Harnessing a novel CRISPR nuclease for programmable counterselection in human cells

CRISPR technologies have revolutionized genome editing in medicine, agriculture, biotechnology, and life-sciences research with their ability to generate virtually any DNA edit at any genomic site in any organism.

However, editing frequencies can be restrictively low, requiring extensive screening to identify cells harboring desired edits. What remains elusive is a way to greatly boost the frequency of editing.

While characterizing CRISPR-Cas systems, bacterial defense systems and the source of CRISPR technologies, we discovered a new mechanism that could kill unedited cells yet spare edited cells, regardless of the type of gene edit.

This versatile and sequence-specific approach can be described as programmable counter-selection, as undesired cells are targeted for removal, and those cells can be targeted in a programmable way.

If proven, this capability could radically boost the effective editing frequencies by removing unedited cells regardless of the underlying edit, providing much-needed relief to the burden of screening imposed on diverse genome-editing applications.

Here, we propose to perform proof-of-concept experiments demonstrating this capability in human cells while exploring which editing applications would best benefit from this capability.

The associated tasks build on my extensive work at the interface of CRISPR biology and technologies and leverages his numerous academic and industrial contacts.

I ultimately aim to translate a novel biological insight from my group’s ERC Consolidator project into an innovative foundational technology, with a clear path toward its broad use in genome editing.