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Rewriting eye disease: Are we ready for gene therapies?

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In 2020, ophthalmology became the first medical field in Australia to secure approval for a gene therapy. The one-off treatment can restore vision in people once resigned to a lifetime of blindness and is expected to pave the way for many more. MYLES HUME analyses the opportunities and challenges posed by ocular gene therapies.

In a new biography on the American biochemist Professor Jennifer Doudna, famous for her pioneering work in CRISPR gene editing, bestselling author Mr Walter Isaacson explains how the world has entered the third great revolution of the modern era.

The first of these began in the early 1900s in the field of physics when geniuses like Albert Einstein published their work. This was followed by the digital revolution in the second half of the 20th century, bringing us the computer and internet. Now, as Isaacson writes in The Code Breaker, the 21st century has brought the life sciences and biotech revolution where scientists can manipulate or rewrite the code of life to overcome disease.

Ophthalmology is one field at the forefront of this revolution, which is now beginning to cement its place in Australia. Doudna’s seminal work with the CRISPR-Cas9 platform – which earned her the 2020 Nobel Prize in Chemistry along with Professor Emmanuelle Charpentier – could shape eye disease in years to come, and is helping to inspire various programs in Australia in the closely related field of gene therapy.

While these approaches have existed as lab experiments for several years, the Therapeutic Goods Administration’s approval of Luxturna was a flashpoint for Australia in August 2020. It marked the country’s first true, ‘in-vivo’ gene therapy for any disease. The therapy helps to restore vision for patients with inherited retinal disease (IRD) caused by pathogenic biallelic RPE65 gene mutations and is expected to be the first of many brought to market for previously untreatable IRDs.

For more common eye diseases like glaucoma and age-related macular degeneration (AMD) – caused by multiple factors rather than a single genetic fault – there is also promise, with several gene therapy trials already advancing to Phase 2 and 3.

The groundswell of gene therapy programs is cause for excitement among Australian practitioners, patients and health systems, but it has also sparked all new considerations around infrastructure, sustainability and health economics.

Gene therapies explained

Before going further into the article it’s important to understand gene therapy. In gene therapy, the effect of a mutation is offset by inserting a healthy version of the gene into the target tissue/organ, and the disease-related genes remain in the genome. In the more complicated gene editing, such as CRISPR-Cas9, the incorrect DNA sequence within the gene is removed and replaced with the correct sequence, thus permanently altering the genome.

Lions Eye Institute (LEI) clinician researcher Dr Fred Chen says some of the early work in retinal gene therapies began in Western Australia when – more than two decades ago – Professor Ian Constable and Professor Elizabeth Rakoczy began developing an approach that uses retinal cells as a bio-factory to continuously secrete anti-VEGF molecules for treating neovascular AMD, avoiding the need for frequent intraocular injections.

Their research was the first in Australia to use a gene therapy in ophthalmology or any other medical field, and was also the first to progress to human trials locally in 2014. The therapy has been licensed by US firm Adverum Biotechnologies (formerly Avalanche Biotechnologies), which plans to advance the therapy to Phase 3 trials later this year.

Dr Fred Chen
Dr Fred Chen, Lions Eye Institute.

Chen says the eye is a perfect organ for gene therapy because cells in the retina rarely divide and they are enclosed in an immune privileged site within the body. Administration of the gene vector is also relatively straight forward, and the effect of gene therapy can be monitored directly and accurately with high-resolution multimodal imaging technology.

He says there are two broad disease groups where gene therapies are being investigated. The first is Mendelian disorders where the eye disease is caused by a single gene. Those that result in IRDs can be due to mutations in any of the >300 retinal genes. These are collectively the most common cause of blindness in working age Australians.

The other group of diseases are more well-known – such as glaucoma and AMD. Although they aren’t specifically genetic diseases, there is a strong genetic component, and genetic manipulations can be performed to treat pathways of these diseases.

One such therapy in this space is GT005 to slow geographic atrophy (GA) progression, which is being commercialised by UK firm Gyroscope Therapeutics. LEI and the Centre for Eye Research Australia (CERA) are participating in trials related to this therapy, which has advanced to Phase 2. GT005 is designed to stimulate a person’s cells to create Complement Factor I (CFI) deficient, a protein that a subset of GA patients are deficient in.

In IRDs, Chen says the groundbreaking Luxturna therapy adopts the most basic form of gene therapy, known as replacement therapy. It involves loading the RPE65 gene into an adeno-associated viral (AAV) vector, which then infects the retinal cell. The genetic segment is then used by the cell’s protein-producing machinery to create functional RPE65 protein.

The adenovirus family structure used for gene delivery to the eye.

“For recessive diseases this approach works well because a functional gene isn’t there, and the missing gene can be replaced by healthy gene copies delivered via an AAV,” he explains.

“But some dominant conditions are more difficult to treat with gene therapy because the disease manifestation is not due to the lack of the normal protein from the gene, but rather due to a build-up of some faulty protein made from the mutated gene. Therefore, simply adding normal gene copies cannot fix this type of problem. The alternative in such dominant-negative disease mechanism is to edit the mutation in the DNA, or alter RNA processing, using molecules that may interfere with splicing.”

Chen says RNA-level therapy is a hot area in gene therapies at present, and LEI is working with Perth company PYC Therapeutics in this space for retinitis pigmentosa 11 (RP11), a dominantly inherited retinal degenerative disease caused by mutations in the PRPF31 (pre-mRNA processing factor 31) gene.

“The RP11 treatment restores the amount of protein coded by the RP11 gene by using an RNA therapy to influence regulators of RP11 gene expression. The end result is greater amount of RP11 protein to overcome insufficiency due to the deleterious mutation,” he says.

Following Luxturna, Chen expects more IRD gene therapies to arrive soon, potentially for choroideremia and X-linked retinitis pigmentosa.

He is hopeful of more gene therapy trials being set up in Australia as the country expands its capability to genetically diagnose patients with IRDs. In WA, patients are being actively tested through either a clinical or a research pathway facilitated by the Genetic Services of WA or Australian Inherited Retinal Diseases Registry, respectively.

“None of these gene therapies can be administered without first genetically diagnosing these patients. There is a significant cost in setting up the infrastructures and genotyping these patients. It is important not to forget that the process of diagnosing these patients can be just as complex and involved as the process of treating them,” he says.

“In the past, serious life-threatening diseases have been prioritised for genetic testing, for obvious reasons. However, clinical geneticists are taking more interest in genotyping IRDs given the increasing number of IRD treatment trials and the approval of Luxturna.

“My hope is that genetic testing for suspected genetic eye diseases becomes standard care in Australia.”

Need for radical thinking

CERA managing director Professor Keith Martin’s gene therapy efforts have focused on glaucoma, by using a recombinant AAV vector system. The virus works by introducing therapeutic genes to make retinal ganglion cells more resistant to damage. Initially, it is hoped the therapy will target the 10 to 15% of patients who don’t respond to regular treatment and are advancing towards blindness.

Martin began developing the therapy while at the University of Cambridge before co-founding Quethera in 2016, now a wholly-owned subsidiary of Japanese firm Astellas Inc. The therapy is making good progress towards human clinical trials.

Prof Keith Martin
Professor Keith Martin, Centre for Eye Research Australia.

Part of his work has also focused on regenerating the optic nerve, with the most recent work in this area combining two molecules thought to improve axon function – brain derived neurotrophic factor (BDNF) and tropomyosin receptor kinase B (TrkB) – in one treatment. Mice with glaucoma treated with this approach showed improved optic nerve activity and signs of improved vision.

“We have now got some strong candidates that can get regeneration back to the brain with a single dose of gene therapy in these models – that’s a bit further away from clinical use, but it shows in principle what we thought was going to be extremely difficult in the past, which is regenerating the optic nerve, may actually be more feasible than many people first thought,” he says.

“Gene therapy is now a tool we can use in a whole variety of situations, and that’s why it’s so powerful. It can be applied in situations where patients are missing a particular gene, but also to toughen up cells and make them more resistant to injury, and stimulate regeneration by tweaking those pathways.”

Martin says one of the major hurdles in the gene therapy space is the amount of energy devoted to developing treatments for individual IRDs. Doing so is time consuming and not all genes associated with IRDs can fit into viral vectors currently being used.

It’s also an incredibly expensive undertaking for companies and health payers. Reports in the US suggest Luxturna costs up to US$850,000 (AU$1.18 million) for both eyes. Companies will seek to recoup many years of research and investment, but because they only treat a narrow patient group, the cost per patient is high.

“Part of setting the price in the US was looking at the cost saving of avoiding blindness in someone who is treated early in life, and that’s not just in terms of cost in care, but what they are able to contribute to the economy throughout their life,” Martin explains.

“One of the issues for Luxturna, for example, is that it may seem very expensive, but there’s probably only between 16 and 20 patients in Australia who would meet the criteria. The cost for something like AMD clearly cannot be that high to be economic. That’s because the years of vision loss that are avoided is likely to be much less, and it’s a more common condition. It is a trade-off: the more common a condition, the more pressure there is going to be to bring that cost down to make sure it’s accessible to health systems and patients.”

Another issue is that many of the target diseases involve the loss of photoreceptor cells, which the most advanced IRD gene therapies need to work. Martin believes more radical approaches to create therapies that are “disease agnostic” are necessary, as opposed to developing a different therapy for each genetic disorder. One example is reprogramming cells within the retina, such as Müller cells to replace photoreceptors to help restore vision. This could be achieved through techniques like CRISPR.

“It might seem crazy turning a glial cell (Müller) – a non-neuronal cell in the retina – into a new photoreceptor, but that’s exactly what happens in amphibians and fish when they injure their retina. The Müller cells within the retina de-differentiate and then repopulate the missing, lost neurons, so we are trying to establish the missing switches that stop us humans from being able to do that because it’s something we have likely lost along the line of evolution. We are trying to work out how it works in other animals and replicate that in the human eye.”

Along with Phase 2 trials for Gyroscope Therapeutics’ GT005 gene therapy to slow the progression of GA, CERA has been selected for several retinitis pigmentosa trials, and is also developing its own single-gene therapies.

Martin says it’s all part of a plan to make CERA and its affiliates (The Royal Victorian Eye and Ear Hospital and University of Melbourne) a go-to gene therapy centre, especially when pharmaceutical companies view Australia as a favourable location and regulatory environment to perform studies.

The organisation is still building its gene therapy trial capacity and has already gone to great lengths for what is a tightly regulated area. That comes down to having the right theatre facilities and appropriately trained staff, while the end-to-end handling and preparation process is practised and heavily scrutinised before given approval. With the gold standard treatments involving a subretinal injection, there’s also the hefty cost of an OCT-integrated microscope to consider.

“For Luxturna, we expect there to be a small number of centres within Australia that will be providing these treatments, both in terms of facilities and expertise, and that will grow. There are currently five surgeons in Australia who have delivered gene therapies and we have two of them [at CERA], but we hope once we get this up and running we will be able to provide training, and information and knowledge transfer,” Martin says.

Administering the treatments only forms part of the puzzle. As Chen pointed out, identifying potential patients before genotyping and phenotyping, and then linking them with therapies and trials they may benefit from requires extraordinary levels of coordination. Inherited diseases also have implications for families, so genetic counselling is also built into the picture.

This holistic approach was the motivation behind the Ocular Genetics Service that opened at the Eye and Ear in 2019. It is dedicated to patients who have an IRD, are at risk of inheriting or passing on an eye condition or have a genetic disease that affects their eyes.

“It’s the first truly integrated ocular gene therapy clinic in Australia, with genetic counsellors on site, alongside optometrists, ophthalmologists and clinical geneticists working closely together in the same space, seeing the same patients,” Martin says.

“We think this is the gold standard model, where you can offer a one-stop-shop for diagnosis and characterisation of disease; you capture this information, so these patients are ready to go both for approved treatments, or recruitment to clinical trials down the line.”

A national approach

Ophthalmic clinical geneticist Professor Robyn Jamieson agrees more coordination is required if Australia is to provide equitable access to ocular gene therapies.

Jamieson leads the Eye Genetics Research Unit at the Children’s Medical Research Institute (CMRI) in Sydney, among other roles, which has established an end-to-end gene therapy program in NSW that – with the collaborations established – will be valuable across Australia.

Robyn Jamieson_2020
Professor Robyn Jamieson, Children’s Medical Research Institute.

The first component involves a multidisciplinary approach to secure the diagnosis. Eye specialists and geneticists work collaboratively to correctly diagnose patients, their stage of disease and determine their suitability for therapies and trials. This approach arose from 30 years of experience with the multidisciplinary Genetic Eye Clinic at Sydney Children’s Hospitals Network, Westmead. But the results aren’t always clear cut, leading to the second component of the system. In 10 to 15% of cases patients display ‘variants of uncertain significance’ – a genetic variant that has been identified through testing but whose significance to the function or health of the individual is not known.

To overcome this, functional genomics can be performed where a sample is taken from the patient and turned into induced pluripotent stem cells. These are then grown into organoids (retina in a dish) over many months, where the diagnostic team can then assess the patient’s mutation more closely and hopefully determine a diagnosis.

These organoids are grown by Dr Anai Gonzalez Cordero, group leader in stem cell medicine and the manager for the Stem Cell & Organoid Facility at CMRI. Aside from functional genomics, the organoids are used for therapeutic genomics whereby researchers test their own novel therapies. Gonzalez Cordero herself is looking into therapies for Stargardt disease and Usher syndrome, a key challenge being that these genes don’t fit into regular adeno-associated (AAV) viral vectors. She’s applying knowledge she acquired during her time working at the University College London’s Institute of Ophthalmology, under Professor Robin Ali, an esteemed Professor of Human Molecular Genetics and pioneer in the field of gene therapy in the eye. There, she investigated six viral vectors to evaluate which performed best in human retinal cells, establishing key principles to treat human organoids with AAV gene therapy in vitro.

A retinal organoid at the Stem Cell & Organoid Facility at Children’s Medical Research Institute in Sydney. The cones are in red and ganglion cells in green.

Meanwhile, Jamieson is developing and using the organoids to test novel therapies for retinitis pigmentosa and cone-rod dystrophy.

The third and final arm of the program is setting up for pharmaceutical clinical trials or administration of approved therapies. Using this approach, Jamieson believes this can bring together the relevant research institutions, clinical trial centres and diagnostic laboratories across Australia for maximum benefit for patients.

With much of the genomic testing in the research setting, she says this creates a bottleneck and inequity in access. Genetic diagnostic capacity could be significantly increased through greater collaboration with NATA-accredited laboratories.

“We have applied for funding to various government organisations so we can get the whole multidisciplinary team approach as a concept across the country, because sometimes these things tend to operate in isolation and people aren’t realising what’s available for patients,” she says.

“We have engaged organisations in all states across Australia to push forward with this idea, and with the funding we are hoping to appoint coordinators in each state and nationally to facilitate that. We’ve also engaged diagnostic laboratories in those states to get extra funding for them to help push this forward for more patients, and also have people there for coordinating the genetic services with the ophthalmic services. The work we are doing now will be a tremendous advantage for when other therapies are approved and more trials come to Australia.”