Programmable Molecular Technologies for Genome Editing and Cell Control
Jonathan Gootenberg, PhD, Principal Investigator, Center for Vaccines and Virology Research, Beth Israel Deaconess Medical Center
Cell Editing: Industry Needs New Toolkit that Allows Reprogramming of Cells
Drug developers should look beyond genomics and find ways of editing and reprogramming cells to treat a broader range of diseases more effectively.
The idea was proposed at TIDES USA by Jonathan Gootenberg, a principal investigator at the Center for Vaccines and Virology Research at Beth Israel Deaconess Medical Center, who pointed to the evolution of genomics tools as an inspiration.
“It’s been about two decades since we’ve really been able to understand and sequence the human genome. And this has given us an amazing parts list, as well as a wide set of potential tools to use. And with that the genome editing toolbox is maturing, and we are starting to see this maturation.
“We have about a fifth of potential, likely pathogenic mutations that we can use to treat. And this is not an academic exercise; we’re starting to see approved therapies,” he said, such as Casgevy from CRISPR Therapeutics and Vertex and Intellia’s product for transthyretin amyloidosis (aTTR).
“But DNA is not the only molecule in your cells. Now, RNA is also, of course, involved in many different layers of cell function. mRNA is probably a largest note, but there’s a large range of noncoding RNAs and functional RNAs in your cells as well. And with this, we also need a set of cognate tools to be able to manipulate these both for basic research and for therapeutics.”
The next stage is the development tools that allow the manipulation of entire cells, according to Gootenberg, who said, “You might actually use it as an analogous to a genome sequencing project of our time, which is the indexing and analysis of single cells.
“How do we manipulate and control not just nucleic acids, but the cells that contain them to both understand their function as well as create new therapeutics? For that we really need not just a genome editing toolbox but a cell editing toolbox.”
Cell editing toolbox
Gootenberg’s vision is based on four pillars: new technologies to manipulate nucleic acids inside living cells; the ability to sense cellular states in real time; a means of reprogramming cells to convert them to a different state; and novel delivery technologies.
“Our lab focuses on these four fundamental pillars of programmable cell editing,” Gootenberg said, using its efforts to develop tools able to insert large sections of DNA as an example.
“How do we have that capability to put large amounts of DNA into the genome in a programmable way? And this is, of course, very useful for many different applications. For one thing, if you think about treating genetic disease, most are not a single mutation. In cystic fibrosis, for example, you have thousands of mutations in the genes responsible.
“So the question is, can we use gene insertion as a way to circumvent this where one gene product can actually treat across the spectrum of different mutations? So how do we do this?”
Gootenberg and colleagues’ solution is Paste, a programmable addition via site-specific targeting elements. The tech is effectively a combination of the CRISPR-Cas9 gene editing system with the serine integrase nonprogrammable, high-efficiency DNA insertion platform.
“You have a programmable system like Cas9 that can write relatively small — 40, or 50 nucleotides — sequences into the genome. And once you write this landing pad you can use a nonprogrammable, high-efficiency system to integrate into the gene of interest into the genome.
“We can now actually put in a large piece of DNA,” Gootenberg said, adding that in trials at two different gene sites the team has been able to insert sequences of up to 36 kilobases.