Explained: A first— how a customised gene-editing tool was used to treat 9-month-old boy

Indian Express

27-05-2025

A nine-month-old boy, born with a rare genetic disorder, has become the first (known) person to successfully receive a custom gene-editing treatment, a report published on May 15 in the New England Journal of Medicine said.
Kyle 'KJ' Muldoon Jr suffers from CPS1 deficiency which causes toxic levels of ammonia to accumulate in his blood. To treat him, scientists and doctors from the University of Pennsylvania and the Children's Hospital of Philadelphia developed a personalised treatment based on 'base editing', a new version of the decade-old CRISPR-Cas9 technology.
Scientists say this technology can potentially treat thousands of uncommon genetic diseases. But there remain many roadblocks to its universal adoption.
What is CRISPR?
Following infection by a virus, humans generate an 'immune memory' in the form of antibodies. When they are infected by the same virus again, these antibodies quickly identify the pathogens and help neutralise them.
CRISPR, short for 'clustered regularly interspaced short palindromic repeats', is an immune system found in microbes such as bacteria which fights invading viruses. When a virus infects a bacterial cell, CRISPR too helps establish a memory — but a genetic one, not in the form of antibodies like in humans.
When a virus enters a bacterial cell, the bacterium takes a piece of the virus's genome and inserts the DNA into its own genome. CRISPR then produces a new 'guide' RNA with the help of the newly acquired DNA.
During a future attack by the same virus, the guide RNA quickly recognises the virus DNA and attaches itself to it. Then, the guide RNA directs an enzyme (a type of protein) called Cas9 to act like 'molecular scissors' to cut and eliminate the virus DNA.
In 2012, scientists Jennifer Doudna and Emmanuelle Charpentier replicated this mechanism found in microbes to develop a gene-editing tool, which they called CRISPR-Cas9, a feat which earned them the Nobel Prize for Chemistry eight years later.
How does CRISPR-Cas9 gene-editing work?
The tool works much like the 'cut-copy-paste', or 'find-replace' functionalities in common computer programmes.
Genetic information in DNA is stored as code made up of four chemical bases — adenine (A), guanine (G), cytosine (C), and thymine (T). These bases exist in pairs, which are then stacked one on top of each other, creating the horizontal layers of the double-helix structure of DNA.
Note that A always pairs with T, and C always pairs with G. Genetic disorders, like the one KJ suffers from, occur due to the presence of an abnormal DNA sequence, that is, a mispairing (A-G or G-T).
The first task for the gene-editing tool is to identify the abnormal DNA sequence behind a patient's ailment. Once the bad DNA is located, scientists create a guide RNA attached to a Cas9 enzyme, which is then introduced to the target cells of the patient.
The guide RNA recognises the bad DNA sequence, then the Cas9 enzyme cuts the DNA at the specified location in a process called a 'double-strand break' (since the cut is made on both strands of the DNA). This gets rid of the DNA sequence causing the illness.
DNA strands have a natural tendency to reattach and repair themselves, meaning there is a chance that the bad sequence regrows. To tackle this issue, scientists also supply the correct DNA sequence after the 'cutting' process which is meant to attach itself to the broken strands of DNA.
Over the years, scientists have made many improvements to the original CRISPR-Cas9 technology, making it safer and more precise. A newer, evolved version of this tool is 'base editing'.
How does base editing work?
Base editing and CRISPR-Cas9 differ significantly in how they modify DNA. Unlike CRISPR-Cas9, base editing does not make a double-strand break. Rather, it enables targeted single-base conversions with the help of a Cas9 enzyme fused to a base-modifying enzyme. This allows scientists to fix mispairing of the bases by changing one specific base. For instance, mispaired A-C bases can be corrected to A-T by converting C to T.
To treat KJ, scientists first determined which mispaired base in his DNA was causing his condition. They then programmed the base editing tool to find and rewrite the target base. This process can be likened to using a pencil and an eraser, rather than scissors and glue, as in CRISPR-Cas9.
'In the older version of CRISPR, scientists were required to provide additional DNA from outside, which would be pasted at the site where the double-strand break takes place. In base editing, however, the system by itself can make a very precise change without the need for a foreign DNA to be inserted,' Debojyoti Chakraborty, principal scientist at CSIR-Institute of Genomics and Integrative Biology, told The Indian Express. 'As a result, base editing has fewer components and is compact, making it easier to package in delivery vehicles, which can take it to target cells,' he said.
In 2023, Chakraborty and his team tried to develop a similar tool to treat a patient with a rare neurodegenerative disease. But she passed away before the experiment could be carried out.
Will base editing become commonplace soon?
Chakraborty said the successful use of base editing for treating KJ has given hope to doctors treating people with rare genetic disorders for whom no medical treatments were currently available.
However, it is unlikely that such technologies will become commonplace any time soon, first and foremost due to the prohibitive costs of such treatments. Even if it were to become widely available, base editing would not be accessible to most people. (KJ's treatment was funded by research institutes and biotechnology. While they did not make any official disclosure regarding its cost, it is likely to be in the range of hundreds of thousand dollars, maybe more).
Also, the base editing tool created to help KJ was a one-off treatment, meaning it was designed specifically for his unique genetic disorder and cannot be used to treat other individuals with different disorders. This poses a unique challenge with regards to scaling up such technologies for mass consumption, something that disincentives pharmaceutical companies to invest in their development.
Getting regulatory approvals is another issue. 'To do such a thing in India is very difficult because it also means that you will have to get rid of red tapism,' Chakraborty said.
It remains to be seen how researchers make such personalised treatments more accessible. Till then, only a few fortunate people like KJ will benefit from base editing therapies.