Patients with overproduction of protein from the chromodomain helicase DNA binding (CHD2) gene can develop a very rare and severe neurodevelopmental disorder with profound implications for their quality of life. This is true for Emma Broadbent, an eight-year-old girl with the condition that has left her wheelchair-bound and nonverbal with severe intellectual delays. Her disease, which has not yet been named, is part of a group of neurodevelopmental disorders called developmental and epileptic encephalopathy (DEE).
Now, scientists have identified the mechanism by which protein overproduction from CHD2 occurs in patients like Emma. It involves the deletion of a copy of a gene that codes for long noncoding RNA (lncRNA) called CHD2 adjacent suppressive regulatory RNA (CHASERR). Details of the study were published in The New England Journal of Medicine in a paper titled, “Neurodevelopmental Disorder Caused by De Novo Deletions in lncRNA Gene.” The scientists explain that their findings indicate that when CHASERR is present, it works like a brake, keeping CHD2 production under control. In patients like Emma who lack the gene, CHD2 protein production goes unchecked.
The findings are the work of an international group of scientists and physician-scientists from the Broad Institute, Northwestern University, the University of Nantes, the Weizmann Institute, and Baylor College of Medicine. It is the kind of collaborative effort that is essential for these types of rare gene discoveries, Vijay Ganesh, MD, PhD, first author on the paper and senior postdoctoral fellow at the Broad Institute and neurologist at Brigham and Women’s Hospital, told GEN in an interview. It also highlights the value of platforms for sharing data before peer review and networking with other scientists who may be studying similar questions. “This is a rare disease so we need to have a large antenna so to speak and be able to survey globally, rare genetic variants,” he said.
The initial link between CHASERR’s deletion and CHD2 protein production in mouse models was made in the lab of Igor Ulitsky, PhD, a senior scientist at the Weizmann Institute of Science who is also listed as a co-author on the NEJM paper. Separately, in the lab of Gemma Carvill, PhD, an assistant professor of neurology, pharmacology, and pediatrics at Northwestern University’s Feinberg School of Medicine and corresponding author on the study, scientists linked variants in CHD2 to the development of DEE, which is characterized by severe seizures and developmental delays.
Specifically, the team found that people with the unnamed disorder lack a chunk of DNA in one copy of the CHASERR gene. Having one broken copy of the CHASERR gene leads to an overabundance of the protein encoded by the CHD2 gene which sits adjacent to CHASERR. It is an unusual result because other studies linking CHD2 to brain development disorders found that the effect was actually due to lower CHD2 abundance.
Importantly, this is the first study to link the loss of a single copy of a lncRNA to a human disease—an earlier study linked the loss of two copies of a lncRNA to a separate developmental disease with effects on the skeleton and the brain. The link between CHASERR and CHD2 redefines CHD2 as a “Goldilocks”-like gene where too much or too little CHD2 disrupts typical human brain development.
With the connection made in three unrelated patients “we were able to finally classify this as a new disorder,” said co-senior author Anne O’Donnell-Luria, MD, PhD, co-director of the Broad Center for Mendelian Genomics, clinical genetics physician at Boston Children’s Hospital, and assistant professor of pediatrics at Harvard Medical School. Furthermore, “the unique mechanism we’ve identified here suggests that there are more long noncoding RNAs underlying rare genetic disorders still to be found, which could potentially bring answers for some of the many families still waiting for a rare-disease diagnosis.”
It’s certainly a compelling case for more research into lncRNAs, which have been largely understudied since their discovery in the 1990s. Thousands of long noncoding RNAs have been discovered in the intervening years, but very little is known about their significance in human disease. For Carvill, the findings are the tip of a much bigger iceberg. “There’s no reason at all to think that this is an isolated case,” she said. It’s more likely that “these long noncoding RNAs and noncoding regions are implicated more broadly across human disorders.”
Putting a spotlight on noncoding elements
As is often the case with ultra-rare diseases, the sequence of events culminating in the NEJM study begins with a family searching for a diagnosis for their daughter. Her challenges began at birth leading her to spend the first weeks of her life in intensive care. By age 8, Emma had spent hundreds of days in the hospital. Her disorder has left her functioning at the level of a 3-5-month-old alongside other major health challenges.
Those early days in the hospital provided some of the earliest clues that Emma’s condition might be something unusual. But there were other pieces of evidence. MRI scans of her brain revealed white matter abnormalities that pointed to a potential genetic disorder. The evidence pointed to a genetic cause for her condition but an analysis of the protein-coding parts of the genome did not provide answers.
Emma’s parents pushed for years for an accurate genetic diagnosis for her with their search leading them to enroll in the Broad’s Rare Genomes Project and the National Institutes of Health’s Undiagnosed Diseases Program (UDN). They knew that identifying the genetic basis of her disorder could help them find patients with a similar disorder, and get the condition formally recognized as a new disease. They could also better advocate for research into new treatments.
At UDN, scientists identified the mutation in a single copy of CHD2 from their analysis of Emma’s DNA and RNA. Armed with that information, the family searched for scientists with expertise in CHD2 which led them to Carvill’s lab at Northwestern University and their work linking CHD2 to epilepsy. They also connected with other families affected by CHD2-related disorders. Those connections furnished additional evidence to the Broadbents that Emma’s condition may not be epilepsy. Specifically, she had more severe physical and mental disabilities. Also, her EEG readings were abnormal but she had less severe seizures than other children with CHD2 variants.
Meanwhile, scientists at the Broad found the same CHD2 variant in Emma but decided to see if there were other changes in the regions near the gene. This was when they learned that Emma’s variant was close to a deletion of a DNA segment that overlapped the CHASERR lncRNA gene, which sits next to CHD2 in the genome. This led them to the work from Ulitsky’s team at Weizmann. In 2019, the lab shared a preliminary report of their discovery that mice with one copy of the CHASERR gene deleted had high levels of CHD2. They also demonstrated that the excess CHD2 observed in these patients came from the DNA strand that lacked CHASERR.
Analyzing both whole-genome and transcriptome data, the researchers found a similar pattern in Emma. Deletion in a single copy of CHASERR decreased its expression by half while CHD2’s expression was up. Next, Carvill’s lab used skin cells from Emma to generate neural progenitor cells. By analyzing the cells, the researchers were able to link the deletion of a single CHASERR allele with increased CHD2 protein expression on the same strand. It explained why Emma’s cells generated too much CHD2 unlike other children with other CHD2 disorders who have too little.
For Emma’s father, Brian Broadbent, a digital marketing executive in Dallas, TX, and a co-author on the study, this diagnosis has been a long time coming and opens the door to a possible cure for his daughter and children like her. The team found the other two children, both of whom are from France, who have similar symptoms to Emma and were participants in the study through the MatchMaker Exchange, a rare disease research. Emma’s father and her mother, Julia Broadbent, are now pushing for more research into CHASERR, how it works, and how it might be treated.
“Emma suffers a lot, and this adds purpose to her life because she’s helping science,” he said. “We felt we had a responsibility to push this forward as much as we can because it’s going to impact future children. This is just scratching the surface of something that could be really important. We intuitively understood that this was a lot bigger than just Emma.”
In fact, there are likely more patients with the disorder that have not been diagnosed, Ganesh said. “We showed, through our analysis of the individuals in the study, that the de novo deletion was caused by recombination of DNA mediated by repetitive elements,” he told GEN. “This was not just sort of a random event of the DNA rearrangement” meaning it occurs at some rate in the population. “It’s highly likely that there are more individuals that are undiagnosed with severe developmental delay due to loss of CHASERR. And that the reason that they’re not diagnosed is because this region in the noncoding genome is not routinely analyzed in standard clinical genetic testing,” he said.
Implications for neurodevelopmental disorders
The impact of these findings may very well extend beyond a single rare disease to include other CHD2-linked neurodevelopmental disorders like autism and epilepsy. In a 2013 study, Northwestern’s Carvill and her team identified a subset of epilepsy and autism patients with a version of CHD2 that produces too little protein.
Advances in gene editing may be the key to manipulating CHASERR to boost CHD2 protein production which could help those patients. Currently, about 30% of patients with epilepsy do not respond to standard antiseizure medications. And even for patients who do respond, the drugs treat the symptoms of the disease. Gene therapies that target CHD2 would go after the source of the disease with effects that are likely to last longer, if they work.
Carvill and her team are open to the possibility. Her lab continues to study Emma’s cells to better understand CHASERR’s impact and she is developing cellular models that could help evaluate potential therapies. “Everything we currently know about disease is rooted in a genetic variant in a gene, and that is because that genetic variant either destroys the function of the protein or it alters the function of the protein, but it’s all protein-based, and that’s mostly because we’ve been doing exome sequencing,” she said. “But we know we’re still missing things because there are still a significant percentage of kids in pediatric epilepsies and other disorders as well where we suspect they have a genetic basis, but we just haven’t found it yet.”
Ganesh hopes that studies like this encourage more scientists to look into noncoding genetic elements like lncRNAs especially when rare diseases are suspected. “This work highlights a regulatory mechanism that’s baked into the genome, for genes that need to be precisely expressed,” he said. “They’re clearly quite active, but they remain hidden to us without the right data and analysis, so there’s a lot of room for progress.”
In future studies, he hopes to identify additional noncoding genes that are linked to rare diseases beyond those involved in neurodevelopment. “The group that we work in at the Broad is focused on getting patients with undiagnosed genetic disease an answer. So we are working to find ways to identify additional genetic variance in the noncoding genome, which is vast and represents the overwhelming majority of the human genome. It’s an unexplored space,” Ganesh told GEN.
For the three children in the study, now that scientists know what caused their disease, the next goal is finding a way to treat it. Ganesh and members of the broader research team are exploring the potential of using a targeted gene therapy to fine-tune CHASERR’s expression of CHD2. In this case, the treatment would be to turn down its expression but ideally they could develop something that would also work in the opposite direction in a different disease. One solution proposed in the paper would be to use an antisense oligonucleotide therapy that partially inhibits either CHD2 or CHASERR or both to provide some therapeutic benefit.
“Much more work needs to be done to demonstrate that sort of optimization of this Goldilocks problem,” he said. But it’s certainly a “worthwhile endeavor.”
