Breakthroughs in Gene Therapy

RECENT BREAKTHROUGHS in gene therapy and genome editing are giving researchers and patients hope that cures are on the horizon for many genetic diseases, including blindness, blood and immune disorders and sickle cell disease. According to the Alliance for Regenerative Medicine’s (ARM) 2021 annual report, clinical advancements included the first proof of concept for an in vivo gene editing therapy, evidence that chimeric antigen receptor T-cell (CAR-T) therapies compare favorably with earlier-line treatments, and compelling early results that cell and gene therapies can treat complex, polygenic diseases. Results even suggest these therapies may be able to reverse damage that has already occurred.

ARM’s report notes that 2021 was the second best year for new product approvals, with six new regenerative medicines approved globally, and the best year for CAR-T products, with three new approvals. Nearly 60 percent of the 2,400 ongoing regenerative medicine trials at the end of 2021 targeted prevalent diseases. Further, gene editing continues to advance as a therapeutic modality. Forty-one trials in gene editing were ongoing at the end of 2021, about one-third of which were in the Phase I stage, with the remainder in the Phase II stage. The vast majority of these trials (80 percent) use clustered regularly interspaced short palindromic repeats (CRISPR), demonstrating the strong foothold this technology has established since the initiation of the first CRISPR gene editing trial in 2019.¹

CRISPR is a customizable gene-editing tool that lets scientists cut and insert small pieces of DNA at precise areas along a DNA strand. An RNA-based system that can be easily modified to target multiple sites, it works by using a Cas9 enzyme to cut a DNA sequence at a specific genetic location, then deleting or inserting DNA sequences, which can change a single base pair of DNA, large pieces of chromosomes or regulation of gene expression levels.² This process is referred to as CRISPR/Cas9.

The results of recent clinical trials and the anticipated results of upcoming trials in regenerative medicine have shown or are expected to show positive results. Following is a look at the most promising breakthroughs for some of the most prevalent genetic diseases.

Three Approaches to Gene Therapy¹⁵

Blindness

The National Eye Institute (NEI), part of the National Institutes of Health, supports basic, translational and clinical research globally to help find therapies for blinding diseases such as genetic forms of retinal neurodegeneration that are largely untreatable today.

Loss of neurons in the retina constitutes the major cause of inherited blindness worldwide. To date, more than 250 genes have been identified as disease-causing for inherited retinal diseases (IRD), and most of these diseases are targets of gene replacement or gene-based therapies.

NEI-funded research has established that adeno-associated virus (AAV) vectors are among the most efficient gene delivery tools for modifying the function in retinal cells. A major breakthrough occurred a few years ago when several scientists used an AAV vector to deliver the RPE65 gene in retinal pigment epithelium cells of patients with a form of childhood blindness called leber congenital amaurosis (LCA). This treatment has now been approved by the U.S. Food and Drug Administration (FDA) and is available for patients. Gene therapy clinical trials using AAV vectors are now being conducted for treatment of several IRDs and have shown promising results in patients.

In addition to funding extramural research in the United States and other countries, NEI has an intramural research program (IRP) located in Bethesda, Md., where several laboratories are involved in finding mechanisms of retinal diseases and developing treatments based on stem cells, small molecule drugs and knowledge of the gene defects. For example, the Neurobiology, Neurodegeneration & Repair Laboratory (NNRL), a division of the NEI-IRP, is working to understand biological pathways that lead to many different types of inherited blindness to design new treatments for several forms of IRDs.²

The NNRL and NEI’s Gene Therapy Core scientists have collaborated on several projects, including preclinical gene replacement therapy for X-linked retinitis pigmentosa, in which long-term efficacy and preliminary safety studies of gene replacement therapy in Rpgr and Rp2 gene knock-out mouse models have paved the way for further clinical development.

For mechanism-based gene therapy for LCA due to CEP290 mutations, NEI is currently seeking mechanism-based gene therapy for the disease based on the existing knowledge of CEP290 protein structure and its interactome. Since CEP290 is a large gene for AAV delivery, NNRL scientists have been exploring the use of minigene and small molecule drugs for treatment of this devastating form of LCA. More recently, NNRL scientists have used retinas generated in a dish from patient stem cells to develop gene therapy for another autosomal dominant form of LCA caused by CRX mutations. Similar work is in progress for LCA caused by mutations in the NPHP5 gene.

Previously, NEI scientists had developed gene replacement therapy protocols for X-linked juvenile retinoschisis (XL-RS) by helping to design and develop the human retinoschisin AAV vector, which is currently being tested in Phase I clinical trials of XL-RS.³

For CRISPR/Cas9 mediated genome editing in postmitotic retinal neurons, NEI’s initial effort will be focused on gene disruption mediated by nonhomologous end joining. This may lead to novel therapies for retinal degeneration caused by gain-of-function or dominant mutations.

CRISPR Gene Editing Market Growth Projection in the United States¹⁵

NEI is also supporting multiple basic and clinical research studies in IRDs. For example, researchers funded by NEI preserved vision in dogs with a disease similar to retinitis pigmentosa in humans using gene therapy for a blinding condition called autosomal dominant retinitis pigmentosa caused by a mutation in visual pigment rhodopsin. The researchers generated a gene therapy construct that knocks down the rod cells’ ability to produce rhodopsin using a technology known as short-hairpin RNA (shRNA) interference. In dogs’ retinas, the construct knocked down approximately 98 to 99 percent of rhodopsin (both mutated and normal). But because normal rhodopsin is required for the rods to detect light, the researchers added a “hardened” shRNA-resistant rhodopsin gene to the same vector. When treated with the combined vector, the dogs maintained healthy, functional photoreceptors, and because the vector was designed to produce human rhodopsin, it could potentially work in humans as well.⁴

In 2017, FDA approved Luxturna (voretigene neparvovec-rzyl), a new gene therapy to treat children and adult patients with an inherited form of vision loss that may result in blindness. Luxturna is the first directly administered gene therapy approved in the United States that targets confirmed biallelic RPE65 mutation-associated retinal dystrophy caused by mutations in a specific gene that leads to vision loss and may cause complete blindness in certain patients. It works by delivering a normal copy of the RPE65 gene directly to retinal cells, which then produce the normal protein that converts light to an electrical signal in the retina to restore patients’ vision loss. Luxturna uses a naturally occurring AAV, which has been modified using recombinant DNA techniques, as a vehicle to deliver the normal human RPE65 gene to the retinal cells to restore vision.⁵

Blood and Immune Disorders

The California Institute for Regenerative Medicine (CIRM) has funded 76 clinical trials for gene-modified cell therapies with more than 3,200 patients enrolled, helping to cure more than 40 children of fatal immunological disorders. Highlights from three of these trials include:

X-linked severe combined immunodeficiency (XL-SCID). Also known as the “bubble boy” disease, XL-SCID is a rare immune disorder that is often fatal within two years of birth. In 2017, researchers took blood stem cells from a child, genetically reengineered them to correct the defective gene and then infused the reengineered cells back into the child. Over time, the cells multiplied and created a new blood supply free of the defect, which helped repair the immune system.⁶ CIRM Director of Patient Advocacy Kevin McCormack says, “The child in this clinical trial is now almost 5 years old and is doing extremely well with no indication of any recurrence and is considered functionally cured because there have been no setbacks and his immune system appears to be functioning normally.”

McCormack says approximately 50 more children have been treated with this same approach in a clinical trial that CIRM funded with Don Kohn, MD, of the University of California, Los Angeles. Last year, Dr. Kohn published a paper in the New England Journal of Medicine reporting that 95 percent of those children are now considered cured.

X-linked chronic granulomatous disease (XL-CGD). XL-CGD is a condition that affects the immune system’s ability to fight off common germs, specifically bacteria and fungi, and can result in infections that would otherwise be mild in healthy people. In 2017, a patient received an infusion of his own blood stem cells that had been genetically modified to correct the X-CGD mutation.⁷ “Five years posttreatment, this patient appears to be doing extremely well with no indication of any recurrence. He is considered functionally cured because there have been no setbacks, and his immune system appears to be functioning normally,” says McCormack.

Cystinosis. Cystinosis is a rare, multisystem genetic disorder characterized by the accumulation of an amino acid called cystine in different body tissues and organs, including the kidneys, eyes, muscles, liver, pancreas and brain. It is caused by mutations of the cystinosin, lysosomal cystine transporter (CTNS) gene and is inherited as an autosomal recessive disease. This disease is classified as a lysosomal storage disorder.⁸

The Cystinosis Research Foundation (CRF) explains that the mutation in the CTNS gene is on the 17th chromosome that encodes a protein called cystinosin. This protein’s function is to transport an amino acid called cystine out of an intracellular compartment called the lysosome. If the cystinosin protein is absent or dysfunctional, cystine accumulates within the lysosome and forms crystals, which kills the cells. Cystinosis slowly destroys organs of the body mentioned previously.⁹

According to CNF research, gene therapy for cystinosis has shown promising results in mice. In 2018, FDA approved a Phase I/II clinical trial for six adult patients to evaluate gene-corrected autologous stem cell transplant as a treatment. The first adult patient received the transplant in October 2019, the second and third patients were transplanted in 2020, the fourth patient was transplanted in November 2021 and the fifth patient received the transplant on March 29, 2022. All five patients are doing well and remain off oral cysteamine medication since their transplants. The sixth and final patient is expected to be transplanted by the end of 2022.

In the October 2019 transplant, the adult patient received an infusion of his own blood stem cells with a functional version of the defective CTNS gene, which reduced cystine buildup in affected tissues. The patient’s gene-modified stem cells are expected to embed themselves in his bone marrow, where they should divide and differentiate into all types of blood cells. Those cells are then expected to circulate throughout his body and embed in his tissues and organs, where they should produce the normal cystinosin protein.¹⁰ “The patient is showing signs of a strong response to the gene-modified hematopoietic stem cell gene therapy and is no longer taking the medication he used to rely on to keep him alive,” says McCormack. “He has drastically cut his medications from 54 pills per day to around 20, and each year he is able to reduce those even more. The patient is not cured, but he is now able to do things that he was not able to do before and is able to imagine a normal life.”

How CRISPR/Cas9 Gene Editing Works

1. RNA identifies a specific portion of DNA
2. Cas9 enzyme cuts double-stranded DNA
3. Targeted piece of DNA is removed
4. New, reengineered sections of DNA are inserted
5. Reengineered genes are automatically incorporated when cells repair broken DNA
6. Disease is controlled going forward

How CAR-T Cell Therapy Works¹⁷

1. Apheresis: T cells are isolated and collected from the body
2. Reprogramming: T cells are sent to a lab where they are genetically modified with
   chimeric antigen receptors that recognize and kill diseased cells
3. Multiplication: Modified cells are multiplied until there are millions of new disease-
   attacking cells
4. Infusion: Modified cells are infused through an IV back into the patient’s blood
5. Cell death: CAR-T cells track down and kill diseased cells

Sickle Cell Disease

In 2014, a team of scientists from the University of California, Los Angeles, the University of California, Berkeley and the University of California, San Francisco (UCSF) collaborated with Benioff Children’s Hospital in Oakland on the first clinical trial to use CRISPR-based therapy on a patient’s own blood stem cells to correct the mutated gene that causes sickle cell disease (SCD). The experimental four-step therapy involves collecting a patient’s blood stem cells; using a brief electrical current to introduce CRISPR/Cas9 enzymes to the extracted stem cells along with a template for correcting the sickle mutation; using chemotherapy to make space in the bone marrow for the edited stem cells; and reintroducing the patient’s own edited cells. This gene editing protocol is expected to correct the sickle mutation in approximately 30 percent of engrafting cells.¹¹

A Phase I/II clinical trial will evaluate the transplantation of CRISPR/Cas9 corrected hematopoietic stem cells (CRISPR_SCD001) in nine patients between the ages of 12 years and 35 years old with severe SCD. The trial is expected to start on Dec. 1, 2022, with an estimated primary completion date of Dec. 1, 2024, and an estimated study completion date of Dec. 1, 2027. The primary endpoint of the trial will determine the safety of CRISPR_SCD001 through a 3+3 design with staggered enrollment and a pause in enrollment for a safety review after each of the first three patients is infused with the drug product. “After safety is assessed in the third patient, enrollment of the next three patients will not be staggered,” say the researchers. “The first six subjects will be adults. If CRISPR_SCD001 is determined to be safe in the first six subjects, the trial will continue to enroll three adolescents between 12 years and 18 years of age to evaluate the safety in younger patients. The younger cohort also will follow staggered enrollment.”¹²

This is the first time clinical researchers have attempted to correct a harmful beta-globin gene mutation in a patient’s own cells with nonvirally delivered CRISPR gene-correction tools, according to Mark Walters, MD, a professor of pediatrics at UCSF and principal investigator of the clinical trial and gene editing project. “This therapy has the potential to transform sickle cell disease care by producing an accessible, curative treatment that is safer than the current therapy of stem cell transplant from a healthy bone marrow donor,” says Dr. Walters. “If this is successfully applied in young patients, it has the potential to prevent irreversible complications of the disease.”¹³

An Exciting Outlook

According to ARM, cell and gene therapy continues to hold great promise for treating rare diseases with high unmet medical needs. It believes 2022 is likely to be a record year for the approval of new gene therapies to treat rare diseases, with a total of four possible approvals in the United States and Europe. (Note: Since publication of ARM’s 2021 annual report, one of the possible approvals was pushed back to 2023.) Two therapies to treat SCD could be available in the United States as soon as 2023 — a gene therapy and a first-ever CRISPR therapy.

“From the approval of CAR-T therapies treating blood cancers to gene therapies treating rare genetic diseases, 2022 is proving to be a strong year for the cell and gene therapy sector,” says Stephen Majors, ARM director of public affairs. “And the strength of the late-stage pipeline bodes well for the next few years, with a variety of therapeutic approaches advancing to treat both rare and prevalent diseases.”