The genetic modifier approach: identifying the right target for rare diseases

Most rare diseases are caused by a single gene defect, but severity can vary considerably among patients. Modifier genes can help explain that variability and can alter or even prevent disease onset and progression, making them appealing therapeutic targets. However, the identification of these genes is challenging. Enabling the systematic discovery of these largely uncharted targets can be a valuable opportunity for development of novel therapies.

Genetic-based therapeutics hold significant promise in the clinic 

Despite the growing number of genes linked to human disease, the proportion of genes targeted by approved therapies remains low. A significant challenge in developing novel therapies is the limited understanding of how the target gene influences the underlying disease biology, which contributes to the considerable attrition observed in investigative therapies.¹ With novel emerging drug modalities further expanding the druggable genome, connecting the right target genes to a disease will only become more relevant. Strikingly, a strong genetic link between target and disease biology is emerging as a predictor for success in clinical trials.^2,3 This is exemplified by drugs that target disease-specific genes or genetically distinct patient subsets which are more likely to succeed in demonstrating efficacy in clinical development.⁴ For the treatment of rare genetic disorders especially, drugs with genetically supported targets are more than twice as likely to be approved⁵, thereby indicating genetics and genomics can empower companies to develop better drugs.

Leveraging genetic evidence to develop new therapeutics has been successful in the past. An example is Vertex Pharmaceuticals’ approved treatment for cystic fibrosis (Kalydeco)⁶, which counteracts the outcome of a specific mutation thereby stabilising the defective CTFR protein, and restoring proper pulmonary function. This is one of many examples where genetic information was critical in generating a clinically effective and efficient compound. As most inherited diseases are caused by gene mutations that lead to a defect or loss of function, the benefit of using genetics to find new drug targets is compelling. Nevertheless, directly targeting a protein encoded by a disease-causing variant is rarely simple.

Genetic modifiers: the safeguard for genetic disorders 

This is where genetic modifiers come into play. Genetic modifiers are genes that can influence the phenotypic outcome of a disease-causing gene variant, thereby either exacerbating or ameliorating the severity of the disease.⁷.This results in a diverse range of symptoms among patients. Especially in rare disorders, individuals with identical pathogenic mutations may present with different clinical symptoms. For example, Gaucher disease, an autosomal recessive lysosomal storage disorder caused by mutations in the GBA1 gene, manifests in different phenotypes even within families that have similar genotypes.⁸ Genetic modifiers that suppress the effects of a disease-causing gene, genetic suppressors, can protect carriers from the disease. They may dampen and, in some instances, even fully overcome monogenic disease traits. A human genetics study involving over half a million genomes from healthy people notably identified a small number of individuals that carried fully penetrant disease mutations, yet did not exhibit any clinical symptoms of the disease.⁹ Such insights highlight the power of genetic modifiers in inherited conditions and their therapeutic potential. Nevertheless, their identification is a challenging task and thus remains an underexplored area of study. However, dvancements have led to renewed interest in genetic modifiers and their prospects in the development of novel therapeutics for rare diseases.

Identifying genetic modifiers as new therapeutic targets

How can we tackle the elusive search for genetic modifiers?

Methods such as human population genetics, model organisms and functional genomics have been effectively employed for that purpose.¹⁰ Furthermore, improved access to patient whole genome sequencing data and recent progress in genome editing are now enabling both observational and experimental approaches to identify modifier genes, notably for rare diseases.

In the human genetics field, genetic modifiers have been successfully identified through family linkage analyses¹¹, genome-wide association studies (GWAS)¹², and using whole-genome (or exome) sequencing.¹³ While the increasing availability of genome sequencing will facilitate the identification of modifier genes in the future, there are a few inherent challenges. For one, these approaches are reliant on the inclusion of individuals with modifier variants. However, resilient individuals are infrequent in the general population⁹ and in more targeted studies examining a specific disease, patients with a modified course of disease may elude inclusion due to effective suppression or a compound phenotype. The modest sample sizes which are typical in rare disease research make it inherenttly challenging to obtain sufficient power to confidently associate gene variants to phenotypes. Lastly, interpreting the functional relevance of gene variants associated with phenotypic outcome is not straightforward. Nonetheless, genomics-based identification will only increase in relevance for the identification of modifier genes as genome sequencing becomes more prolific and the analysis toolbox expands.

Studies in model organisms have long observed that the genetic background is a major determinant of phenotypic outcome.¹⁴ In particular in baker’s yeast, researchers could systematically identify gene-gene interactions, including genetic suppressors.¹⁵. Access to complex libraries of mutant strains yielded significant insights into genetic suppressor interactions which suggests similar genetic connections are relevant to human phenotypes.¹⁶ Since directly translating genetic interactions from simple model organisms into human traits or diseases is not clear-cut, more complex model organisms such as flies, worms, zebrafish, mice, and dogs have been used to identify modifier genes. For example, a study conducted in dogs with Duchenne’s Muscular Dystrophy (DMD) singled out two specimen with a mild form of the disease. Using a combination of sequencing-based approaches and experimental validation in zebrafish, researchers showed that increased jagged1 activity could suppress the disease in dogs.¹⁷ Nevertheless, the use of complex model organisms for  the systematic identification of  genetic modifiers is challenging due to longer generation times and high costs, and is therefore most frequently reserved for reverse genetic approaches that examine a small number of candidate modifiers or for characterising a few healthy carriers.

 A highly complementary approach to uncover genetic modifiers is by using functional genomics  in human cells. Innovative functional genomics platforms have been set up by companies such as Maze Therapeutics, Scenic Biotech, generating interesting results with clinical studies in process.

Using functional genomics to find genetic modifiers

Functional genomic approaches can explore the whole genome of mammalian cells to not only identify modifier genes but also establish their relation to a relevant cellular disease phenotype. Many rare metabolic disorders feature disrupted elementary processes, the consequences of which can frequently measured in cells carrying disease mutations. Thanks to high-throughput genome editing approaches, activating or inactivating mutations can be introduced on a genome-wide scale and their effects on measurable disease traits can easily be analysed. This in contrast to population genetics studies which rely on the presence of rare individuals carrying modifier variants. Although there are limitations to modeling diseases in cell systems, the use of human cells increases the likelihood of identifying robust and species-relevant genetic interactions. Hence, functional genomic approaches offer a highly complementary path toward the rapid identification of modifier genes, which has become more and more valuable in both academic and industry settings.

Maze Therapeutics, for instance, has developed the Compass platform which combines functional genomics with human genetic data in order to develop new precision medicines for genetically validated drug targets. One of their programs focuses on amyotrophic lateral sclerosis (ALS), a fatal neurodegenerative disorder that translates into progressive muscle weakness and eventually death within 2-5 years. The knowledge that in some ALS cases patients live well beyond this prognosis has led Maze Therapeutics to identify a genetic modifier that impacts the severity of the disease. Inhibition of the modifier was found to restrict the toxicity of the protein TDP-43, which participates in pathologic aggregates observed in ALS patients.¹⁸ The company is now attempting to develop a microRNA therapy that targets the gene ATXN2 and has already shown that loss of this gene has a positive effect on survival in preclinical models.

Pioneering research on genetic modifiers is also performed at Scenic Biotech to develop a new generation of therapeutics. Their proprietary Cell-Seq platform uses human haploid cells (harboring only one copy of each chromosome) which are amenable to random mutagenesis.^19,20 Mutations are introduced across the genome of these cells through gene-trap mutagenesis and the resulting phenotypes can be monitored with fluorescent markers in both wildtype cells and cells with an engineered disease mutations.²¹ The gene trap mutations introduce a molecular tag into the genome to pinpoint the genetic modifiers that affect the disease phenotype. This approach can be applied to a wide range of disorders to search systematically for genetic modifiers within the genome. This concept has led to a collaboration with Genentech, a member of the Roche Group, under which Scenic uses its platform and insight to discover novel therapeutics that target genetic modifiers.

Scenic Biotech’s therapeutic focus now is on unveiling genetic modifiers for rare diseases, with Niemann-Pick Type C (NPC) and Barth Syndrome as some of the diseases under investigation. Barth Syndrome is an inherited mitochondrial disorder that arises from mutations in the gene encoding for Tafazzin. Patients with Barth’s syndrome have a reduced life expectancy and there are currently no effective treatments available other than symptomatic care. Niemann-Pick Type C is a rare lipid storage disorder caused by a mutation in the NPC1 gene, which results in disruption of lipid metabolism. NPC is mainly treated with miglustat, a glucosylceramide synthase (GCS) inhibitor that delays the appearance of neurological symptoms.²² However, this therapy is only approved for NPC in Europe and the illness provokes many other symptoms, with a current high unmet medical need as a result. In February 2023, Scenic Biotech announced a Cooperative Research and Development Agreement (CRADA) with the National Institutes of Health (NIH) to support the identification of genetic modifiers for this severe indication with patient genomic and clinical data to further complement and reinforce Scenic’s proprietary target discovery platform.  Genetic modifier-based approaches could eventually provide a pharmacological recourse to not only delay but also reverse the damage caused by the disease on both a neurological and physiological level. Identifying and targeting genetic modifiers therefore presents as a promising path towards such treatment options.

Genetic modifiers: the path ahead

The therapeutic potential of genetic modifiers is gradually emerging for an array of indications, as their influence on inherited disease phenotypes becomes more evident and their identification more attainable. Indeed, targeting genes that impact disease representation, rather than the disease-causing genes, constitutes a particularly novel therapeutic approach that companies like Scenic Biotech and Maze Therapeutics are now equipped to employ in their search for new drug targets. Their cutting-edge platforms should allow them to overcome the hurdles that uncovering genetic modifiers implies to develop breakthrough medicines. The coming years will be critical in conquering the genetic modifiers field and demonstrating this area of research is a strong therapeutic avenue for the treatment of diseases with high unmet medical needs.

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