CRISPR-TO bridges a critical gap left by sequencing and imaging technologies and will greatly accelerate the functional study of spatial transcriptome in the future.

CRISPR-TO-enabled screening in primary neurons identifies Stmn2 mRNA localization as a driver of neurite outgrowth.

In primary cortical neurons, we demonstrate that repositioned mRNAs undergo local translation, which regulates neuronal morphology and axonal regeneration.

CRISPR-TO effectively functions in primary neurons for ultra-long distance RNA transport, in which spatial transcriptomes are crucially linked to pathological processes.

It allows for inducible and reversible bidirectional RNA transport along microtubules via motor proteins.

CRISPR-TO enables targeted localization of endogenous RNAs to diverse subcellular compartments.

Spatial RNA organization has a pivotal role in diverse cellular processes and diseases. However, its functional implications remain largely unexplored due to limited technologies for perturbing endogenous RNA localization.

Spatial RNA organization has a pivotal role in diverse cellular processes and diseases. However, its functional implications remain largely unexplored due to limited technologies for perturbing endogenous RNA localization.

Programmable control of spatial transcriptome in live cells and neurons - Nature CRISPR-TO, a system for programmable control of spatial localization of cellular RNAs, is presented and enables functional investigation of endogenous RNA localization in diverse living cells.

www.nature.com/articles/s41...

Thrilled to share our paper in
@nature.com led by @MengtingHan123
on CRISPR-TO technology, which paves the way for treatments for neurodegenerative diseases by precisely delivering therapeutic RNA to the damaged sites. A 🧵@Stanford_ChEMH, @bioe_stanford, @Stanford

We look forward to seeing further applications enabled by the technology! 🔬

Applying Oligo-LiveFISH to study enhancer-promoter interaction, we found that stimulating FOS transcription led to reduced 3D distance, increased confinement, and slower dynamics between the FOS enhancer and promoter.

Combined with polymer-based dynamic modeling, Oligo-LiveFISH revealed two distinct modes of chromatin communication: 1D cis-communication, predominated at short distances (up to 300 kb), and 3D trans-communication, which is significant over long distances (> 1 Mb).

Integrated with 3D super-localization microscopy, Oligo-LiveFISH tracked genomic regions at high spatial (20-nm) and temporal (50-ms) resolution, revealing highly sub-diffusive chromatin motion consistent with fractional Brownian motion.

Oligo-LiveFISH enables the tracking of chromatin dynamics in diverse cell types, including hard-to-image cells such as primary T cells and induced neurons (iNs) derived from human embryonic stem cells.

Utilizing machine learning, we characterized key parameters of chromatin and gRNA features on imaging efficiency and established gRNA design principles for live chromatin imaging.

To address this, we exploited approaches to generate effective gRNA pools to image non-repetitive loci by computational design, in vitro transcription, and chemical labeling, delivered as ribonucleoproteins.

The 3D chromatin dynamics is crucial for gene transcription and cellular function. However, real-time, live-cell DNA visualization remains challenging.

Oligo-LiveFISH is a high-resolution, reagent-based platform for studying 3D genome dynamics and their links to cellular processes in diverse cell types, including primary cells.

www.cell.com/cell/fulltex...
authors.elsevier.com/c/1kxK7L7PXu...

Thrilled to share our paper, led by Dr. Yanyu Zhu @yanyuzhu.bsky.social in collaboration with Prof. W.E. Moerner and Prof. Andrew J. Spakowitz, on developing Oligo-LiveFISH technology, in Cell @cellcellpress.bsky.social. A🧵

@stanford-chemh.bsky.social @bioe-stanford.bsky.social

Our study establishes trogocytosis as a novel, programmable framework for cell-based macromolecular delivery. We look forward to seeing further applications enabled by the technology!

TRANSFER demonstrated superior programmability by (1) recognizing a combination of cell surface markers, and mediating delivery under AND gate logic; (2) being applicable to the delivery of Cre and ZFN for gene editing, and prodrug-converting enzymes for targeted cell ablation.

To expand trogocytosis beyond surface molecules, we introduced a pH-sensitive cleavable linker, enabling the translocation of membrane-recruited Cas9 cargos to the nucleus upon transfer. We termed the system trogocytosis-based transfer and functional effector release (TRANSFER).

However, trogocytosed molecules were found to be unfunctional in recipient cells. To tackle this challenge, we engineered donor cells with pH-sensitive membrane fusogens, which get co-transferred to recipient cells through trogocytosis and mediate endosomal escape of cargos.

We were inspired by trogocytosis, where cells transfer membrane fragments and associated molecules in a contact-dependent manner. We showed that donor cells with engineered receptors can transfer surface molecules in a ligand-specific manner through direct cell-cell contact.

Programmable macromolecule delivery via engineered trogocytosis Trogocytosis, the transfer of plasma membrane fragments during cell-cell contact, offers potential for macromolecular delivery but is limited by uncertain fate of trogocytosed molecules, constraints t...

www.biorxiv.org/content/10.1...

In this work, we explored the use of engineered cells as delivery vehicles, with the potential of constantly producing and transferring cargos, and targeting specific recipient cells.

Thrilled to share our preprint led by @xinyi-chen.bsky.social on programmable molecule delivery via engineered trogocytosis called TRANSFER! a 🧵 @stanford-chemh.bsky.social @bioe-stanford.bsky.social

Bioengineering lab provides affordable gene-editing kits Stanford researchers introduced affordable gene-editing kits ready for the classroom, aiming to make the field more accessible for high school students.

We are excited to make #CRISPR accessible to high school education. 🧬 Go check out the article in The Stanford Daily to read about our frugal CRISPRkits.
#democratizingscience #scienceaccessibility

@bioe-stanford.bsky.social @stanford-chemh.bsky.social

stanforddaily.com/2025/02/03/c...