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Special Report on Gene Therapy: Finding the pathfinders

Researchers move beyond cut-and-paste to address genetic disorders
Written byRandall C Willis
| 17 min read

A few years ago, someone asked me to give a layman explanation of CRISPR/Cas9 gene editing. They had heard about it in the evening news for several months by this point, but they never felt like they fully grasped what it did at the DNA level.

A word processing cut-and-paste metaphor was my immediate response, explaining that the complex effectively finds the defective form of a gene sequence and replaces it with a preferred form.

As CRISPR/Cas9 continued to evolve, so too did my metaphorical thinking; it was less cut-and-paste than find-and-replace.

Even though the gene-editing platform continues to be a hot topic, in both the public and scientific eyes, the technology itself continues to evolve as we see a transition from find-and-replace to something more akin to spellchecking.

From gene to base

For genetic disorders, the progression from small-molecule and biologics interventions to cell and gene therapies has been an effort to find deeper and longer-lasting treatments that—in their ultimate form—could be curative.

Some disorders have been more amenable to genetic exploration—e.g., stable monogenic disorders—whereas others have been more intractable—e.g., molecularly heterogeneous tumors.

The University of Victoria’s Francis Choy and Chloe Christensen work in the former category, focusing on mucopolysaccharidoses (MPSs), lysosomal storage disorders where the absence of a single metabolic enzyme leads to a buildup of toxic byproducts. Effectively, the cellular garbage disposal is broken, and the molecular trash overwhelms the cell.

“Enzyme replacement therapy [ERT] has really been the interest over the years for lysosomal diseases and MPS in particular,” Christensen explains, but this approach offers a variety of limitations, not the least of which is the inability of ERT to cross the blood-brain barrier (BBB).

Thus, for conditions like MPS IIIB (aka Sanfilippo syndrome), ERT can ameliorate the bodily impacts of the disorder, but not the neurological impacts.

“There is also the issue of ERT being a chronic therapy, something that needs to be used over time,” she continues. “Patients have to go back for repeat treatments, and for that reason, as well as because the MPSs are quite rare, ERT can be very expensive.”

To find a longer-lasting solution, Choy’s lab and others have looked at gene therapy as a potential solution, using vehicles like adeno-associated viruses (AAVs) to deliver the missing genes to cells where they would produce the deficient enzyme.

Because this genetic material doesn’t integrate into the patient’s DNA, however, even this is not a permanent solution. Over time, as infected cells divide, the AAV-delivered genes dilute out, requiring additional treatments.

“Even more recently, more interest has been in gene replacement therapies, where the gene can actually be knocked-in to the genome of the patient,” Christensen notes, pointing to the recent CHAMPIONS and EMPOWERS clinical trials led by Sangamo Therapeutics.

“They’ve taken the IDS and the IDUA genes—which are implicated in MPS I and MPS II, respectively—and delivered them using AAVs to patient hepatocytes,” she explains. “The idea is that if this is delivered alongside a zinc-finger nuclease (ZFN), which is like the first version of genome editors, that this gene could be knocked-in to a safe harbor locus and could produce the enzyme long term.”

What makes this approach particularly attractive for lysosomal storage diseases is a phenomenon called cross-correction, says Choy. When lysosomal enzymes are produced in the cell, they are secreted into circulation and ultimately interact with, and are taken up by, other cells via a ligand-receptor interaction. In MPSs, the ligand on the enzyme is typically mannose-6-phosphate. Thus, even if a cell is not gene-modified, it can benefit from its neighbors.

“The beauty of the concept of cross-correction is related to what we call the disease threshold,” offers Choy. “For example, in MPS I (Hurler’s syndrome), researchers have documented the threshold amount of normal enzyme to correct the major disease effects is quite low.”

Most MPS I patients have near-zero enzyme activity, he explains, but research has shown that as little as 1 to 5 percent of normal enzyme levels can treat most of the outcomes.

“Because of this low disease threshold for the enzyme correction level, cross-correction becomes the method of choice,” he states.

“This is particularly interesting to us because MPS IIIB disease has a neurological component,” adds Christensen, suggesting that they are applying similar genome editing ex vivo to patient-derived induced stem cells.

“Once edited for a patient-specific mutation, you can take those cells, differentiate them into neuronal and glial precursors, and deliver them back into the patient using intracerebral transplantation,” she remarks. “Then, hopefully, those precursors would turn into neurons and glia, be able to produce functional enzyme, and secrete the enzyme to be taken up by existing neurons in the patient brain.”

This is not to say that genome-editing platforms don’t have their challenges.

ZFNs, for one, are owned by Sangamo, and therefore can be expensive to acquire. As well, they can be difficult to bioengineer because of the protein-DNA interaction that guides their genomic site-specificity.

“The success recently, particularly with the CHAMPIONS and EMPOWERS studies, has resulted from the focus on this single locus, the safe-harbor locus in the albumin gene,” Christensen notes. “So, they were essentially able to just design one version of the zinc finger and use a different gene knock-in construct to insert into that particular location.”

She contrasts that with CRISPR/Cas9 genome editing, where targeting relies on RNA-DNA interactions, making them much easier to design and much less expensive to use.

The challenge with CRISPR/Cas9, she points out, comes with its induction of a double-strand DNA break (DSB) and its reliance on host cell DNA repair machinery to induce the genome modification.

If DSB repair occurs via non-homologous end-joining (NHEJ), the result is likely a gene knock-out, whereas if it occurs via homology-directed repair (HDR), the sequence of an endogenous homologue or introduced DNA fragment is used to specify how the DSB is fixed.

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