for new treatments. "It potentially identifies a whole other class of genes that could be targeted to rescue the expression of a nearby gene," Ganesh said. "If those can be more definitively identified."