Gene therapy has a history of presenting possibilities that stay out of reach for a long time. The tantalizing idea of using exogenous “good” DNA to replace defective DNA was suggested by Stanfield Rogers in 1970. Then, in 1972, the idea was elaborated upon by Theodore Friedmann and Richard Roblin, who wrote that viruses could be tweaked to contain human genes and allowed to infect patients. Once copied into patients’ cells, the genes could start to function, compensating for defective and disease-causing genes.1

Despite these conceptual advances, clinical progress was slow. Indeed, there were dead ends and reversals. In 1971, Rogers deployed a naturally occurring virus in an attempt to treat an arginase deficiency. And in 1980, Martin J. Cline tried to treat b-thalassemia by using an ex vivo procedure in which bone marrow cells were transfected with a recombinant human globin gene and then reintroduced to patients. Both these efforts were, at best, inconclusive.

Finally, a partial and temporary gene therapy success was reported in 1990. Scientists led by William French Anderson used an ex vivo procedure to treat a four-year-old girl suffering adenosine deaminase–deficient severe combined immunodeficiency disease. They infected the patient’s own white blood cells with a virus that had been engineered to carry a gene encoding a functional variant of the adenosine deaminase gene. For two years, transfusions were administered that incorporated transfected white blood cells. The transfusions didn’t bring about a cure, but they did help reduce the patient’s symptoms.

Then, in 1999, the field suffered a major setback when an 18-year-old patient with a metabolic disorder died after suffering an immune overreaction to an adenovirus designed to restore a missing liver enzyme. And a few years later, several patients with immunodeficiencies developed leukemias after receiving gene therapy, as the viruses caused insertions into cancer-related genome sites. The U.S. Food and Drug Administration (FDA) reacted swiftly, putting many gene trials on hold.2 The development of gene therapy stalled.

In subsequent years, however, researchers learned from these setbacks. For instance, safer viral vectors were identified, such as adeno-associated viruses (AAVs). The genes they deliver typically remain in the cell cytoplasm and are expressed there, rather than being integrated into human cells’ genomes, making them less likely than some earlier vectors to trigger cancer.

Since 2017, the FDA has approved several gene therapies for disorders caused by defects in single genes, including Luxturna for retinal dystrophy, Zolgensma for young children with spinal muscular atrophy, and Zynteglo for certain patients with b-thalassemia. The agency has also green-lighted several cell-based gene therapies which alter patients’ cells and reinfuse them into patients. For example, approvals have been granted to several therapies that use modified T cells, specifically, chimeric antigen receptor (CAR) T cells. They have proven effective in treating certain blood cancers.

Meanwhile, hundreds more gene therapy trials are underway. To get a sense of what these trials tell us about the current status and near-term future of gene therapy, GEN spoke with representatives of companies at various stages of clinical development. They took the opportunity to expand on the results they shared at the 25th Annual Meeting of the American Society of Gene and Cell Therapy (ASGCT), which was held last May in Washington, DC. They emphasized that for many diseases—hereditary monogenic disorders, complex diseases, and even cancer—single-dose gene therapies held disease-modifying potential.

Getting to the heart of Friedrich’s ataxia

The New York City–based Lexeo Therapeutics has been developing a treatment for Friedreich’s ataxia (FA), a rare condition that is currently incurable. It’s caused by a mutation in the frataxin gene FXN which leads to progressive degeneration of the nervous system. Rather than targeting the disease’s neurological pathology, which is tricky as the viruses fail to transduce efficiently and specifically in affected brain areas, Lexeo tackles the oft-fatal cardiac disease associated with FA, said Jay Barth, MD, Lexeo’s executive vice president and chief medical officer.

Lexeo’s therapeutic, LX2006, employs an AAV that’s effective at infecting cardiac cells, introducing the FXN gene, increasing frataxin levels, and thereby restoring mitochondrial function. According to data presented at the ASGCT conference, mouse models of FA that received a single intravenous dose of LX2006 had improved heart function, general mobility, and survival compared with untreated rodents, “even after they developed fairly advanced cardiac disease,” Barth noted.3

LX2006 a gene therapy candidate
Lexeo Therapeutics is developing LX2006, a gene therapy candidate to treat Friedreich’s ataxia cardiomyopathy. The disease causes mitochondrial dysfunction and deficient energy production in myocardial cells (upper panel). To restore mitochondrial function and improve cardiomyocyte function, intravenously administered AAVs deliver a functional frataxin gene to myocardial cells (lower panel). LX2006 has shown promise in preclinical studies, and an IND application for the drug has been cleared by the FDA.

Lexeo is planning a Phase I/II trial to assess safety of the therapy in 10 FA patients with cardiomyopathy. One of the goals is to identify the maximum safest dose for LX2006.4 Investigators are taking a cautious approach, Barth said, as overexpression of frataxin has been associated with safety issues.

The first study cohorts will receive the lowest dose that’s shown efficacy in mice, and the dose will be incrementally increased in subsequent groups. Frataxin levels will be monitored through heart tissue biopsies. Patients will be followed for one year, and then for an additional four years as the FDA requires. In Barth’s view, the study could help “find some way to prolong the lives of these patients beyond what the disease would give them.”

A new weapon against solid tumors

While many gene therapy companies focus on restoring lost functions to normal cells, the Australia-based immuno-oncology company Imugene is employing the method to help kill cancer cells. In 2019, the company acquired an oncolytic virus called CF33, a chimeric vaccinia that infects and selectively replicates in malignant solid tumor cells.5

Imugene scientists have tinkered with CF33 in various ways that are already being tested in patients with specific cancer types. But according to Leslie Chong, the company’s chief executive officer and managing director, the “crown jewel of Imugene” is a version of CF33 that contains a gene encoding the CD19 protein.

This surface protein is expressed on B cells and is the target of several CAR T-cell therapies. Using CF33 to induce uniform expression of CD19 across tumor cells could make CAR T-cell therapy work against solid tumors, which has proven a challenge as the tumors often express a heterogeneous mix of cell surface antigens. But with CF33, Chong explained, “We line all your solid tumor [cells] with the CD19-directed targets, such that when you add a CD19-targeted therapy, you then obliterate the solid tumor where it hasn’t had markers before.”

In 2020, scientists at the City of Hope National Medical Center published data in support of this approach.6 Specifically, the scientists used mouse models of various cancer types to study the effects of administering the CD19-carrying CF33 virus followed by CD19-directed CAR T-cell therapy. Mice that received the antigen-matched therapy survived significantly longer than mice that received only mock T cells or CD19-CAR T cells.

Imugene looks forward to identifying indications that may benefit the most from this “onCARlytics” approach. The company is also planning a human trial. “In our initial in-clinic study, we will be focused on certain indications,” Chong noted. “However, I think the application could be huge.”

onCARlytics diagram
onCARlytics, a combination immunotherapy that is being developed by Imugene, unleashes a CD19-expressing oncolytic virus to target and eradicate solid tumors that are otherwise difficult to treat with CAR T-cell therapy alone: 1) The oncolytic virus infects tumor cells. 2) Virus replication leads to production of CF33-CD19 on the cell surface, enabling CD19 CAR T-cell targeting. 3) Tumor cell lysis leads to viral particle release, and the combination promotes endogenous immune cell recruitment to tumors. 4) Released viral particles reinitiate virus infection of surrounding tumor cells.

A new approach to tackling complex disease

The North Carolina–based gene therapy company Asklepios BioPharmaceutical (AskBio) is also pursuing a target that falls outside the usual paradigm of monogenic disorders: congestive heart failure (CHF), a chronic and progressive condition in which the heart cannot pump blood sufficiently. “There’s a high unmet medical need to develop additional medicines to reduce mortality … and improve quality of life for the patients,” said Canwen Jiang, MD, PhD, AskBio’s chief development officer and chief medical officer.

NAN-101 gene therapy
AskBio has been conducting clinical research to determine if NAN-101, a gene therapy that induces the expression of constitutively active inhibitor-1 (I-1c), can improve heart function and provide a new approach to treating congestive heart failure. A Phase II trial, designated GenePHIT, is
being organized.

AskBio’s approach to tackling this complex disease has been to deliver a gene encoding the phosphatase-1 inhibitor-1, a key protein in regulating cardiac contractions. Introducing the gene via an AAV that’s engineered to target cardiac cells could improve heart function as well as reverse and prevent the detrimental remodeling of cardiac muscle that occurs in CHF, Jiang said. The therapy, NAN-101, is delivered via a one-time injection into the heart’s coronary arteries.

After collecting robust preclinical data, AskBio launched a Phase I study in 2019, enrolling eight individuals with Class III CHF. According to preliminary results presented at the ASGCT meeting, investigators observed efficient transduction of NAN-101 in heart cells of one trial participant from whom a tissue biopsy could be obtained.7 A cohort consisting of three patients who had completed their 12-month follow-up appeared to tolerate the treatment well and saw consistent improvements in heart function.8

If successful, such studies will not only motivate AskBio to expand into broader CHF indications, but also bolster the idea that gene therapy is useful beyond monogenic disorders. “It would be a … confidence-building example for the industry, for the academic community, as well as for the regulatory agencies,” Jiang said.

Advancing gene therapy for muscular dystrophy

One of the companies at the Phase III stage is Sarepta Therapeutics, a Cambridge, MA–based biotech firm specializing in rare diseases such as Duchenne muscular dystrophy (DMD), a monogenic disease that causes progressive muscle deterioration.

The gene therapy SRP9001 is based on an AAV virus subtype with an affinity for reaching muscle cells. It contains a gene encoding a form of the dystrophin protein, which is lacking in DMD patients’ tissues, coupled with a promoter that causes selective expression in skeletal and cardiac muscle cells, explained Jake Elkins, MD, Sarepta’s senior vice president of research and development and chief medical officer.

In a pilot study that tracked four DMD patients aged four to seven, data was collected four to five years after SRP9001 was taken. The treatment was well tolerated, and patients showed a 7-point improvement on a 17-step mobility scale (the North Star Ambulatory Assessment), despite being at an age where they’d typically experience rapid deterioration of mobility.9 A randomized Phase II study of 41 pediatric participants has so far bolstered these observations at one year of follow up, Elkins noted.10

Currently, Sarepta is closely tracking 120 boys with DMD aged four to seven in a Phase III study. The first half of patients are receiving gene therapy in the first year, during which the second half will receive a placebo until being rolled onto gene therapy after one year. “At one year, we’re able to document clinically meaningful effects of the therapy,” Elkins said. “We view it … as a confirmatory study of our early findings, but [it] will really expand our knowledge base of how this treatment works across the range of ambulatory patients with DMD.”

Repairing broken sugar metabolism

Ultragenyx Pharmaceutical, a California-based rare disease-focused company, has also reached the Phase III stage with DTX401, which tackles glycogen storage disease type IA (GSDIa). This condition is caused by a genetic deficiency of the enzyme glucose-6-phosphatase, which breaks down glycogen reserves into glucose during fasting periods. GSDIa causes low blood sugar and accumulation of glycogen in the liver and kidneys, and patients need to regularly take cornstarch to maintain normal blood sugar levels, explained Eric Crombez, MD, Ultragenyx’s chief medical officer for gene therapy and inborn errors of metabolism.

DTX401 is based on a liver-targeting AAV designed to restore glucose-6-phosphatase expression in patients’ hepatocytes. According to results presented at the ASGCT meeting, a Phase I/II study of DTX401 reported only mild adverse events in adult GSDIa patients.11 And all 12 participants were able to reduce their daily cornstarch intake by around 70% over three years. When interviewed at 52 weeks, most of the patients reported having more energy and better mental clarity.

“If the transgene wasn’t working, they would be having a lot of problems,” Crombez asserted. “[We can see that] they don’t, [which] shows that we’ve established the normal breakdown of glycogen to produce glucose.”

Motivated by these results, the company launched a Phase III study in 50 patients to compare the efficacy of DTX401 to that of a saline infusion. Primary endpoints—including patients’ ability to taper cornstarch use—will be assessed after 48 weeks, but investigators hope to follow patients for as long as possible.

As the liver has high cell turnover, and the therapy doesn’t integrate into the genome, the transgene will eventually be lost, Crombez said. That’s why he doesn’t describe gene therapy as a “cure” in the strictest sense. However, he emphasizes that “even if you need [another] dose 20 years down the road, [you’ve still] treated it for a very long period of time.”

 

References
1. Friedmann T, Roblin R. Gene Therapy for Human Genetic Disease? Proposals for genetic manipulation in humans raise difficult scientific and ethical problems. Science 1972; 175(4025): 949–955
2. Pollack A. FDA halts 27 gene therapy trials after illness. New York Times. Published January 15, 2003.
3. Zuluaga CM, Gertz M, Yost-Bido M, et al. Identification of the Therapeutically Beneficial Intravenous Dose of AAVrh.10hFXN to Treat the Cardiac Manifestations of Friederichs’s Ataxia. Paper presented at: 25th Annual Meeting of the American Society of Gene and Cell Therapy; May 16–19, 2022; Washington, DC.
4. Lexeo Therapeutics. LEXEO Therapeutics Announces FDA Clearance of Investigational New Drug Application for LX2006, an AAV-Based Gene Therapy Candidate for Friedreich’s Ataxia Cardiomyopathy. Published February 16, 2022.
5. Imugene. Today we enhanced our portfolio with a compelling oncolytic virus technology. Published July 15, 2019.
6. Park AK, Fong Y, Yang SK, et al. Effective combination immunotherapy using oncolytic viruses to deliver CAR targets to solid tumors. Sci. Transl. Med. 2020; 12(559): eaaz1863.
7. Tretiakova AP, Ozkan T, Sethna F, et al. Rationally designed cardiotropic AAV capsid demonstrates 30-fold higher efficiency in human vs. porcine heart. Paper presented at: 25th Annual Meeting of the American Society of Gene and Cell Therapy (ASGCT), Washington, D.C., May 16-19, 2022
8. Henry T, Chung ES, Egnaczyk GF, et al. A first in-human phase 1 clinical gene therapy trial for the treatment of heart failure using a novel re-engineered adeno-associated vector. Presented at: 25th Annual Meeting of the American Society of Gene and Cell Therapy; May 16–19, 2022; Washington, DC.
9. Sarepta Therapeutics. Sarepta Therapeutics’ Investigational Gene Therapy SRP-9001 for Duchenne Muscular Dystrophy Demonstrates Significant Functional Improvements Across Multiple Studies. Published July 6, 2022.
10. Sarepta Therapeutics. Sarepta Therapeutics’ SRP-9001 Shows Sustained Functional Improvements in Multiple Studies of Patients with Duchenne. Published October 11, 2021.
11. Ultragenyx Pharmaceutical. Ultragenyx Announces Positive Longer-Term Durability Data from Two Phase 1/2 Gene Therapy Studies at American Society of Gene & Cell Therapy (ASGCT) 2022 Annual Meeting. Published May 19, 2022.