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Base editing to correct the root cause of genetic disease: A breakthrough for progeria patients and a blueprint for future approaches in other genetic diseases.

Contributor: Heidi Grabenstatter, PhD, Science Director, IFCR

Article: Koblan LW, Erdos MR, et al. In vivo adenine base editing rescues Hutchinson-Gilford progeria syndrome. Nature. Online January 6, 2021. DOI: 10.1038/s41586-020-03086-7

Abstract:

Hutchinson–Gilford progeria syndrome (HGPS or progeria) is typically caused by a dominant-negative C•G-to-T•A mutation (c.1824 C>T; p.G608G) in LMNA, the gene that encodes nuclear lamin A. This mutation causes RNA mis-splicing that produces progerin, a toxic protein that induces rapid ageing and shortens the lifespan of children with progeria to approximately 14 years. Adenine base editors (ABEs) convert targeted A•T base pairs to G•C base pairs with minimal by-products and without requiring double-strand DNA breaks or donor DNA templates. Here we describe the use of an ABE to directly correct the pathogenic HGPS mutation in cultured fibroblasts derived from children with progeria and in a mouse model of HGPS. Lentiviral delivery of the ABE to fibroblasts from children with HGPS resulted in 87–91% correction of the pathogenic allele, mitigation of RNA mis-splicing, reduced levels of progerin and correction of nuclear abnormalities. Unbiased off-target DNA and RNA editing analysis did not detect off-target editing in treated patient-derived fibroblasts. In transgenic mice that are homozygous for the human LMNA c.1824 C>T allele, a single retro-orbital injection of adeno-associated virus 9 (AAV9) encoding the ABE resulted in substantial, durable correction of the pathogenic mutation (around 20–60% across various organs six months after injection), restoration of normal RNA splicing and reduction of progerin protein levels. In vivo base editing rescued the vascular pathology of the mice, preserving vascular smooth muscle cell counts and preventing adventitial fibrosis. A single injection of ABE-expressing AAV9 at postnatal day 14 improved vitality and greatly extended the median lifespan of the mice from 215 to 510 days. These findings demonstrate the potential of in vivo base editing as a possible treatment for HGPS and other genetic diseases by directly correcting their root cause.

Commentary:

In this landmark study, Dr. David Liu’s lab in collaboration with Dr. Francis Collins and others demonstrate for the first time in mice that of a second-generation CRISPR gene-editing technology called “base editing” has the potential to correct the root cause of Hutchinson-Gilford Syndrome and other lifelong genetic diseases (1).  Hutchinson-Gilford Progeria Syndrome (or Progeria) is a progressive genetic disorder that causes children to age rapidly. Few Progeria patients live past the age of 13 and early death is usually caused by cardiovascular disease. Progeria is caused by a mutation, a mis-spelling consisting of a single C-to-T change in the gene LMNA that encodes the protein lamin A.  Lamina A plays a key structural role in the cell’s nucleus (2).

Base editing is a precise solution to correct point mutations.

The progeria mutation in lamin A is a dominant negative mutation. While there may be a good copy present, the mutant copy is sufficient to generate the toxic protein, progerin, and cause disease.  First-generation CRISPR technologies are good molecular “scissors” used to cut genes, but do not have the precision needed to correct a single-letter mutation. Base editing is a newer genome editing approach that uses components from CRISPR systems together with other enzymes to directly install point mutations into cellular DNA without making double-stranded DNA breaks (DSBs). The cellular response to DSBs can lead to gene disruption and undesired byproducts including the introduction of insertions, deletions, translocations, or other DNA rearrangements at the site of a DSB (3).  To avoid this issue, Dr. Liu’s team modified enzymes to make them more precise and fused them to CRISPR to create fusion proteins called “base editors”. Since CRISPR technology is good at reading DNA and finding a target, it can effectively deliver the editors to the gene that needs to be changed.  Base editors can change one base pair (or single letters) of the genetic code into another base pair using a guide RNA template. For example, enzymes can convert an A (adenine) to a G (guanine), or a C (cytosine) to a T (thymine). By design, base editors change letters, but do not cut DNA like CRISPR scissors to avoid the risk of large chromosomal deletions and potential damage to cells. (4,5).

To learn more about base editing:

Watch a video of the Sheeky Scientist show covering this study and base editing basics.

Encouraging results expressing base editors in human cell lines and in a mouse model of progeria.

A lentivirus expression system was used to express base editors in fibroblast cell lines derived from patients with progeria and adeno-associated virus 9 (AAV) was used as a vector to express base editors in the cells of progeria mice. The relevant base-editing enzyme (the base editor ABE 7.10max-VRQR was programmed to target the LMNA gene and convert the mutated T•A base pair back to the normal C•G pair) was tested in cells taken from children with progeria.  These experiments successfully demonstrated that 90 percent of progeria cells were edited, subsequently lowering levels of progerin mRNA and protein.

With these encouraging results in hand, the team injected adeno-associated virus 9 (AAV) carrying base editors programmed to target the LMNA gene to the progeria mice three days or 14 days after birth.   A single injection increased the lifespan of the mice engineered to carry the progeria mutation.  The treated progeria mice lived 2.5 times as long as progeria mice injected with saline.  Additionally, treated mice maintained healthy tissue in key organs and demonstrated the gene correction at levels between 10 and 60 % by 6 weeks of age. The investigators noted that follow up experiments confirmed aorta samples were comparable to normal mouse samples. Cells from the base-edited mice were making the corrected human lamin A protein instead of progerin at 6 months.

Moving forward on the heels of a ground-breaking study

This work paves the way for further preclinical studies developing a therapy for progeria and provides a blueprint for addressing other genetic diseases with base editing.  The goal of the team comprised of physician scientists partnered with industry is to develop this approach for humans, but there are remaining questions that need to be addressed first in these model systems.

The team spent years optimizing the base editors and it is encouraging that significant off-target edits were not observed using this approach.  The treated mice with the longest lifespans developed liver tumors, a known long-term complication when AAV is used as a vehicle to deliver genes into mice. The investigators will conduct additional safety and efficacy studies to better understand these results and investigate potential ways to reduce risks of adverse side effects. Next steps will likely include further preclinical studies, with the eventual goal of launching a clinical trial for the progeria population.

Applications in CDD

About 50% of pathogenic variants within the CDKL5 gene are point mutations (6,7).  If these mutations are single-letter mutations in a A•T base pair or C•G base pair, then it is possible those root causes of CDD could, hypothetically, be targeted by cytosine base editors and adenine base editors.  Cytosine base editors convert a C•G base pair into a T•A base pair and adenine base editors convert an A•T base pair to a G•C base pair. Collectively, CBEs and ABEs can mediate all four possible transition mutations (C to T, A to G, T to C, and G to A). The evidence presented here demonstrating proof of principle in progeria human cells and a mouse model of progeria has not yet been demonstrated using base editors in CDD models.  Those experiments are the necessary first steps required to demonstrate the ability of programmed base editors to repair CDD point mutations and subsequently restore CDKL5 protein production.  Additional experiments will also be required on the road to clinical trials not unlike our friends from the progeria community.

References

1. Koblan LW, Erdos MR, et al. In vivo adenine base editing rescues Hutchinson-Gilford progeria syndrome. Nature. Online January 6, 2021. DOI: 10.1038/s41586-020-03086-7

2. Eriksson, M. et al. Recurrent de novo point mutations in lamin A cause Hutchinson–Gilford progeria syndrome. Nature 423, 293–298 (2003).

3.HA Rees and DR Liu. Base editing: precision chemistry on the genome and transcriptome of living cells. Nat Rev Genet. 19(12): 770–788 (2018).

4. Komor, A. C., Kim, Y. B., Packer, M. S., Zuris, J. A. & Liu, D. R. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 533, 420–424 (2016).

5. Gaudelli, N. M. et al. Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage. Nature 551, 464–471 (2017).

6. Olson, H.E.; Demarest, S.T.; Pestana-Knight, E.M.; Swanson, L.C.; Iqbal, S.; Lal, D.; Leonard, H.; Cross, J.H.;Devinsky, O.; Benke, T.A. Cyclin-dependent kinase-like 5 (CDKL5) deficiency disorder: Clinical review. Pediatr. Neurol. 97, 18–25 (2019) 7. Hector RD, Kalscheuer V, Hennig F, Leonard H, Downs J, Clarke A, Benke T, Armstrong J, Pineda MM, Bailey MES, Cobb SR. CDKL5 variants: understanding of a rare neurological disorder improving our. Neurology: Genetics. 3(6), (2017)