Abstract
The White House executive order on Advancing Biotechnology and Biomanufacturing Innovation for a Sustainable, Safe, and Secure American Bioeconomy, issued last month, highlights the importance of biotechnologies. In the context of CRISPR and genome editing, global competition is fierce, with strong commitments in technology development around the world, especially in agriculture in Asia, as well as regulatory challenges in the European Union.
The urge to deploy genome editing commercially at scale is also a reminder that, beyond human genome editing, many complexities remain to editing various genomes. There are important technical and practical considerations to ponder. The development of the CRISPR effector toolbox has been well chronicled, including here, but its deployment in nonmodel commercial species across phylogenetic groups warrants attention. In an ocean of possibilities, the article depicted on the cover of this issue, from Zhang and colleagues, represents a timely example of efforts in metagenomic mining.
Researchers now have access to a portable CRISPR toolbox enabling flexible editing from a single nucleotide (e.g., a base editor) to large-scale genome manipulation (e.g., removing genomic islands in excess of 100 kb), spanning nearly six orders of magnitude in the size of the edit. This elasticity also applies to the size of the organisms that are being manipulated, from submicroscopic viruses (<10−7 m) to trees that exceed 10 m in height—that is more than eight orders of magnitude in the size of the edited organism. This obviously correlates with the size of the genomes in play, from tens of kilobases to tens of gigabases, respectively (seven orders of magnitude in the size of the genome being manipulated).
Some of these theoretical combinations consequently add up to sobering orders of magnitude, from a single base edit in a 30-kb bacteriophage delivered in a single 1-mL dose to 1 kb inserted in a 30-Gb tree genome scaled up to 100,000 hectares of a commercial forest. The depth of our knowledge of most commercial trees and crops oftentimes pales in comparison with how well we know the genomes of some model phage and bacteria. (This too spans orders of magnitude!)
Editing the World
Once a particular genome has been edited for a particular purpose in a select species, one must contemplate the scale at which the edited genome will be deployed. Small viruses such as CRISPR-engineered phages targeting bacteria for infectious disease may be delivered in a single dose (e.g., 1010 particles in 1 mL) released locally at a site of infection in a single patient. Bacteria used in food fermentations may be scaled up industrially to manufacture dairy products such as cheese and yoghurt (humankind consumes ∼1021 CRISPR-enhanced starter cultures annually).
Genome-edited crops are anticipated to be planted in 100 million farms (up to 15% of all farms on the planet) by 2030, accounting for ∼2% of our global agricultural production. Applications of genome editing in the realm of forestry will of course take more time, but there are already plans to scale up to hundreds of thousands of hectares of edited forests by 2050. Lifespan elasticity is also in play, from simple organisms that replicate in 20 min in ideal conditions to long-lived trees that will hopefully thrive for hundreds of years.
Straightforward Approach, Complicated Processes
Despite the seemingly simple processes inherent to using CRISPR effectors to edit genomes, each species presents unique difficulties (delivery, efficiency, and specificity) and scale up challenges (across space and time). This is compounded by our relatively primitive understanding of important processes (DNA repair pathways and controlling editing outcomes) and limited toolbox (delivery in many plant species).
Thankfully, some enabling technologies will help mitigate certain challenges, such as the affordability of high-throughput sequencing technologies to deepen our understanding of genotypes (what genes should be targeted), machine learning and artificial intelligence to inform editing strategies (how many and what kind of edits should be designed, with multiplexing typically needed for complex traits), and, as always, delivery modalities (RNA-only payloads, viral discovery, and synthetic biology).
Inspired by the pioneers leading CRISPR-based clinical trials, an army of livestock, crop, and tree breeders are already defining the next era of agriculture. Meanwhile, molecular microbiologists are manipulating viromes and microbiomes to shape the environment, with hopes to do so at scale.
The White House executive order also tasks regulatory agencies to engage with industrial innovators to ensure we collectively do so responsibly, safely, and transparently to mitigate risks. Time will tell whether technical hurdles or regulatory challenges are the limiting factor, in a globally competitive context where geopolitical considerations are also in play, not to mention fears of climate change and economic uncertainty.