BHP Industry Report: Gene Therapy

Gene therapy is an innovative and rapidly growing treatment modality, poised to redefine how diseases of all types are treated over the coming decades. Spun out of advances in genomics, molecular biology, and computational research, the field corrects genetic malfunctions driving disease with a suite of novel biological and physical science technologies. With an annual compounded market growth rate greater than 20% through 2030, such paradigm-shifting innovation in gene therapy has attractive market potential (1). Successful gene therapies still face several surmountable hurdles, which offer avenues for investment across multiple sub-verticals.

Across indications, gene therapies need to traverse several common checkpoints to successfully achieve therapeutic genetic modification. First, a therapy needs to target the right cells for modification and, once in the cell, break into the nucleus. This targeting is achieved either in vivo or ex vivo, with each method presenting unique technical and clinical challenges. Upon entering the nucleus, the therapy needs to modify the deleterious gene by identifying the correct point of the genome to adjust and leveraging an enzyme from a repertoire of insertion and deletion tools. The desired sequence is optimized for an effective and healthy edit. Because a single patient might require hundreds of thousands to millions of viral cells or high throughput ex vivo processing of their own cells, manufacturing technologies of gene therapies need to be scaled significantly to meet this demand. Given this broad set of challenges, rapid innovation is happening in gene therapy at each of these important technological milestones.

Tools for in vivo delivery represent a diverse set of molecular and cellular vectors that shuttle genetic payloads into the nucleus of diseased cells within the patient. They are commonly divided into nonviral and viral subtypes. Viral vectors leverage a virus’ natural ability to navigate their genetic information through the body and into cell nuclei. Yet, their natural history is equally problematic for gene therapies, as patient immune systems react seriously, sometimes fatally, to high viral doses. Recent work has focused on engineering viral vectors, through high value computational platforms or molecular biology solutions, that are unrecognizable to the immune system but retain their cell specificity. However, given high profile failures within gene therapy trials using viral vectors, investors and investigators are now approaching these technologies with caution. Another response to the immune challenge is to engineer nonviral vectors with the same functionality. Research in this nonviral space has created a broad set of technological solutions, all of which attempt to localize a genetic payload to specific cell types while evading the immune system. Nonviral vectors have diverse chemical formulations, from lipid nanoparticles (the casing of the Moderna and Pfizer COVID-19 mRNA vaccines) to double stranded DNA molecules. In addition to reduced immunogenicity, nonviral vectors offer an avenue to deliver larger gene sequences, which otherwise do not fit in kilobase-constrained, naturally occurring viruses. Despite these improvements over viral vectors, companies have increased onus to show that nonviral vectors can localize to cell nuclei with the skill of a virus.

To scale in vivo treatments to the clinic, advances in viral and nonviral manufacturing need to be made. Currently, viral vectors are biomanufactured using cell lines by either transfecting cells with viral DNA to initiate replication or inducing the production of viruses from cells with viral DNA preprogrammed into their genome. While transfecting cells with viral DNA is cheaper and quicker, the method does not scale to high yields easily. In contrast, preprogrammed cell lines can produce high viral yields but remain costly to generate. Nonviral vectors also suffer from manufacturing constraints. For example, DNA vectors require high throughput synthesis at a low error rate, which is currently being pursued by developers.

Ex vivo delivery tools offer alternatives to immunogenicity, cell targeting, and manufacturing challenges, but remain limited to certain tissue types and by their efficacy. Once cells are removed from the body, genetic payloads can be delivered either chemically, virally, electrically, or mechanically. Electrical and mechanical insertion are fields of intense research and development but suffer from reduced cell viability. Using both methods, cell membranes are loosened to allow the passage of genetic cargo, and this loosening threatens the health of the cell. Nanotechnologies that can make small incisions in the cell and nuclear membrane currently hold the most promise for protecting cell viability. However, given the limited number of patient cells extracted, maximizing cell viability remains a looming task for ex vivo therapies.

Maintaining healthy cells and viruses outside the body is crucial before dosing a patient. Viral vectors need to be scanned to ensure they all contain the genetic payload, and cell lines need to be cloned to ensure there is no heterogeneity in the product being produced. Ex vivo therapies require the transfer and modulation of delicate patient cells over the course of multiple days, which need to remain healthy despite such disruptions. As genetic therapies progress from the innovation stages to the clinic, technologies at these steps to ensure efficiency and safety will need to be built out. Companies in the gene therapy space are leveraging robotics and automated solutions to address such quality issues.

Aside from developing delivery technologies, another major aspect of genetic therapy is optimizing the edit being made with the editing machinery and the edited sequence. Editing machinery is typically an enzyme derived for a specific type of edit and a method to guide that enzyme to the right part of the nucleus. Most famously, CRISPR-Cas systems are used to make cuts in the DNA, which are then repaired with a variety of insertion, deletion, or substitution methods. However, companies are navigating away from traditional CRISPR-Cas systems to develop enzymatic tools for defined purposes, such as primer editors to make highly specific nucleic acid edits. A key determinant of success for editing tools is their ability to target the proper spot in the genome for an edit that will ensure expression of the modified gene and avoid disruption of adjacent genetic components. This targeting can include accurately identifying the location of the deleterious nucleic acid sequence or finding safe places for gene insertion. A diverse set of companies is developing computational models that incorporate data about cell type and epigenomics to find areas of the genome that are most amenable to genetic modification. Such precision is important for limiting harmful off-target edits in the genome and non-diseased cell types.

Lastly, a successful gene therapy requires designing and manufacturing the final gene sequence. Optimal gene expression is dependent on multiple cell specific factors, such as the cell’s preference for a certain amino acid code and specific transcription promoting factors. Newly minted computational products are devoted to this task by generating massive libraries of potential sequences and identifying the best candidates. Whole workflows are dedicated to a subset of the gene, such as identifying a strong promoter sequence given multiple platform-generated options. The final optimized sequence is synthesized using chemical or biologic techniques. This synthesis requires a low error rate, which can be achieved with proprietary biologic and chemical technologies.

In Conclusion

Technology in the gene therapy space is making rapid advancement, on the cusp of clinical success in the next decades. Advances occupy computational, molecular biological, and manufacturing spaces creating high yield therapeutic products with optimized genetic edits, while minimizing immunogenic and toxicity side effects. With such rapid market movement, the challenges gene therapies face moving into patient care offer opportunities for investors to support high potential innovation.

Sources

1. Vikita and Onkar. Gene Therapy Market. Allied Market Research. 2022.