University of Toronto researcher, Dr. Lucy Osborne, aims to discover novel genetic factors contributing to the wide spectrum of phenotypes observed in cognitive disorders. She strives to help families better predict the clinical implications of such complex conditions.
Neta Pipko and Celia Pennimpede
Identifying the correct diagnosis for a child’s underlying behavioural and learning disabilities is challenging since the same symptoms can be caused by a number of disorders. Therefore, when the pieces of the puzzle finally begin to form a picture, parents start to experience an immense sense of relief when placing a concrete label on their child’s symptoms. A diagnosis, however, may often serve as a double-edged sword when it comes to neurodevelopmental disorders (NDDs).
NDDs are a group of complex conditions that affect brain development and growth, impairing several cognitive and behavioural features such as learning, self-discipline, language, and social communication1. Common NDDs include conditions such as intellectual disability, autism spectrum disorder (ASD), and attention-deficit/hyperactivity disorder (ADHD). Signs and symptoms appear early in childhood development and can fall within a wide spectrum, ranging from mild to severe phenotypes1. Pinpointing the correct diagnosis is particularly challenging since symptoms often overlap and co-occur amongst different NDDs. Consequently, therapeutic interventions should be tailored to the specific NDD and its characteristic features. Therefore, an official diagnosis can offer parents a tremendous wave of comfort and ease. However, the battle does not end here, since the large spectrum of phenotypes adds a layer of uncertainty to managing this diagnosis.
Toronto-based researcher, Dr. Lucy Osborne, hopes to help parents get some of the answers they are looking for. Dr. Osborne is a principal investigator and professor at the University of Toronto in the Departments of Medicine and Molecular Genetics. She also holds the title of Canada Research Chair in Genetics of Neurodevelopmental Disorders. Her work largely focuses on two rare NDDs, Williams-Beuren syndrome (WS) and 7q11.23 duplication syndrome (Dup7). WS and Dup7 are caused by the reciprocal deletion and duplication of the same ~25 genes on human chromosome 7, respectively (Fig 1)2. Deletions and duplications are structural genetic changes called copy number variants (CNVs) that lead to the loss and gain of genetic material3. Studying reciprocal CNVs of the same genetic segment offers Dr. Osborne a golden opportunity to evaluate how the copy number of a gene may impact neuronal development.
“A small set of genes can have such a huge impact on cognition and behaviour,” Dr. Osborne answers when asked what fascinates her about the two NDDs she studies. “It really changes how somebody appears and sees the world.”
WS and Dup7 are distinct disorders with overlapping and opposing phenotypes (Fig 2), likely attributed to the varying copy number of some of the genes in the 7q11.23 critical genetic region2. While unique in their own ways, both of these NDDs are associated with a wide spectrum of clinical manifestations. “A syndrome is not written in stone. You have a list of phenotypes spread across all the people you see, and very few have all of those symptoms, but the question is why,” says Dr. Osborne. She revealed that the greatest challenge is having no way of predicting the extent of a child’s disability despite reaching a final diagnosis. “Parents want to make some sort of plan or have some expectation about what that diagnosis is going to mean, but there is huge variation,” says Dr. Osborne. “We have no predictors right now and that is [a huge burden] for families.”
Interestingly, two children with the same CNV and diagnosis may fall on opposite ends of a phenotypic spectrum. Dr. Osborne aims to unravel what might be contributing to this widespread continuum to find some predictors for families. In a recent collaborative study with SickKids genetic scientist Dr. Ryan Yuen, the two research groups investigated why some individuals with Dup7 have an additional ASD diagnosis. “Anecdotally, a lot of the [Dup7] kids coming into our study already had a diagnosis with autism, but most of them did not have autism,” Dr. Osborne explained. By virtue of their separation anxiety and shy nature, those kids got labeled and lumped in with other ASD children without going through a formal diagnostic test. However, after putting them through the proper assessment, it was identified that most of the Dup7 kids were misdiagnosed, rather only ~20% of them had an additional clinical ASD diagnosis5. Notably, 20% appears as a striking increase when compared to the general population’s ASD prevalence rate of ~1.5%6. Therefore, Dr. Osborne wondered, “could they (Dup7 kids with ASD) have a ‘second hit’ layered on top of this one CNV that pushes them over the edge that the others do not?”
Unlike monogenic diseases that are caused by a single gene, complex disorders have an array of different variants (mutations) and environmental factors contributing to the disease outcome. Thus, Drs. Osborne and Yuen hypothesized that Dup7 children diagnosed with ASD are likely to carry additional rare damaging variants in ASD-relevant genes. These additional variants are known as genetic modifiers, which suppress or enhance the phenotype of the primary disease-causing gene7. Typically, the more additional variants or ‘hits’, the more severe the phenotype8. This is known as the ‘multiple hit model’, which contributes to the wide variability and overlap in symptoms observed in individuals with NDDs2,8.
To test their hypothesis, they performed whole-genome sequencing (WGS) on twenty Dup7 individuals, half of whom had an ASD diagnosis. WGS is a tool that reads the entire DNA sequence of an individual, which they used to look for second hits across the genome that may be contributing to the ASD phenotype. Unfortunately, they did not identify any variants that could explain the ASD diagnosis9. Surprised by this analysis, Dr. Osborne states, “It wasn’t as simple as that. It wasn’t the CNV and one additional hit that will push you towards autism. It’s more complicated than that”. She explains that rather than one large second hit, there may be a collection of smaller hits with smaller impacts that ultimately add up.
This concept can be visualized as a cup with two thresholds, one for Dup7 filled about halfway, and one for the ASD phenotype bordering the top of the cup (Fig 3)2. Dr. Osborne describes that on their own, modifier genes with small effects are not enough to fill up the cup and push you over either threshold. However, for those with Dup7, their cups are already half full and have surpassed the first threshold. Therefore, Dr. Osborne presumes that unlike in typically developing children, these additional small modifiers may be the distinguishing factors that push the kids with Dup7 and ASD, over the edge (Fig 3, Threshold B).
Even though they failed to identify a clear correlation between having a second hit and an ASD diagnosis, it does not mean these hits are not present. Dr. Osborne explains that the smaller hits are much more difficult to find. In fact, the effects of genetic modifiers are becoming more apparent in complex diseases, including NDDs, and will likely become a major focus of genomics research moving forward.
When asked whether the lack of association with ASD was discouraging, Dr. Osborne said, “No, not really. You ask questions and do not know what answer you will get”. In fact, the team discovered a phenotypic association when shifting their focus towards examining Dup7 as a whole, rather than splitting the children into groups based on ASD diagnosis. They successfully found that some rare variants correlate to various clinical phenotypic measures, such as intellectual ability and adaptive behavior9. This finding could lead to the future development of polygenic risk scores for Dup7. Polygenic risk scores estimate an individual’s relative risk of developing a disease by calculating the weighted sum of all genetic and environmental contributors10. This cumulative measure can hold predictive value in estimating severity in such phenotypic features. In the case of Dup7, polygenic risk scores can estimate an individual’s level of cognition and aspects of behaviour. Ideally, this information could help inform families about whether their child will be shy, socially independent, communicative, and what their intellectual abilities may look like in the future. “Being able to place your child at one extreme or the other would be valuable,” Dr. Osborne explains. This study “gives us hope that there will be other measures that we will be able to find” to further increase the predictive value of these symptoms.
The degree of success attained in identifying such predictors sparked a similar study in children with WS. Dr. Osborne shared that they are in the process of examining whole genomes of ~250 WS children for potential correlations between rare variants and scores measuring cognitive abilities, patterns in social behavior, as well as cardiovascular outcomes. Like Dup7, Dr. Osborne hopes this research brings them one step closer to finding enough predictors to develop polygenic risk scores for WS as well. Identifying an individual’s relative risk can allow for the introduction of personalized therapeutic interventions early on in life, such as speech therapy or cardiovascular monitoring. While these scores hold some predictive power, they should always be taken with a grain of salt, as they should not be used for diagnosis.
Despite not finding the associations they were looking for with ASD, Drs. Osborne and Yuen did find associations with phenotypic measures that may explain some of the variation observed with NDDs. Shifting gears when studying complex disorders is often needed as many different genetic, environmental, and lifestyle factors contribute to the overall clinical manifestation of a disease. “Don’t be afraid to tackle something that is complex,” says Dr. Osborne. “You can still find answers for things even if you know it’s going to be complicated, and it really does take teamwork.” Dr. Osborne shares that while the research field was previously quite competitive, the scientific community is beginning to realize that there is large value in collaborating and integrating patient data. Examining syndromes from different angles will give you a more comprehensive insight into NDDs, ultimately granting families more certainty when planning and investing in their child’s future.
References
1. Morris-Rosendahl, D. J. & Crocq, M.-A. Neurodevelopmental disorders—the history and future of a diagnostic concept. Dialogues Clin. Neurosci. 22, 65–72 (2020).
2. Osborne, L. R. & Mervis, C. B. 7q11.23 deletion and duplication. Curr. Opin. Genet. Dev. 68, 41–48 (2021).
3. Hastings, P., Lupski, J. R., Rosenberg, S. M. & Ira, G. Mechanisms of change in gene copy number. Nat. Rev. Genet. 10, 551–564 (2009).
4. About Us | Osborne Lab. http://individual.utoronto.ca/osbornelab/.
5. Klein-Tasman, B. P. & Mervis, C. B. Autism Spectrum Symptomatology Among Children with Duplication 7q11.23 Syndrome. J. Autism Dev. Disord. 48, 1982–1994 (2018).
6. Lyall, K. et al. The Changing Epidemiology of Autism Spectrum Disorders. Annu. Rev. Public Health 38, 81–102 (2017).
7. Rahit, K. M. T. H. & Tarailo-Graovac, M. Genetic Modifiers and Rare Mendelian Disease. Genes 11, 239 (2020).
8. Guo, H. et al. Genome sequencing identifies multiple deleterious variants in autism patients with more severe phenotypes. Genet. Med. 21, 1611–1620 (2019).
9. Qaiser, F. et al. Rare and low frequency genomic variants impacting neuronal functions modify the Dup7q11.23 phenotype. Orphanet J. Rare Dis. 16, 6 (2021).
10. Lewis, A. C. F. & Green, R. C. Polygenic risk scores in the clinic: new perspectives needed on familiar ethical issues. Genome Med. 13, 14 (2021).
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