Predicting The Trajectory Of Prime Editing: Lessons From Base Editing:

7 min readSep 22, 2021

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DNA base editing, a technology that emerged from Dr. David Liu’s labs at the Broad Institute, Harvard University, and Howard Hughes Medical Institute (HHMI), which was first introduced in 2016 and has since become widely used by the academic life science community, as well as by companies such as Beam Therapeutics (BEAM). ARK believes that if you review base editing’s trajectory, prime editing could be following a similar course.

Since the introduction of CRISPR-Cas9, two new technologies have added increased functionality, namely a deaminase for base editing, which causes a single letter replacement, and a reverse transcriptase for prime editing, which causes large chunk replacements. The main advantage of base editing and prime editing over targeted nucleases such as CRISPR-Cas9, transcription activator-like effector nuclease (TALENs), or Zinc-finger nucleases (ZFNs) is they do not simply mediate target gene disruption but instead allow target gene correction, even in most therapeutically relevant cell types, which generally do not support homologous-directed repair (HDR). Therefore, these technologies can correct the cause of disease, by correcting mutated DNA letters that cause thousands of genetic diseases, which cannot be done in most cell types by simply cutting DNA with a nuclease.

Base and prime editors nick only one strand of DNA but do not make double-stranded DNA breaks. In addition, unlike nucleases, base and prime editing do not generate uncontrolled mixtures of insertions and deletions (indels) as their major editing outcomes. Since base and prime editing do not make double-strand DNA breaks, they also avoid the production of large deletions, chromosomal translocations, chromothripsis, p53 activation, and other adverse consequences of cutting both strands of DNA. Cells are thought to naturally experience thousands of nicks every day, but only rarely experience double-strand DNA cuts, and tolerate double-strand cuts far less well.

Like nucleases, base and prime editors can also generate gene knockouts. They do so by precisely installing or mutating splice sites, start or stop codons, or regulatory sequences, without the uncontrolled mixture of products and other downsides of double-strand DNA breaks. As a result, it is difficult to imagine a therapeutic application of a nuclease such as CRISPR-Cas9 that cannot be achieved with a base editor or prime editor.

Both base editors and prime editors began as fusion proteins of DNA-manipulating enzymes with inactivated forms of CRISPR-Cas9 that can no longer make double-strand DNA cuts. Initial base editors consisted of an inactivated Cas9 fused to a deaminase enzyme and, in some cases, other proteins involved in DNA repair. The resulting fusion proteins allow targeted transition mutations (C to T, G to A, A to G, or T to C) in living systems including primates. Later versions of base editors use TALE repeat arrays instead of Cas9 to target DNA, allowing base editors in mitochondria, where CRISPR has not been successfully used due to difficulty importing guide RNAs.

Prime editors, in contrast, consist of an inactivated Cas9 fused to a reverse transcriptase. This Cas9-reverse transcriptase fusion protein allows for virtually any small (<~100 bp) DNA sequence to be replaced by virtually any other DNA sequence in living systems. As a result, prime editing is highly versatile, allowing all 12 possible base-to-base conversions, as well as small insertions and deletions. Approximately 89% of known human pathogenic mutations, in theory, can be corrected by prime editing. Unlike the case with base editors, prime editors that do not use CRISPR have not yet been described.

Scientists are actively assessing whether prime and base editing will have drawbacks. For example, prime editors are larger machines, and prime and base editing have the reverse transcriptase or deaminase that are “on,” whereas CRISPR Cas9 is only turned on after hybridization of the guide RNA and the proper PAM sequence is reached. Recent publications suggest that the reverse transcriptase of prime editors do not themselves cause unwanted effects on the DNA or RNA in a human cell, but more data will be needed.

Both base and prime editing have garnered a lot of interest from the academic and investment community. The number of academic papers in base editing has proliferated since its debut in 2016 and continues to expand. Prime editing seems to be following a similar trajectory (Figure 1).

Figure 1.

In 2019, Dr. Liu’s team published the first prime editing study, which has gained significant traction in both general interest and academic circles (Figure 2). According to our research, more than 1,000 labs have obtained prime editing technology from Addgene and published more than 50 research publications and preprints involving a wide range of organisms, including adult mammals. For example, scientists at the Hubrecht Institute, UMC Utrecht, and the Oncode Institute, recently published the use of prime editing to correct the causal mutation of cystic fibrosis in cultured human stem cells. Other scientists at Yonsei University in Korea recently published the use of prime editing in adult mice to treat liver and eye genetic diseases, ameliorating the diseases in the animals.

Figure 2.

When comparing the percentage of prime editing papers in academic journals as a total of base editing and prime editing papers, it is clear that prime editing research has continued to rise since 2019 (Figure 3).

In 2019, prime editing was 2% of the total base editing and prime editing papers, whereas in 2020 the percentage grew to 20%. In 2021, we continue to see growth.

Figure 3.

Base editing went from a technology in a lab to a publicly traded company, BEAM Therapeutics, in four years (Figure 4).

Figure 4.

ARK believes that Prime Medicine, the company that has exclusively licensed prime editing for therapeutic applications from the Broad Institute, and then sublicensed prime editing to Beam Therapeutics in certain fields, could follow a similar or even accelerated trajectory (Figure 5). The company was founded the same year as its first academic paper was published and because of recent advances in artificial intelligence (AI), next-generation sequencing (NGS), gene editing technologies, and in vivo delivery methods, if Prime Medicine follows Beam Therapeutics’ trajectory, Prime Medicine could IPO in 2023. However, given the pace at which the space is developing 2022 is conceivable, for a turnaround time from the first technology publication to IPO in three years.

Figure 5.

*Forecasts are inherently unpredictable and cannot be relied upon.

ARK believes that the increased functionality of base and prime editing over CRISPR nucleases may unlock the possibility of creating potential cures for many genetic diseases with unmet need. The pace of innovation in gene editing is unprecedented with CRISPR being developed in 2012, base editing in 2016, and prime editing n 2019. We see innovation continuing to proliferate because of the advances in AI, sequencing, gene editing, and in vivo delivery. Because of this, we believe the translation of these technologies into new companies and patient benefit could occur unusually quickly.

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Predicting The Trajectory Of Prime Editing: Lessons From Base Editing:

Written by Ali Urman