Over the last 30 years the gene therapy community has been constructing its map. In September 1990 W. French Anderson and colleagues at the US National Institutes of Health (NIH) performed the first gene therapy procedure on a 4-year-old girl (Ashanti Desilva) born with severe combined immunodeficiency (SCID).

Despite a few horror stories reported in the popular press, the trial was a success and Ashanti is still alive.^1,2 In 2017 and 2019 we witnessed the first two gene therapies approved by the US Food and Drug Administration (FDA) for commercial use: LUXTURNA, for inherited retinal blindness due to mutation of the RPE65 gene, and ZOLGENSMA, for spinal muscular atrophy (SMA) in patients less than 2 years old.^3,4 In addition, over the last 2 years we have seen approval of three other products by either the U.S. Food and Drug Administration (FDA) or European Medicines Agency (EMA) or both, including ZYNTEGLO for adult and pediatric patients with β-thalassemia; SKYSONA for cerebral adrenoleukodystrophy; and LIBMELDY for metachromatic leukodystrophy in the European Union, with another 5 approvals expected in 2023.⁵  In addition to these approvals is a healthy pipeline of gene therapies in the clinical trial setting, including over 376 active trials.⁶

But the gene therapy map is not all peaks; there have been some valleys as well. In 1999 Jesse Gelsinger died during a gene therapy for ornithine transcarbamylase deficiency when he had a fatal immunologic response to an adenovirus vector.⁷ More recently, we have seen additional high-profile safety issues, including deaths associated with AAV vector gene therapies that have raised safety concerns among the public and regulators.^8,9 We have also recently seen a 70% reduction in follow-on funding across cell and gene therapy companies that have impacted how they are approaching development, especially regarding manufacturing.⁵ There are looming questions about how health systems will afford gene therapy as a modality when there are 50 gene therapies on the market or when these therapies are developed for more prevalent diseases. The objective of this article is to look at future directions for gene therapies by describing three future trends and how they might impact safety, manufacturing development, and reimbursement and payment.

Trend 1: Enhanced and More Specific Vectors and Delivery Mechanisms:

Generally, the gene therapy delivery mechanism has been shown to be safe; however, there have been a few fatal cases of adverse events associated with adeno-associated viruses (AAV) viral vectors. To proactively confront some of the safety issues we are and will be seeing the advancements in virus vector design, new delivery mechanism and nonviral vector development.

Tissue-Specific Promoters for AAV Vectors:
For a gene therapy to work there needs to be a therapeutic gene and polyadenylation signal. The promotor’s job is to control the gene expression.¹⁰ The traditional promotors have not been tissue specific sometimes leading to low expression by silencing the transgene or overexpression resulting in cell damage and toxicity. One of the trends we see in the future is a movement towards using tissue-specific promotors. Tissue specific promoters are promoters that only work in specific cell types and can minimize over- and under expression.

Better Device Delivery Mechanisms:

Another trend we predict is the use of new devices to deliver more vector in a more localized manner to increase efficacy and minimize toxicity. We are starting to see this trend especially in central nervous system (CNS) disorders.  For example, many gene therapies targeting the CNS deliver the vector through a bolus injection into the lumbar spine often with minimal brain penetration and cellular targeting. New approaches being developed uses computer models to understand the cerebral spinal flow dynamics in an individual to deliver vector more precisely.¹¹

Non-Viral Vectors:

According to a recent analyst, more than 92% of vectors used for gene therapy are viral. With that said, we are seeing a growing interest in using nonviral vectors, especially for therapies requiring larger payloads and as a mechanism to immunogenicity. There are 2 main ways nonviral vectors deliver material: physically and chemically. Physical methods allow researchers to directly deliver genetic material to target cells. Ex vivo electroporation is an example. Chemical methods use natural or synthetic materials that are compatible in vivo and include lipids, polymers, nanoparticles, and ministring DNA.Presently, there are 60 therapies in the pipeline exploring the use of nonviral vectors.⁶

Trend 2: A Phased Approach to Manufacturing:

As mentioned earlier, follow-on funding for gene therapy companies has declined, putting more financial pressure on companies. As a result, we are observing more companies taking a phased approached to a manufacturing build out, helping to extend capital. The typical phased approach starts with limited capital investment for non-Good Manufacturing Practice (GMP) operations, including process development and analytical development (PD/AD), then grows incrementally with small-scale GMP capabilities until enough clinical data are available to drive funding and further large-scale investment.

When companies make large-scale investment and either build or enter a long-term lease, we see the best management of downside for those that position their facility as a flexible asset. Flexibility is an important element in manufacturing design in that it can accommodate multiple modalities and scales. A flexible design can mitigate the risk of a modified platform within one’s company, as well as position the facility as an asset. If a facility has flexible design, with modular walls and acceptable ceiling clearance, then the facility becomes a strong asset to accept a modified platform, or worst case, repositioning to the market.

Trend 3: Cost-Effectiveness vs. Cost-Effectiveness and Affordability:

Cost-Effectiveness: To date most of the gene therapies on the market or approaching approval have been for relatively rare diseases with very high unmet clinical need. This presents unique challenges to payers:

• Limited data: Often small, single-arm trials due to rareness and/or the transformational impact do not provide wide-reaching results
• High price points: The promise of long-term patient benefits means that these therapies can be cost-effective or even cost-saving at very high price points, putting them among the highest priced pharmaceutical options
• Upfront cost: Single dosing may mean that payers need to pay the entire cost of treatment up front and in advance of knowing the full longevity of effect

Despite some of these challenges, payers have been covering and paying for gene therapies based on the value they have been demonstrating in cost-effectiveness models and the limited budgetary exposure.

Cost-Effectiveness and Affordability:
The gene therapy pipeline is large. Currently there are 376 active gene therapy trials with 59 of those in Phase 3. Of the Phase 3 trials, 40 of them are for rare disorders, whereas 19 are for more prevalent disorders.⁴ With the potential for many more gene therapies on the market over the next 3 to 5 years and some of them for more common disorders, payers will become much more concerned about the overall budget impact.

We are starting to see this trend both in the United States and in Europe. In the United States we have observed the emergence of gene therapy “carve outs.” For example, Cigna, eviCore, Accredo, and Express Scripts have created a gene therapy “carve out” aimed at the self-funded, self-insured employer population, in which the employer pays $0.99 per member per month to insure that individual for gene therapy.¹² This reduces the financial risk to the employer, but we have yet to see how these carve outs will impact patient access. In Europe some countries are employing dynamic approval models, in which conditional approvals at a price are given and then reevaluated once additional clinical trial and/or real-world data are available.¹³ For example, in Germany the G-BA may apply a time limit to the benefit assessment granted, meaning that that the product must undergo another benefit assessment (and rebate price negotiation).¹⁴ The gene therapies Libmeldy and Luxturna were both subject to time-limited benefit resolutions in Germany.

Parting Thoughts

As these trends illustrate, gene therapies are evolving across every aspect of the development cycle. There are now “more places that we might go.” The potential impact of gene therapy is fundamentally so profound that we must take this journey.

References

1. Anderson WF. September 14, 1990: the beginning. Hum Gene Ther. 1990;1:371-372.

2. Springen K. Using genes as medicine. Newsweek, December 6, 2004. https://www.newsweek.com/using-genes-medicine-123277.

3. FDA News Release. FDA approves novel gene therapy to treat patients with a rare form of inherited vision loss. Accessed November 11, 2022. https://www.fda.gov/news-events/press-announcements/fda-approves-novel-gene-therapy-treat-patients-rare-form-inherited-vision-loss.

4. FDA News Release. FDA approves innovative gene therapy to treat pediatric patients with spinal muscular atrophy, a rare disease and leading genetic cause of infant mortality. Accessed November 11, 2022. https://www.fda.gov/news-events/press-announcements/fda-approves-innovative-gene-therapy-treat-pediatric-patients-spinal-muscular-atrophy-rare-disease.

5. Alliance for Regenerative Medicine. Regenerative Medicine: The Pipeline Momentum Builds H1 2022 Report. Accessed November 12, 2022. https://alliancerm.org/sector-report/h1-2022-report/.

6. Watt A. A gene therapy landscape analysis of rare vs. common disorders. Gene Therapy for Rare Disorders Conference. 2022. Boston, MA.

7. Gene-therapy trials must proceed with caution. Nature. 2016; 534:590. https://doi.org/10.1038/534590a.

8. Masson G. Another Pfizer gene therapy is free of FDA hold, but delay continues. Fierce Biotech. 2022. Accessed November 12, 2022. https://www.fiercebiotech.com/biotech/fda-frees-pfizers-hemophilia-gene-therapy-clinical-hold.

9. Keown A. Another patient dies following treatment with Astellas’ experimental gene therapy. Biospace. Accessed November 12, 2022. https://www.biospace.com/article/patient-dies-following-treatment-with-astellas-pharma-s-experimental-gene-therapy/.

10. Zheng C, Baum BJ. Evaluation of promoters for use in tissue-specific gene delivery. Methods Mol Biol. 2008; 434:205-19.

11. Alcyone Therapeutics. Accessed November 16, 2000. https://alcyonetx.com/science-technology/falcon/.

12. Embarc Benefit Protection Plan. Accessed November 16, 2022. https://www.cigna.com/employers/cost-control/embarc-benefit-protection.

13. National Institute for Health and Care Excellence. Managed Access. Accessed November 29, 2022 https://www.nice.org.uk/about/what-we-do/our-programmes/managed-access

14. Macaulay R, Wang G, Majeed B. Time-limited G-BA Resolutions – A tool to Appropriately manage reimbursement of innovative therapies receiving expedited regulatory approval. European International Society of Pharmacoeconomics and Outcomes Research Conference, (2018). Barcelona, Spain.

What Are AAV Vectors?

Wild-type AAVs are some of smallest viruses (approximately 25 nm) with a linear single stranded DNA genome of 4.7 Kb in length with 2,145 nucleotide inverted terminal repeats. The linear DNA has 3 genes encapsulated in 60 outer coat capsid, which include rep (replication) gene encoding 4 proteins required for viral genome replication and packaging, cap (capsid) that encodes the proteins in the capsid, and aap (assembly activation protein) that provides the structure for the capsid.^1-3 In order to make AAV viruses usable for gene therapies, they are engineered into recombinant AAVs (rAAVs), where the viral genome is replaced with a promoter, the gene or genes of interest, and a terminator.⁴ Recombinate AAVs cannot replicate in vivo and need a helper virus to replicate and are not passed on during cell division. These properties make them very safe vehicles to drive long-term gene expression after a single infection.^5,6 Presently, there are 11 serotypes (AAV1 through AAV11) cloned, and they can have specific affinity to tissues. For example, AAV1, AAV2, AAV4, AAV5, AAV8, and AAV9 are optimal for central nervous system (CNS) disorders.⁷

What Are Major Considerations When Selecting an AAV Vector?

There are 3 major considerations when selecting the appropriate AAV:

1- Selecting the right capsid and promoter: Selection can improve targeting of cell transduction and increase expression, which has implications for the dosage required for effective therapy.

2- Selecting the best dosing regimen: The choice of dosage can lead to either reduced efficacy when the doses are too low or can lead to toxicities when the dosing is too high. Dosages that are too low could lead to inefficient transduction; dosages that are too high can result in delivery and transduction-related toxicities.8 Inflammatory toxicities have been seen with increasing doses of gene therapies resulting in complement activation, cytopenia, and severe hepatotoxicity. Therefore, it is ideal and safest to have as minimal dose as possible while still being clinically effective. Majority of the deaths associated with AAV vector have been seen at higher doses.                

3- Development of immune responses to the vector (immunogenicity): Many individuals have already been exposed to one or more serotypes of wild type AAV, and thus may have some degree of pre-existing immunity to the vectors used that includes binding antibodies and neutralizing antibodies (NAbs), which may negatively impact clinical efficacy and could increase post-therapy prevent re-administration. The prevalence of pre-existing anti-capsid NAbs varies by AAV serotypes, ranging from approximately 40% for AAV8 to 74% for AAV2.9

Strategies for Mitigating Safety Issues with AAV Vectors

Presently, there are multiple strategies being deployed or developed to mitigate risk associated with AAV vector usage and to increase performance, including excluding individuals with some level of existing NAbs, depleting NAbs, vector engineering removing immunogenic features during vector design lowering therapeutic dosing, and immunosuppression.  

Excluding Patients with Naturalizing Antibodies (Nabs):

Often patients with pre-existing Nabs against the specific AAV capsid are precluded from receiving the gene therapy. This occurs often in clinical trials with 45% excluding patients with a pre-specified Nab levels. With that said, this exclusion in clinical trials is quite variable among therapeutic areas, where approximately 90% of the blood disorder trials exclude patients, and ophthalmologic and CNS clinical trials excluding 10% and 21%, respectively. This represents the current hypothesis that NAbs are of greater concern for systemic delivery of AAV than for targeted therapy to immune privileged sites.⁵

Tissue-Specific Promoters for AAV Vectors:

For a gene therapy to work, there needs to be a therapeutic gene, promotor, and polyadenylation signal. The promotor’s job is to control the gene expression.¹⁰ The traditional promotors have not been tissue-specific, sometimes leading to low expression by silencing the transgene or overexpression, resulting in cell damage and toxicity. One of the trends we anticipate is a movement towards using tissue-specific promotors. Tissue-specific promoters work only on specific cell types and can minimize over- and under expression.

Transgene Optimization:
Modifying the transgene to produce more-effective therapeutic

Proteins is another method beginning to be employed, with the hope that greater therapeutic efficacy will lead to lower doses and better safety with similar efficacy. An example of this is FIX-Padua, a variant of FIX (Factor “9”) with a hyperactivating R338L mutation, which resulted in increasing the efficacy by up to 5–10-fold in hemophilia B patients at lower doses with no liver enzyme elevation in the majority of the patients.¹⁰

Better Device Delivery Mechanisms:
Another strategy being employed is the development and use of new devices to deliver more vectors in a more localized manner to increase efficacy and minimize toxicity. We are starting to see this trend, especially in CNS disorders. For example, many gene therapies targeting the CNS, delivering the vector through a bolus injection into the lumbar spine, often with minimal brain penetration and cellular targeting. New approaches being developed use computer models to understand the cerebral spinal flow dynamics in an individual to deliver vector more precisely.¹¹

Immunosuppression:
It is becoming more common to administer immunosuppressive agents as part of a AAV gene therapy. In the first few AAV gene therapies trials, corticosteroids were used reactively after the therapy administration when liver enzymes became elevated. The introduction of the immunosuppressants usually corrected the elevated enzymes. Recently, it has become prevalent to administer immunosuppressants proactively. Common immunosuppressants used are corticosteroids, rapamycin, tacrolimus, mycophenolate, rituximab, eculizumab, and hydroxychloroquine. All of these immunosuppression agents can have significant side effects, so it is important to factor in the safety profile of the immunosuppressant in conjunction with patient clinical presentation before administering.¹²

FDA on Safety Issues with AAV Vectors

In May of 2020, the US Food and Drug Administration (FDA) issued general guidance for the industry on human gene therapy (GT) for rare diseases. In that guidance, the FDA notes that “pre-existing antibodies to any component of the GT product may pose a potential risk to patient safety and limit its therapeutic potential.” In addition, antibodies to the gene therapy may also limit the re-administration of the therapy to a one-time use. The FDA also stated “Sponsors may choose to exclude patients with pre-existing antibodies to the GT product.” If patients are excluded based on pre-existing antibodies, the sponsor should strongly consider development of a companion diagnostic to detect antibodies to the to the gene therapy. If an in vitro companion diagnostic is needed to appropriately select patients for the clinical study, then there should be coordination of the companion diagnostic marketing application with the biologic license application for the gene therapy.¹³

In response to a few high-profile adverse events seen in clinical trials and surveillance of AAV gene therapies, on September 2^nd and 3^rd of 2021, the FDA’s Cellular, Tissue, and Gene Therapies Advisory Committee held a meeting to discuss toxicity seen with AAV vectors. The meeting centered on the following adverse events: hepatotoxicity, thrombotic microangiopathy (TMA), dorsal root ganglion (DRG) toxicities, neurotoxicity – MRI findings, and oncogenicity. The FDA questions to the committee centered around:

Hepatotoxicity: (1) Role of animal studies? (2) Before AAV administrations, how should patients be screened and categorized for risk of liver injury? (3) What strategies could be implemented to prevent or mitigate the risk of liver injury? (4) Beyond weight of the patient, what factors (e.g., level of disease severity) should be considered to determine the vector dose for systemic administration? (5) Considering the risk of toxicities observed in clinical trials with high doses of AAV vectors, should an upper limit be set for the total vector genome dose per subject?

Thrombotic Microangiopathy (TMA): (1) What factors may increase the risk of TMA following AAV vector administration? (2) What strategies could be implemented to prevent or mitigate the risk of AAV vector-mediated TMA? (3) Should an upper limit be set for the total vector dose? (4) Discuss whether an upper limit should be set on the total capsid dose.

Dorsal Root Ganglion (DRG) Toxicities: (1) based on the published data, please discuss the relevance of the non-human primate (NHP) cases of DRG toxicity to human subjects. (2) Please provide recommendations on preclinical study design elements, such as animal species/disease model, age, in-life and post-mortem assessments, and duration of follow-up, post-dose that may contribute to further characterization of DRG toxicity. (3) In addition to periodic neurological examinations, please provide recommendations on other methods to mitigate the risk of DRG toxicity in clinical trials.

Oncogenicity: (1) Discuss the merits and limitations of animal studies to characterize the risk of AAV vector-mediated oncogenicity. (2) Discuss benefit-risk considerations for AAV vector-mediated oncogenesis, such as patient age at the time of treatment, pre-existing liver conditions (e.g., infection with hepatitis B or C virus), and high vector dose.

Although there has not yet been a formal guidance issued from this meeting, the meeting did serve to help define some of the major questions regarding AAV vectors.¹⁴

Parting Thoughts The final comments from Peter Marks MD (US FDA) frame the situation well: “I would say the fact that we’re discussing this is evidence that they (gene therapies) very much are becoming a reality. And it’s actually a good sign because with every medical therapy, as it comes along, we have to deal with the side effects that may come up and address them.”¹⁴ As Hagrid said to Harry Potter, not all wizards are good. Well, not all AAV gene therapies are bad. AAV gene therapies hold tremendous promise, and we are engaged in the iterative process of refining AAV therapies. We are turning magic into science!