Summary: Researchers have developed a CRISPR-based technology that transports RNA to specific locations inside neurons, enabling local repair and regrowth. Unlike conventional CRISPR approaches that edit DNA, this system repurposes CRISPR-Cas13 to act as a targeted carrier, using molecular “zip codes” to deliver therapeutic RNA precisely where it is needed. This advance, named CRISPR-TO, could open a new field of “spatial RNA medicine” with applications for neurodegenerative diseases, spinal cord injury, and other neurological disorders.
In laboratory tests, CRISPR-TO increased neurite extension by up to 50% within 24 hours, demonstrating robust promotion of neurite outgrowth and highlighting the therapeutic potential of controlling RNA localization inside cells. The approach offers a path to safer, more effective RNA-based interventions by ensuring molecules act at the correct subcellular site.
Key Facts:
- CRISPR-TO System: CRISPR-Cas13 is engineered to transport RNA to precise neuronal locations using molecular localization signals.
- Enhanced Regrowth: Guided delivery of selected RNAs promoted up to 50% greater neurite growth in injured neurons within 24 hours in vitro.
- New Therapeutic Class: Establishes the concept of “spatial RNA medicine” for targeted cellular repair and regeneration.
Source: Stanford
When a neuron is damaged, local RNA segments are translated into proteins that support repair. In conditions such as amyotrophic lateral sclerosis (ALS), spinal muscular atrophy, and after traumatic spinal cord injury, the cellular systems that mobilize these RNAs can fail. When essential RNAs cannot reach the injury site, repair processes falter and damage may become permanent.
Scientists at Stanford have created a tool that actively transports RNA to defined locations inside neurons so those molecules can perform repair functions or stimulate regrowth. Their work, funded in part by the National Institutes of Health, lays the groundwork for therapies that work by repositioning RNAs within cells rather than changing the genetic code.
“For the first time, we’ve harnessed CRISPR to create a precise spatial ‘zip code’ that directs RNA molecules to the exact subcellular locations where they are needed,” said Stanley Qi, associate professor of bioengineering and senior author of the paper published May 21 in Nature. “Imagine targeting a damaged region within a neuron, repairing it, and promoting regrowth—this is what our technology enables.”
A CRISPR-based mailman
Recent work has emphasized that where an RNA molecule resides inside a cell can be as important as its sequence or function. Neurons, which can extend over a meter in humans, rely on precise transport systems to shuttle RNA to distant sites such as axon terminals and growth cones. Aging, injury, or genetic mutations can disrupt that transport, preventing RNAs from reaching sites of need.
To address this, Qi and colleagues adapted CRISPR-Cas13, a CRISPR family member that targets RNA rather than DNA, and repurposed it to move RNA instead of cutting it. Rather than editing sequences, the team disabled Cas13’s nuclease activity and fused it with localization signals that act as molecular addresses. These signals instruct the modified Cas13 where to deliver bound RNAs inside the cell.
“Cas13 normally functions like molecular scissors, but we engineered it to perform as a mail carrier,” Qi explained. “By combining Cas13 with different localization signals, we can program where a given RNA will be deposited within the neuron.”
Using this platform, named CRISPR-TO, the researchers screened dozens of endogenous RNAs to identify candidates that promote neurite outgrowth when relocalized. In cultured mouse neurons, CRISPR-TO transported selected RNAs to neurite tips—specialized protrusions that form synapses—and several RNAs produced notable increases in neurite length. One RNA boosted neurite extension by as much as 50% over a 24-hour period.
“We are identifying RNA targets that enhance neurite outgrowth and regeneration,” said Mengting Han, a postdoctoral scholar in Qi’s lab and lead author on the study. “This adds a new capability to the CRISPR toolbox: programmable control of RNA localization inside cells, a capability not previously available.”
Safer, more effective RNA medicine
Beyond discovery, CRISPR-TO can be used to evaluate which endogenous RNAs best support repair in mouse and human neurons and to test therapeutic RNAs delivered as medicines. By placing RNA exactly where it can act, the platform has potential to improve both efficacy and safety of RNA therapies, avoiding unwanted activity elsewhere in the cell.
“Location matters,” Qi said. “A therapeutic molecule must be at the right place at the right time. With programmable spatial control, CRISPR-TO can target any RNA in any cell type and move it to the site of need.”
Funding: This work was supported by the National Science Foundation, the National Institutes of Health, the National Center for Research Resources, the Stanford School of Medicine Dean’s Postdoctoral Fellowship, and the American Heart Association Postdoctoral Fellowship.
About this CRISPR and neuroscience research news
Author: Chloe Dionisio
Source: Stanford
Contact: Chloe Dionisio – Stanford
Image: Image credited to Neuroscience News
Original Research: Open access. “Clonal tracing with somatic epimutations reveals dynamics of blood ageing” by Stanley Qi et al. Nature.
Abstract
Clonal tracing with somatic epimutations reveals dynamics of blood ageing
Current methods for tracking stem cell clones across differentiation typically require genetic engineering or depend on rare somatic DNA variants, limiting broad application. The authors report that DNA methylation at specific CpG sites encodes two layers of information: one subset reflects cellular differentiation state, while another subset accumulates stochastic epimutations that can serve as digital barcodes of clonal identity.
They demonstrate targeted single-cell profiling of DNA methylation at single-CpG resolution to extract both differentiation and clonal identity information. The team developed EPI-Clone, a transgene-free lineage-tracing method scalable to large datasets. Applied to mouse and human hematopoiesis, EPI-Clone captured hundreds of clonal differentiation trajectories across tens of individuals and over 230,000 single cells.
In aged mice, the study showed that myeloid bias and reduced output of old hematopoietic stem cells stem from a small number of expanded clones, while many clones retain young-like function. In humans, clones with and without known driver mutations of clonal hematopoiesis form a spectrum of age-related clonal expansions with similar lineage biases. EPI-Clone enables accurate, transgene-free single-cell lineage tracing across hematopoietic cell-state landscapes at scale.