Recent results from gene therapy trials give hope for new treatments that will improve vision
Clinicians and scientists from the Eye Genetics Research Group, at Save Sight Institute in Sydney, are working to identify and treat blinding genetic eye conditions which affect both the anterior (cornea and lens) and posterior (retina) parts of the eye. This includes offering a genetic diagnosis for conditions, which affect millions of people worldwide, such as congenital cataracts, glaucoma, retinal dystrophies and other inherited eye diseases. The vision impairment associated with these conditions is often irreversible, untreatable, and worsens with age.
A genetic diagnosis is helpful in providing clarity about the specific type of genetic eye condition, potential prognostic information, and is also a critical element in the subsequent development of highly targeted emerging treatment options, such as genome engineering and stem cell applications.
Genetic diagnosis is especially useful where there may be no-one else affected in the family. This can help parents understand future genetic considerations, and can also help affected individuals once they reach adulthood to know the chances of their children inheriting the condition. Depending on the inheritance pattern, this can be a less than 1 per cent chance, or it can be up to 50 per cent.
Next Generation Sequencing (NGS) has been a game changer…
Until recently, we’ve rarely been able to provide people with this information because the human body has around three gigabytes of data wound up in its chromosomes, with coding for about 21,000 genes.
In the past, it was almost impossible to offer families a genetic diagnosis because it cost around AU$2,000 and three months to analyse just one gene with the previous gold-standard, Sanger sequencing methodology. When you consider that there can be 50–100 genes on the suspect list, you realise that in some cases it may have taken $200K and 25 years for a result. This was not particularly helpful or feasible!
The challenges of obtaining, managing and analysing such enormous amounts of data in the past, made genetic diagnosis extremely difficult and expensive.
Advances in Genetic Diagnosis
Excitingly, there are recent striking advances in technology allowing breakthroughs in genetic diagnosis and potential treatment approaches.
Next Generation Sequencing (NGS) has been a game changer, offering high-throughput sequencing of large quantities of DNA data for analysis, and incorporating a number of different technologies which allow us to sequence DNA more quickly and less expensively than in the past, revolutionising the study of genomics and molecular biology. There are a number of possible genomic techniques including targeted NGS, clinical exome sequencing (CES), whole exome sequencing (WES) and whole genome sequencing (WGS). These offer increasing amounts of sequence data generation, and can be used in various research applications. We are analysing these techniques for best possible applications in the clinical diagnostic setting in genetic eye disease, and these will become increasingly available as the costs fall with improvements in the technology.
We are collaborating with national and international next-generation sequencing facilities and have already made molecular diagnoses in patients where this was previously not possible. We have so far looked at around 160 children and adults, achieving a detection rate of about 70 per cent for patients with congenital cataracts and about 60 per cent for those with retinal dystrophies. There are still patients and families where a genetic diagnosis has not been possible so far, but we are making good progress in this area, using detailed research applications of the genomics technology. Using these approaches we have identified several novel candidate disease genes.
Identification and Investigation
After discovering a novel disease gene, our task is to understand how it works. Model systems are used to determine the underlying pathophysiological mechanisms and for preclinical work to develop new treatment strategies for the vision impairment.
One of the areas on which we focus includes the anterior segment disorders, which can be complicated by glaucoma and cause debilitating and progressive vision loss. Disorders of the anterior segment of the eye include primary congenital glaucoma (PCG), abnormalities of iris development, congenital cataracts and corneal abnormalities.
At Eye Genetics Research Group, we have used genomics, cell-based and animal model studies in our identification and investigation of the novel disease gene Signal Induced Proliferation Associated 1 Like 3 (SIPA1L3). This novel disease gene is implicated in congenital cataracts, which encodes a previously uncharacterised member of the Signal Induced Proliferation Associated 1 (SIPA1 or SPA1) family, with a role in Rap1 signalling.
This work was recently published in the prestigious journal, Human Molecular Genetics, which used an image from Eye Genetics Research Group’s publication on the journal cover.
We undertook cell-based studies and showed that SIPA1L3 downregulation in 3D cell culture revealed morphogenetic and cell polarity abnormalities. Our studies showed that decreased expression of Sipa1l3 in zebrafish and mice caused severe lens and eye abnormalities. Sipa1l3-/- mice showed disrupted epithelial cell organisation and polarity and, notably, abnormal epithelial to mesenchymal transition (EMT) in the lens.
Our findings showed that abnormalities of SIPA1L3 in human, zebrafish and mice contributed to lens and eye defects, and we identified a critical role for SIPA1L3 in epithelial cell morphogenesis, polarity, adhesion and cytoskeletal organisation. Intriguingly, interrogation of the cBioPortal for Cancer Genomics revealed that somatic abnormalities of SIPA1L3 were present in over 40 cancer types, many of epithelial origin, suggesting that dysfunction of SIPA1L3 may also contribute to the phenotype of some malignancies, paving the way for further investigation in this field.
In our retinal work, we have made significant headway in genomic strategies for novel disease gene and variant identification particularly in the retinal dystrophies (Prokudin et al, 2015).
At Eye Genetics Research Group, we are now translating our genomics research to clinical availability of next generation sequencing (NGS) for diagnostic testing. We are using our expertise in cell-based and animal model assays for functional investigation of novel retinal disease genes we discover.
Two exciting avenues we are particularly interested in pursuing are genome engineering, using CRISPR technology and human induced pluripotent stem (iPS) cell applications:
Genome engineering, including CRISPR technology, can be used to investigate the function of disease genes and application to novel treatment strategies
The CRISPR technology allows precise gene editing to create specific mutations that can be used for disease modelling, and is also a technique for specific correction of gene mutations.
iPS Cell Applications
Induced pluripotent stem (iPS) cell applications are patient skin cells made into cells that can be differentiated to relevant eye cells and used in the development of therapeutic approaches.
Induced pluripotent stem (iPS) cell applications are particularly useful as a cell-based model system in the retinal dystrophies, since these tissues are not generally accessible pre-mortem.
Studies in rodents have shown that stem cells differentiated to retinal cells can deliver healthy retinal cells into the diseased retina, and these approaches are being tested in early trials in humans. We now have expertise in differentiation of hiPSCs to retinal pigment epithelial (RPE) cells (hiPSC-RPEs), through work with our collaborator Associate Professor Alice Pebay, University of Melbourne.
Induced Pluripotent Stem Cells
Induced Pluripotent Stem Cells (iPS) are adult cells, sourced from skin biopsies for instance, that have been genetically altered to more closely resemble human embryonic stem cells.
The ability to do so, using viruses to change gene expression, was discovered in 2007. Since then, researchers have begun to find new, permanent ways to reprogram, and make harmful changes to cells. Their purpose is to create specific diseases then study the disease development and progression, which may assist in developing and testing new drugs for treatment.
Another aim is to be able to create iPS cells safely and on a large scale. This may provide a source of cells to replace those damaged following illness or disease. Researchers believe that it may also be possible to make stem cells for therapy from a patient’s own cells, thereby avoiding the need to use anti-rejection medications.
We are applying these techniques in investigation of a recently identified novel retinal disease gene, which we identified using whole genome sequencing. We have determined that this gene is expressed in specific layers of the retina, but little is known about the function of the encoded protein. We have used CRISPR technology, to generate two mouse lines: one with the precise orthologous missense mutant allele, and a second with a frameshift, loss-of-function mutation. We have developed a functional genomics pipeline to determine the disease mechanism using our cell and animal based models.
The significance of this project is underlined by the fact that many of the genetic retinal dystrophies currently lead to incurable blindness. There is hope for treatment with recent results from gene therapy trials indicating encouraging signs of success towards vision improvement, and stem cell studies in the first phases of investigation in humans. Success of our approaches in functional investigations and steps in gene correction and other experiments towards treatment for this gene, will be able to be applied to other patients and families with mutations in disease genes that are identified.
Associate Professor Robyn Jamieson heads up the eye genetics research group at Save Sight Institute in Sydney. She was recently granted research funding for work on genomics, genome engineering and model systems related to this work.
Described as “game-changing”, CRISPR – or Clustered Regularly Interspaced Short Palindromic Repeat – technology enables researchers to make precise changes in the DNA of humans, other animals, and plants faster and more easily than other DNA modifying techniques.
CRISPR sequences are a crucial component of the immune systems of bacteria and other simple microorganisms, providing protection by identifying and destroying the genome of an invading virus.
Early in 2015 CRISPR technology was used in adult mice to replace a mutant form of a gene with its correct sequence, in the process, reversing symptoms for a rare liver disorder.
Additionally, the technique has been used to give white blood cells immunity to HIV. Researchers believe CRISPR technology has the potential to pave the way for the development of more specific antibiotics that target disease-causing bacterial strains, leaving beneficial bacteria to survive.