Reacción a "CRISPR used for the first time to treat a rare metabolic disease in a baby"

Base editors represent the second generation of CRISPR tools and have been developed by David Liu, a researcher at the BROAD institute, who has also developed the third generation of editing tools, the quality editors. The base editors were created in 2016 by David Liu by combining two activities that had never been together in any living being throughout evolution, which underlines the talent and vision of this researcher in creating from scratch tools capable of chemically changing the identity of nucleotides, without requiring cutting the DNA double strand, which is the characteristic limitation of the first-generation CRISPR tools (and which therefore generates so much diversity of results, not all of which are necessarily correct). There are at least two types of base editors, depending on whether they can convert an A to a G (called ABE) or a C to a T (called CBE) in a precise sequence of the selected gene.

Base editors were used to cure the T-cell acute lymphoblastic leukaemia of Alyssa, a medically hopeless 12-year-old British girl who was resistant to chemotherapy and radiotherapy treatments, but nevertheless managed to pull through with the use of these base editors, which, in this case, were used to inactivate several genes, interrupting their translation, before proceeding to give her CAR-T cell therapy.
Base editors have also been used to inactivate the PCSK9 gene , which encodes the repressor of the low-density lipoprotein (LDL) receptor, which transports cholesterol in the blood, and whose therapeutic effect is to significantly lower serum cholesterol as a potential therapy for people with familial hypercholesterolaemia. This study was validated preclinically in mice, in non-human primates and is currently being evaluated in a clinical trial. In both the case of Alyssa and the PCSK9 gene, base editors were used to inactivate a gene by changing a codon in the sequence coding for an amino acid to a stop codon, which interrupted the synthesis of the protein, which, being truncated, was unable to perform its function.

The work with the base editors to inactivate the PCSK9 gene was led by researcher Kiran Musunuru, from the University of Pennsylvania and the Children's Hospital of Philadelphia (USA). His team now reports in the New England Journal of Medicine (NEJM) the use of base editing technology not to inactivate, but to correct a mutation in a gene associated with a severe congenital rare disease, a metabolic disorder called deficiency in the enzyme carbamyl phostate synthetase I (encoded by the CPS1 gene), which is an essential urea cycle protein responsible for removing residual ammonium from protein metabolism. Mutations in the CPS1 gene inactivate this enzyme and cause severe symptoms in children within days of birth, with vomiting, hypothermia, hypotonia, epileptic seizures and coma, and may lead to death. Treatment involves dialysis to eliminate ammonium, reduction of dietary protein and eventually liver transplantation, which, however, does not resolve the neurological disorders that also occur. It affects about 1 in 300,000 births, about half of whom will eventually die.

In this case, researchers diagnosed the presence of two mutations (one of paternal origin and one of maternal origin) in a child affected by CPS1 deficiency. One of them was chosen to be treated with an ABE-based editor. The strategy was validated first in cultured liver cells and then in a mouse model. All this occurred during the first six months of the child's life. The researchers applied to the regulatory agency (FDA) for approval of this therapy for a single patient and, after obtaining approval, proceeded to administer the base publishers encapsulated in lipid nanoparticles (the same ones used for the covid-19 mRNA vaccines) on two occasions, at months 7 and 8 of life. The child, despite suffering several viral infections, recovered and reduced his blood ammonium levels while increasing the presence of protein in his diet without causing harmful effects. The researchers have been able to assess little else about the treated child, as liver biopsy is not recommended at this age. Nor about the safety of the treatment, about the possible other modified genome sites or about the unlikely (due to previous experiments on mice and macaques) editing of the child's gonads (testicles), which would mean that he could pass on his edited DNA to his offspring. Medium- and long-term study of the treated patient, as well as other similar patients, will be necessary to draw more robust conclusions.

This is a paradigmatic case of developing an ad hoc therapy for a mutation in a single person, a single patient. An economically and ethically debatable initiative (because of the massive and always limited resources that must be invested to treat a single person) and hardly scalable or universalisable, given that each patient will carry different mutations. From the experimental point of view, the approach of single-patient therapies is very risky, given that the lack of controls or variables means that only the success of the treatment can be explained, when it occurs, but not its failure, which may be caused by multiple factors that have not been controlled for in the experimental design. The FDA allows such experimental treatments in cases of very serious diseases, such as CPS1 deficiency, which are incurable and life-threatening.
The researchers anticipate a near future in which these treatments will become more common and even routine. They also predict that, due to previous experience, validation in mice and macaques will no longer be necessary and the patient will be treated after validation of the strategy in cell models only. I consider these to be very optimistic and ambitious wishes, which may have to be revised if success does not follow these pioneering treatments. The important question that the article does not address is the accessibility and affordability of these treatments for children with these diseases. How much will this treatment cost? Where can it be administered? How many children will these new individual therapies reach?