Decoding life:
Key milestones in the CRISPR odyssey

The story of CRISPR’s development, from its humble beginnings as a bacterial defence mechanism to its current status as a groundbreaking tool for gene editing and beyond, is a fascinating journey through scientific discovery and innovation, illustrating the collaborative and cumulative nature of research.

Initially observed as peculiar sequences in microbial genomes, CRISPR’s true potential has been unlocked through decades of curiosity-driven exploration. Following landmark approvals in the UK and US, we reflect on the key milestones that helped to transform a biological curiosity into a powerful tool that promises to revolutionise medicine, agriculture, and beyond.

A sign of things to come

The first sign of CRISPRs emerged in the late 80s, when, while studying a gene in E. coli, Japanese scientist Yoshizumi Ishino and his team stumbled across something unexpected – repeated sequences interspersed with shorter unique ‘spacer’ segments. These ‘Clustered Regularly Interspaced Short Palindromic Repeats’ had never been seen before. Unfortunately, due to a lack of DNA sequence information at the time, the actual biological function of these sequences would remain a mystery for more than a decade.

Of course, this unanswered question didn’t deter scientists from exploring ways to use the information found in CRISPR loci. Just a few years after Ishino’s initial discovery, in 1993, researchers in the Netherlands observed that different strains of Mycobacterium tuberculosis had different spacer sequences between the DNA repeats. Using a technique called ‘spacer oligonucleotide’, the team began to characterise strains based upon their spacer sequences.

Identification of CRISPR’s adaptive immune function

By the turn of the century, Spanish molecular biologist and microbiologist Francisco Mojica had already made quite a name for himself in the world of CRISPR, being the first to characterise what we now call a CRISPR locus (originally dubbed short regularly spaced repeats) in 1993. Throughout the 90s, Mojica devoted his work at the University of Alicante to uncovering the secrets of these sequences, and by 2000 he had observed CRISPR loci in 20 different microbes, identifying common features that are now recognised as CRISPR hallmarks.

Distinció de la GVA al mèrit científic: Francisco Martínez Mójica.(Photo: Alberto Sáiz)Image: Distinction of the Generalitat Valenciana for Cultural Merit: Francisco Martínez Mójica [left]. (Photo: Alberto Sáiz)

Mojica’s dedication paid off in 2005. After years of painstaking research, he discovered that CRISPR sequences matched parts of the bacteriophage genomes. This breakthrough led him to conclude that CRISPR serves as an adaptive immune system in bacteria, that protects microbes against specific infections; a notion confirmed by further research and parallel discoveries by others.

Hijacking the system

A major breakthrough came in 2012 when Jennifer Doudna and Emmanuelle Charpentier demonstrated the ability to programme CRISPR to precisely target and edit specific DNA sequences. Simply put, the researchers identified a way to re-engineer the Cas9 endonuclease with single RNA molecules that could hunt down and cut the DNA target specified by the guide RNA.

Attribute ”© Johan Jarnestad/The Royal Swedish Academy of Sciences”Attribute ”© Johan Jarnestad/The Royal Swedish Academy of Sciences”

Their landmark paper, published in 2012, demonstrated how CRISPR-Cas9, originally part of bacteria’s immune system against viruses, could be harnessed to cut DNA at specific locations. This discovery provided scientists with a powerful tool to edit genomes with unprecedented precision, speed, and flexibility. However, despite the revolutionary implications of the results, when the study was published in June 2012, it wasn’t met with the accolades one might expect for such a discovery, and it would take a long time before CRISPR-Cas9 would become headline news.

The race to expand the CRISPR toolbox

In the scientific community, the race was on to push the boundaries of the technology. For months after her initial discovery, Doudna and her team worked tirelessly to find out if the test-tube success of CRISPR could also be translated to living cells. At the same time, four other research teams were also working towards the same goal.

In January 2013, five teams of scientists published studies demonstrating successful use of CRISPR in living animal or human cells. The first came from Feng Zhang and his team at the Broad Institute. The study, published in the journal Science saw CRISPR-Cas9 used as a tool for genome editing in eukaryotic cells of humans and mice. Around the same time, George Church, a pioneering geneticist at Harvard University, also published his research on genome editing in mammalian cells using CRISPR-Cas9.

The CRISPR toolbox expanded further with the discovery of additional CRISPR systems beyond Cas9, such as Cas12 and Cas13, each offering unique capabilities for gene editing and manipulation. This diversification enhanced the versatility and precision of CRISPR technology.

Later in the year, Doudna, Church, and Zhang joined forces with respected scientists David Liu and J Keith Joung from Havard university to explore ways to commercialise CRISPR-Cas9 technology. The result came in September 2013 in the form of a company – Gengine, Inc (which was swiftly renamed Editas two months later).

First in-human trials commence

Naming issues firmly in the past, Editas soon began making its potential known. Just a few short years after the creation of CRISPR-Cas9, the company (alongside co-sponsor Allergan) was granted unanimous approval by a federal biosafety and ethics panel in the US to begin the first ever in-human trial of the technology.

The groundbreaking BRILLIANCE trial of EDIT-101 focused on gene editing treatment for patients with Leber congenital amaurosis, a genetic disorder causing severe vision impairment from birth. Patients would receive the treatment via a subretinal injection to reach and deliver the gene editing machinery directly to photoreceptor cells – marking a significant step towards in-vivo editing.

The ‘CRISPR babies’ scandal

The meteoric rise of CRISPR technology brought with it a wave of possibilities and opportunities; concerns over the ethics of gene editing were also growing louder.

While the scientific community seemed to be united in the need to balance the excitement of innovation with cautious and careful consideration, one ‘rogue’ scientist had other ideas, ideas that would thrust CRISPR under a very public ethical microscope.

In 2018, Chinese scientist Dr He Jiankui made the groundbreaking, and highly controversial, claim of having created the world’s first genetically edited babies using CRISPR-Cas9 technology – having altered the DNA of two human embryos to make them resistant to HIV.

VOA - Iris Tong, Public domain, via Wikimedia CommonsPictured: Dr He Jiankui speaking at the Second International Summit on Human Genome Editing. Credit: Iris Tong, Public domain, via Wikimedia Commons

If Dr He had been anticipating his work to be met with global acclaim, he was in for a big shock. The technology was still in its infancy, with potential unforeseen consequences and safety risks still unknown. His actions triggered widespread and high-profile condemnation, fuelling ethical concerns as experts criticised the experiment’s lack of transparency, proper oversight, and consent processes.

The incident prompted calls for stricter regulations and guidelines surrounding gene editing, particularly emphasising the importance of balancing scientific advancement with ethical responsibility. Moreover, for his actions, Dr He was found guilty of forging ethical review documents, misleading doctors into unknowingly implanting gene-edited embryos into two women, for which he was handed a three-year prison sentence.

Tightening the reins on CRISPR innovation

Rather unsurprisingly, amid fallout from the public ‘CRISPR babies’ scandal, the World Health Organization (WHO) convened an Expert Advisory Committee on Developing Global Standards for Governance and Oversight of Human Genome Editing. The 18-member committee approved the first phase of a new global registry to track research on human genome editing, as well as an online consultation on the governance of genome editing.

Addressing the second meeting of the committee, Dr Tedros Adhanom Ghebreyesus, WHO’s Director-General, said: “New genome editing technologies hold great promise and hope for those who suffer from diseases we once thought untreatable. But some uses of these technologies also pose unique and unprecedented challenges – ethical, social, regulatory, and technical.”

That same year, Chinese authorities also prepared gene-editing regulations, stressing that anyone found manipulating the human genome by gene editing techniques would be held responsible for any related adverse consequences.

Recognising pioneers

While 2020 will likely be remembered for another significant development in the history book of global health, it was also a standout year in the story of CRISPR. One of the year’s most notable achievements was the awarding of the Nobel Prize in Chemistry to Emmanuelle Charpentier and Jennifer Doudna for their development of the CRISPR-Cas9 gene editing technology, marking an historic recognition of CRISPR’s transformative potential. This accolade cemented the two women as pioneers in the field and underscored the technology’s profound implications for genetic research and its potential for therapeutic applications.

The year also saw advancements in CRISPR’s therapeutic applications, with the first human clinical trials using CRISPR-Cas9 showing promising results in treating genetic disorders. Notably, a study reported in the New England Journal of Medicine demonstrated success in using CRISPR to edit the genes of patients with sickle cell anaemia and beta-thalassemia, offering hope for curing these hereditary blood disorders.

Elsewhere, in the phase I/II BRILLIANCE trial, researchers at Casey Eye Institute, Oregon Health & Science University, administered EDIT 101 to the first patient. This was the first time a CRISPR therapy had been successfully applied directly inside the human body.

© Nobel Prize Outreach. Photo: Bernhard LudewigPictured: Emmanuelle Charpentier © Nobel Prize Outreach. Photo: Bernhard Ludewig

© Nobel Prize Outreach. Photo: Brittany Hosea-SmallPictured: Jennifer Doudna © Nobel Prize Outreach. Photo: Brittany Hosea-Small

A new era of medicine

A decade after Doudna and Charpentier quietly showcased the potential of programming CRISPR to target and edit DNA sequence, in late 2023, CRISPR made mainstream media headlines once again. The first-ever CRISPR-based gene editing therapy had been approved for marketing in the UK.

The Medicines and Healthcare products Regulatory Agency (MHRA) cleared Vertex Pharma and CRISPR Therapeutics’ Casgevy (exagamglogene autotemcel or exa-cel) in in the UK as a one-shot therapy that involves harvesting bone marrow stem cells from patients and using CRISPR to modify them outside the body (ex vivo) before reinfusing them to treat the diseases.

In the context of medical research, where treatments can take decades to reach patients, it was an extraordinary achievement.

Just a few weeks later, regulators in the US followed suit, making Vertex Pharmaceuticals’ Casgevy the first every FDA-approved gene therapy to utilise the CRISPR method. With the ball now rolling, the FDA lost no time in clearing Casgevy for a second indication (transfusion-dependent beta thalassaemia) in January 2024, more than two months before its deadline.

The future of CRISPR

CRISPR technology is still in its early stages, but it has the potential to revolutionise medicine. Researchers are working on developing new CRISPR-based therapies for a wide range of diseases, including cancer, genetic diseases, and infectious diseases. The future of CRISPR is bright, and it is likely to play a major role in healthcare in the years to come.

About the author

Eloise McLennan is the editor for pharmaphorum’s Deep Dive magazine. She has been a journalist and editor in the healthcare field for more than five years and has worked at several leading publications in the UK.

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