This Christmas, DNA engineering is giving the families of leukaemia sufferers hope

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In May 2022, a clinical trial quietly got under way in London when a British teenager named Alyssa became the first patient to receive an experimental treatment generated using “base-editing”, an emerging form of DNA engineering. Alyssa, 13, had exhausted all conventional treatments for a difficult-to-treat blood cancer, and was enrolled to receive immune cells from a healthy volunteer that had been programmed to hunt and kill leukaemia cells. Within a month, the disease was undetectable.

Whether this highly sophisticated form of cell therapy, undertaken by our team at London’s Great Ormond Street Hospital, has cleared the cancer permanently, and whether subsequent patients will also respond, only time will tell. Nonetheless, the breathless pace of research developments around gene therapies, with ever impressive technological improvements, are with good reason, providing scope for optimism.

It is almost 20 years since the Human Genome Project, an international research programme involving 20 universities across six countries, completed a decade-long quest to sequence the DNA code, which makes up our genes and chromosomes. Some 3 billion pairs of letters – or bases – were found to be organised into 20,000 or more genes, and which ultimately guard and control the secrets of life in every nucleated cell.

The code encrypted into bundles, or genes, relies on just four DNA bases and carries instructions to molecular machinery found inside cells and orders the production of proteins. If DNA code is the script, proteins are actors playing out their roles to determine how cells assemble, develop, function, interact, sleep, wake, replicate and die.

At the turn of the millennium, there was still a great deal of uncertainty around how quickly these enormous data sets might be exploited to improve human health. Variations in the DNA code arise naturally between individuals, and occasionally some changes – commonly known as mutations – give rise to diseases. Some dominant mutations – for example, for the neurodegenerative disorder Huntington’s disease – act alone. Other mutations – as in the case of the inherited blood disorder beta thalassemia or lung disease cystic fibrosis – are problematic only in combination.

A microscope image by the National Cancer Institute Centre for Cancer Research in 2015 shows human colon cancer cells with the nuclei stained red. NCI Centre for Cancer Research via AP

The question being asked then was, how can mutations be permanently corrected or their effects reversed? A handful of early reports of successful “genetic therapies” were emerging at the time.

The holy grail of gene therapy remains a quest to replace or change DNA 'on site' in a single, efficient and reliable therapy

For example, in France in 2001, the paediatric immunologists Alain Fischer and Maria Cavazzano used a modified virus, gutted of its own genes, to carry a therapeutic gene into bone marrow cells collected from infants born without a functioning immune system. Return of these “repaired” stem cells back to the infants supported life-saving recovery, restoring immunity and clearing infections.

Later, it became apparent that pushing extra copies of genes randomly into chromosomes can disrupt how cells proliferate and might, in some circumstances, cause cancer. This prompted researchers to revise and upgrade the virus delivery systems. As a result, today there are dozens of experimental treatments being investigated to add extra copies of genes to cells. Some therapies have reached the stage of market authorisation, including for beta thalassemia and certain forms of haemophilia, which otherwise require life-long blood product support. Overall, numbers treated to date are relatively small, and long-term monitoring will give us a better picture of their effectiveness and safety. For now, exceptional price tags will raise eyebrows and restrict access, but developments continue at a rapid pace, and improved, safer and more effective strategies are all but inevitable.

The holy grail of gene therapy remains a quest to replace or change DNA “on site” in a single, efficient and reliable therapy. That aspiration was boosted in 2012, when an enzyme system called Crispr/Cas9, first discovered in bacteria, was repurposed to precisely cut or snip human DNA. This was not the first such platform to be developed. In fact, our team had deployed existing molecular scissor tools for editing “T cells” – a type of white blood cells that are a part of the immune system – against leukaemia. However, Crispr is a highly adaptable, inexpensive and easy-to-use technology. It is indeed a breakthrough technology that earned its developers, Emmanuelle Charpentier and Jennifer Doudna, the 2020 Nobel Prize in Chemistry.

Simultaneous advances in sequencing technologies and computing power now enable an entire genome to be sequenced within hours. A new wave of therapeutic strategies are already in development. A number of clinical trials using Crispr/Cas9 are under way, mostly to disrupt genes, including at our hospital where earlier this year, we published how Crispr can more efficiently engineer T cells.

This week, at the American Society of Haematology annual conference in New Orleans, we reported how an even newer generation of molecular tools – called base-editors – are being applied to generate “off-the-shelf” T cells to treat other types of aggressive leukaemia.

Base-editors were invented at the Massachusetts Institute of Technology, as recently as 2016, and can chemically change single letters of the DNA code. The technology draws on the guidance system of Crispr to reach very precise locations on chromosomes, deep inside the centre of cells. Rather than cut DNA, the molecular machines deploy localised chemistry to change letters just within reach of their enzyme arms. The cells that Alyssa received were the most complex generated so far, and she went into remission within a month of treatment.

All this is very encouraging, but of course more patients will need to be treated and followed over a much longer period of time, in this and other clinical trials.

Nonetheless, a quite remarkable technological leap is under way, and it seems highly likely that there will be further iterations and clever refinements to come. Solutions to address delivery into other types of cells, and to limit possible immune responses, are being investigated. New questions and dilemmas will be certain to arise, not least around regulatory oversight, costs and accessibility of these cutting-edge technologies as the revolution unfolds.

For now at least, one relieved family will celebrate the holidays together, and there is hope for others into a new year.