Nature's new RNA-based editing tool, CellREADR, can accurately edit any type of cell

In a new study, researchers from Duke University and Cold Spring Harbor Lab in the United States developed an RNA-based editing tool that targets individual cells, not genes
.
It can precisely target any type of cell and selectively add any protein
of interest.
The tool may be able to control disease
by modifying very specific cells and cellular functions.
The results will be published online in Nature on October 5, 2022, in the paper "Programmable RNA Sensing for Cell Monitoring and Manipulation.
"

Until now, almost all genetic methods for obtaining cell types have relied on DNA-based transcriptional regulatory elements to express effector genes (such as sensors, effectors, and markers) that mimic cell-specific RNA expression, primarily through germline engineering in a few organisms
.
However, all germline approaches, including CRISPR-based approaches, are inherently cumbersome, slow, difficult to scale and generalize, and raise ethical questions, especially in
primates and humans.
Finally, all DNA- and transcription-based approaches are essentially indirect means
of mimicking and exploiting cell-specific RNA expression patterns.

By using RNA-based probes, neurobiologist Z.
The team led by Dr.
Josh Huang and postdoctoral researcher Dr.
Yongjun Qian demonstrated that they can introduce fluorescent tags into cells to label specific types of brain tissue
.
They developed CellREADR, which uses RNA sensing and editing mechanisms prevalent in all animal cells to detect specific cellular RNAs and then begin translating effector proteins to monitor and manipulate the cells
.

Their selective cell monitoring and control system relies on the ADAR enzyme, which is found in
the cells of every animal.
While CellREADR (endogenous ADAR-sensing cell access via RNA) is still in its early stages, its possible applications appear endless, Huang said, and it could play a role
throughout the animal kingdom.

CellREADR is a string of customizable RNA consisting of three main parts: a sensor, a stop sign, and a set of blueprints
.
First, the authors decided on the specific cell type they wanted to study and identified the target RNA
that was uniquely produced by that cell type.
The significant tissue specificity of the tool depends on the fact that each cell type produces characteristic RNA
that other cell types do not.

Figure 1
.
Design and implementation
of CellREFR in mammalian cells.

Later, they designed a sensor sequence as a complementary strand
of the target RNA.
Just as rungs on DNA are made up of complementary molecules paired with each other, RNA has the same characteristics
.
If it has a matching molecule, RNA has the same magnetic potential to connect
with another piece of RNA.
After this sensing sequence enters the cell and finds its target RNA sequence, the two fragments combine to form a double-stranded RNA
.
This new RNA aliasing triggers the ADAR enzyme to examine the newly produced substance and then change the individual nucleotides
of its code.

ADAR enzymes, a cellular defense mechanism whose purpose is to edit double-stranded RNA as it occurs, are thought to be present in
all animal cells.
Knowing this, Qian designed the stop signal
for CellREADR using the same specific nucleotides that ADAR edited in double-stranded RNA.
The stop signal that blocks protein blueprint expression is removed only when the sensing sequence of CellREADR binds to its target RNA sequence, making it highly specific
for a given cell type.
Once the AFAR deletes the stop signal, cellular machinery can read the blueprint to build new proteins
within the target cell.

The careful planning and design of Huang's team paid off as they were able to demonstrate that Cell REDER accurately labeled specific populations of brain cells in live mice and effectively added activity-monitoring molecules and control switches
.
It is also effective
in rat and human brain tissue collected by epilepsy surgery.

With the ability and flexibility to program cell physiology, CellREADR will facilitate the next generation of precision diagnostics and therapeutics, such as detecting cancer cells using its RNA markers and eliminating cancer cells by inducing programmed cell death or recruiting immune cells
.
Although gene-editing and RNA-editing-based therapies focus almost exclusively on correcting single-gene disease mutations, many complex diseases, such as neuropsychiatric disorders and developmental disorders, are caused by polygenic susceptibility that affects the functional connections of brain circuits and may not be correctable
by gene or transcript editing.
CellREADR, in synergy with genomic and transcriptome engineering technologies, will facilitate research into the elucidating of genotype-to-phenotype biological information flow principles across cell types and enable a new generation of programmable cell-specific RNA drugs
.