he identification of the gene and causative mutation for a human disease is an important breakthrough for patients and clinicians. It provides a DNA diagnosis, which can help with family planning, connecting families affected by the same condition or clinicians who could better define or study the condition. However, it is fundamentally a descriptive, hypothesis-generating milestone. The question immediately becomes how knowledge of the causative mutation can be used to better treat the patient. The answer almost invariably lies in understanding the disease gene’s function and how it is regulated within its biological pathway. This is where the experimental power of model organisms plays such an important role.

Advances in genomics have transformed our ability to identify the specific gene and set of gene mutations that cause a rare disease. Yet for most rare disease genes, we lack insight into the gene’s normal biological function, how the identified mutations cause disease in patients, or what therapies could be useful. Model organisms (yeast, worm, fly, zebrafish, mouse, and others) offer powerful experimental tools to confirm the pathogenicity of rare disease gene variants, characterize the gene’s biological function, and identify potential therapeutic targets and therapies. For these reasons, the Canadian Rare Diseases: Models and Mechanisms (RDMM) Network was established in 2014 to catalyze connections between clinicians discovering new disease genes and researchers able to study equivalent genes and pathways in model organisms.

A rare disease is generally defined as occurring in <1 in 2,000 people, and although individually rare, in aggregate it represents a significant medical burden. It has been estimated that there are >10,000 rare diseases affecting over 400 million people globally, and about 70%-80% of these diseases result from the mutation of a single gene. To date, Online Mendelian Inheritance in Man (OMIM) documents mutations in >4,000 disease genes that are responsible for >6,000 single-gene highly penetrant inherited disorders, and these numbers continue to grow.

Because of the small number of patients for any single rare disease, the conventional approach of genetically mapping the position of an inherited causative gene mutation in families, and then using that positional information to clone the corresponding gene, has not been feasible for thousands of rare diseases. However, thanks to a technological breakthrough in the late 2000s that dropped the cost of DNA sequencing 10,000-fold, it became economically feasible to sequence the entire genomes (or entire exomes, referring to the 1%-2% of the genome which encodes proteins) of multiple patients that have the same rare disease. Computational analysis is then used to identify the candidate causative disease gene mutation common across all the patients, which is then further validated in follow-up experiments.

The first examples of this approach were reported in 2010 (e.g., Miller syndrome), and since then, there has been a tsunami of rare disease gene discoveries (on the order of 250 new disease gene discoveries per year). There are still thousands of unsolved rare diseases, so the identification of the genetic mutations that cause additional rare diseases is ongoing, and the catalogue of rare disease genes will continue to grow over the next decade.

The Experimental Power of Model Organisms

Comparison of the genome sequences of yeast, worm, fly, zebrafish, mouse, and human revealed how all organisms are built from the same set of genes that are evolutionarily conserved. Thus, the experimental tractability of model organisms can be used to understand the effects of a disease-causing mutation in a biological context through the analysis of the equivalent (orthologous) gene. Orthologous genes are genes found in different species that evolved from a common ancestral gene. These genes usually retain identical or similar functions in the organisms in which they are found. By studying these conserved genes in various organisms such as yeast, worm, fly, zebrafish, and mouse, scientists can study the consequences of human gene mutations in these model organisms and shed light on the underpinnings of the human disorder.

Due to the unique biology and the complementarity of the genetic toolboxes available for each model, the value of this group of model organisms, in aggregate, far outweighs any one alone. The biological insights obtained for understanding human disease gene function can guide the identification of candidate therapeutic targets and the development of experimental platforms for drug discovery.

The Canadian RDMM Network

The Canadian RDMM Network has created a rapid and direct pathway from gene discovery to functional characterization studies in model organisms. The overarching goal is to connect a clinician scientist, immediately at the time of a novel rare disease gene discovery, with a basic scientist who is poised to study the orthologous gene in a model organism. RDMM essentially serves as a matchmaker. The central resource of the RDMM Network is a web-based directory of Canadian model organism researchers (“the Registry”) built to facilitate identifications of suitable collaborators for applying clinicians.

As of May 2024, 770 model organism researchers have registered 17,117 genes of interest. With the aid of the computational inference built into the registry, this translates to the coverage of 9,993 human genes. RDMM uses a committee process to identify and review potential clinician-basic researcher matches and approve $30,000 Canadian dollars in seed funding. Furthermore, through collaborations with specific disease foundations, the RDMM regularly organizes joint open calls to encourage submissions for a specific disease or category of diseases.

Since 2014, RDMM has made 125 clinician-MO scientist connections and funded more than 150 functional characterization proposals. In many cases, the establishment of these connections has led to scientific insights into the molecular mechanisms of rare disease, high-impact papers, and in some cases a rationale for identifying novel therapies. In addition, these connections foster long-term collaborations through external grants.

For example, a connection was made between a clinical investigator, Clara van Karnebeek (Vancouver), and a zebrafish scientist, Xiao-Yan Wen (Toronto). Biallelic mutations in NANS, the gene that encodes the synthase for sialic acid, were found to be the cause of infantile-onset severe developmental delay and skeletal dysplasia. Knockdown of this gene in zebrafish embryos resulted in abnormal skeletal development. Furthermore, it was found that exogenously added sialic acid into the zebrafish embryo water partially rescued the skeletal phenotype, suggesting a therapeutic approach for future studies.

In 2019, RDMM established international linkages with emerging similar networks in Europe, Australia, and Japan. To facilitate community uptake, the RDMM Registry was made portable, customizable, and linkable with other instances, and the RDMM committee structures and process were made freely available. This allows potential cross-border connections of clinicians and basic researchers when a match is not found within the regional network. The open software also facilitates easy establishment of additional regional networks to support regional and global collaborations. In 2023, in collaboration with the Canadian Stem Cell Network, RDMM expanded the scope of model systems to include the use of human cell models, including primary patient-derived cells, cell lines derived from iPSCs (induced pluripotent stem cells), and organoids.

What’s Next?

Within the next 10-15 years, we can expect that essentially all the variants and genes that are mutable to a disease phenotype will have been identified. Gene and pathway functional studies in model organisms will continue to play a key role in translating these discoveries to the benefit of patients well into the future. The way forward is to maintain an appropriate balance of research funding between fundamental studies aimed at mechanistic understanding of gene function, and translational studies aimed at direct application to human disease. A key to success in maximizing benefit to patients will come from the continued establishment of connections, collaboration, and crosstalk between basic and clinician scientists. The Canadian RDMM Network will continue to help initiate meaningful collaborations between clinicians and model organism researchers at the earliest timepoint of disease gene discovery to help advance rare disease research locally and globally.