Interview Roundup: Base Editing To Correct Rare Genetic Diseases

Base editors are derived from CRISPR-Cas technology and have the potential to cure many genetic diseases by precisely correcting single pathogenic point mutations. While base editors have yet to enter the clinic, results from animal models are compelling and a number of pre-clinical stage therapeutic programmes are underway. In this roundup, we look back on interviews with scientists working with base editors to develop cures for rare diseases.

By: Karen O'Hanlon Cohrt - Oct. 27, 2021

Base editors are fusion enzymes that can modify the genome by making precise single base changes without introducing a double-stranded break. This relatively new class of designer nucleases may offer safe correction of genetic diseases that are caused by a single-point mutation. Learn more about how base editors work in our CMN Base Editing Explainer.

Dr. David Liu led the development of the CRISPR gene-editing tool, base editors, that now tackles... — Dr. David Liu led the development of the CRISPR gene-editing tool, base editors, that now tackles the root cause of the devastating premature-ageing disease Hutchinson-Gilford progeria. Credit: The Broad Institute.

One-time treatment for Hutchinson-Gilford Progeria Syndrome

Hutchinson-Gilford Progeria Syndrome, or simply Progeria, is an extremely rare but fatal genetic disease that is estimated to affect only 350-400 people worldwide. Progeria is not heritable, as it is typically caused by a randomly-occurring single-point mutation that results in a truncated form of the protein progerin. This leads to cell death and severe developmental issues, and makes young children appear as though they are aging rapidly.

Affected children experience diverse health problems including slowed growth and skeletal abnormalities and life expectancy is about 14.5 years, with most dying from heart disease. The first dedicated treatment, Lonafarnib (Eiger BioPharmaceuticals, Inc.), which works by preventing the buildup of defective progerin, was approved by the FDA late last year, but the disease remains incurable.

Research led by Luke Koblan from David Liu’s lab at Harvard University earlier this year demonstrated that base correction of a single point mutation doubled the lifespan in a mouse model of progeria, raising hopes that base editing may one day provide a cure for the disease.

In the study, the team treated a humanised mouse model of progeria — that had been bred to carry a mutated form of the human LMNA gene — and cultured fibroblasts from children with Progeria with an adenine base editor (ABE) that was delivered via an adeno-associated virus (AAV). The ABE was designed to target the affected sequence in the LMNA gene and correct the mutant thymine base by converting it to a healthy cytosine. About 90 % of the fibroblasts were corrected after a single base-editing treatment, while about 20-30 % of mouse cells were corrected. Treated mice showed huge overall improvements with signs of normal cardiac health, and reached an average age of 510 days, which corresponds to old age in mouse terms.

Although very early days, David Liu, who spoke to CRISPR Medicine News shortly after the study findings were published in Nature, told us:

»The hope is that an affected Progeria child would get a one-time injection into their bloodstream — a base editor packaged into some kind of delivery vehicle that could then directly and permanently correct the root cause of the disease,« and that this would »potentially, offer them a one-time treatment that could rescue at least some of the symptoms of the disease. That's the hope.«

You can read our full interview with David Liu here.

Susie Suh, MD PhD student in Professor Krzysztof Palczewski’s lab at University of California Irvine... — Susie Suh, MD PhD student in Professor Krzysztof Palczewski’s lab at University of California Irvine and co-first author on the recent publication demonstrating that a CRISPR base editor can correct LCA and restore visual function in adult mice.

Correction of Leber congenital amaurosis and restoration of sight in base-edited mice

A study from Krzysztof Palczewski’s lab at University of California Irvine (UCI), which was published in Nature Biomedical Engineering late last year, lends support to base editing as a potentially new way to treat Leber congenital amaurosis (LCA), a rare group of incurable and progressive inherited retinal diseases that manifest early in life and lead to blindness by the 3^rd or 4^th decade.

LCA arises from loss-of-function mutations in any one of at least 27 known genes that play a role in retinal function, and mutations in the RPE65 gene are the most prevalent. Until the recent approval of the RPE65 cDNA gene replacement therapy Luxturna (first approved in the US in 2017), which is suitable for a subset of LCA patients, treatment was limited to symptom control and supportive care.

Susie Suh, MD PhD student was the lead author of the study that demonstrated base correction of a disease-causing mutation in an rd12 reporter cell line and in rd12 mice.

The rd12 cell line and mice carry a mutation in the RPE65 gene that results in LCA phenotypes, and the rd12 mouse is an established disease model for human LCA. The team used a codon-optimised adenine base editor to correct the RPE65 mutation and found biochemical evidence that served as a surrogate for a healthy visual cycle in reporter cells. A range of sight tests carried out in base-edited versus control rd12 mice revealed that the eyes of edited mice behaved similarly to healthy eyes with respect to photoreceptor function and downstream retinal interneurons in response to flash stimuli, suggesting substantial sight restoration.

In the study, the team chose to deliver the base-editing reagents using lentivirus because it has a larger cargo capacity than the safer adeno-associated virus (AAV) delivery method, and lentevirus has a natural tropism for the retinal pigment epithelium (RPE). The lentiviral construct carrying its cargo was injected sub-retinally.

During our interview, Susie Suh revealed plans to further optimise the base editing efficiency, explore its potential in older rd12 mice, i.e., the potential to treat advanced disease, as well as plans to evaluate additional clinical phenotypes in the rd12 mice.

You can read our full interview with Susie Suh here.

A potential cure for sickle cell disease

Within the CRISPR medicine field, sickle cell disease (SCD) is among the most widely targeted diseases in ongoing clinical trials. SCD results from a single point mutation in the beta globin (β-globin) gene, HBB, which results in the production of defective haemoglobin and a range of symptoms and life-limiting complications.

The clinical-stage CRISPR therapies currently under investigation (see a previous roundup on some of these clinical trials here) are primarily designed to compensate for the lack of functional adult haemoglobin by reactivating foetal haemoglobin (HbF) expression in patient-derived stem cells through CRISPR-mediated disruption of the BCL11A gene, which is a negative regulator of HbF expression, or through CRISPR-based modulation of the HBB gene promoter to reawaken HbF expression.

Given that all SCD patients are believed to have the exact same underlying HBB mutation, David Liu’s group envisioned base editing as a simple approach to curing SCD. This could both restore healthy adult haemoglobin and eliminate the presence of defective haemoglobin, unlike strategies based on HbF reactivation whereby defective haemoglobin continues to be produced in affected individuals.

In a study published in Nature this summer, David Liu’s team, along with collaborators at St. Jude Children’s Research Hospital in Memphis demonstrated base correction of the pathogenic HBB mutation in patient-derived haematopoietic stem cells. This ultimately converted the defective β-globin protein to the rare non-pathogenic Makassar β-globin variant, which exhibited high enough efficiencies to produce therapeutic effects in lab mice. We interviewed David Liu shortly after the work was published.

The group developed a custom base editor in order to achieve the high editing efficiencies (80 % conversion from pathogenic to Makassar variant in cells) reported in the paper, which they tested in patient-derived cells in vitro and in vivo in mice following implantation of the edited patient cells. Transplanted mice showed improvements for every disease parameter measured with effects that lasted at least 16 weeks, which was the duration of the study. Base-editing company Beam Therapeutics, of which David Liu is a co-founder, has the BEAM-102 lead optimisation candidate in its pipeline, which is designed to correct the SCD mutation.

You can read our full interview with David Liu here.

For a complete overview of CRISPR IND approvals and ongoing gene-editing clinical trials, check out CRISPR Medicine News' Clinical Trials Database.

ArticleNewsIn vivoViralAdeno-associated virus (AAV)Hutchinson-Gilford Progeria SyndromeLeber Congenital AmaurosisSickle Cell Disease, SCDRare DiseaseBase editors