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Stanley Qi

@stanleyqilab.bsky.social
81 followers 16 following 43 posts

Stanford BioE

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Reposted by Stanley Qi
Nature Reviews Genetics @natrevgenet.nature.com · 15/04/2026
ICYMI: New online! CRISPR–Cas-based live cell imaging of genome dynamics
dlvr.it
CRISPR–Cas-based live cell imaging of genome dynamics
Nature Reviews Genetics, Published online: 08 April 2026; doi:10.1038/s41576-026-00949-zIn this Review, Zhu et al. outline the various CRISPR-based tools recently built for dynamic DNA and RNA imaging, which have provided insights into various molecular mechanisms. The authors also discuss the important parameters to consider when using these tools, and how to approach the quantitative image analysis.
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Stanley Qi @stanleyqilab.bsky.social · 18/04/2026
Incredibly proud of lead author Dr. Yanyu Zhu @yanyuzhu.bsky.social for this impressive review on CRISPR imaging of the genome. Honored to collaborate with Prof. W.E. Moerner. #CRISPR #GenomeDynamics #Imaging #3DGenomics @bioe-stanford.bsky.social @stanford-chemh.bsky.social @natrevgenet.nature.com
nature.com
CRISPR–Cas-based live cell imaging of genome dynamics - Nature Reviews Genetics
In this Review, Zhu et al. outline the various CRISPR-based tools recently built for dynamic DNA and RNA imaging, which have provided insights into various molecular mechanisms. The authors also discu...
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Stanley Qi @stanleyqilab.bsky.social · 12/04/2026
From cancer dysfunction to T cell exhaustion, the "live" 3D genome holds the answers. Read our definitive reference in @NaturePortfolio : nature.com/articles/s41... #CRISPR #Genomics #Biophysics #Stanford #3DGenomics #ScienceTwitter (5/5)
nature.com
CRISPR–Cas-based live cell imaging of genome dynamics - Nature Reviews Genetics
In this Review, Zhu et al. outline the various CRISPR-based tools recently built for dynamic DNA and RNA imaging, which have provided insights into various molecular mechanisms. The authors also discuss the important parameters to consider when using these tools, and how to approach the quantitative image analysis.
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Stanley Qi @stanleyqilab.bsky.social · 12/04/2026
This wasn't possible in a silo. It required the convergence of CRISPR, chemical biology, and the pioneering single-molecule 3D microscopy of W.E. Moerner. We are moving from "Where is the genome?" to "How does it decide?" (4/5)
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Stanley Qi @stanleyqilab.bsky.social · 12/04/2026
The hard problem was the "logic" of life: Promoters and Enhancers. With technologies like LiveFISH, we’ve moved from imaging telomeres to tracking virtually any locus in primary neurons & T cells. We can now watch enhancer and promoter interact in real time. (3/5)
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Stanley Qi @stanleyqilab.bsky.social · 12/04/2026
12 years ago, we repurposed dCas9: not to "cut," but to "label." Today, in @nature.com , we map the arc of CRISPR live-cell imaging from that first 2013 proof-of-concept to the 20nm/50ms resolution we achieve today. Huge work by lead author Yanyu Zhu @yanyuzhu.bsky.social ! (2/5)
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Stanley Qi @stanleyqilab.bsky.social · 12/04/2026
For centuries, the microscope showed us the genome's static architecture. But the genome is not a static blueprint; it’s a living choreography. It breathes, communicates, and decides in real-time. To understand it, we must watch it MOVE. (1/5)
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Stanley Qi @stanleyqilab.bsky.social · 02/04/2026
Ever heard of 'cellular nibbling'? In our @NatureCellBio paper, we’ve turned trogocytosis into a delivery tool for programmable medicine. Congrats to @xinyi-chen.bsky.social and team! Link: rdcu.be/fa90i @StanfordBioE @StanfordChEMH @CZBiohub #GeneTherapy #SyntheticBiology
rdcu.be
Programmable macromolecule delivery via engineered trogocytosis
Nature Cell Biology - Chen et al. engineer TRANSFER (trogocytosis-inspired receptor transfer and functional effector release), a method to deliver functional cargos from donor to recipient cells in...
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Stanley Qi @stanleyqilab.bsky.social · 02/09/2025
We’re excited to share that Maylin Fu, Ph.D. student in the Qi Lab, has been accepted into the NIH-funded Pathways to Neurosciences program at Stanford, supported by the Wu Tsai Neurosciences Institute. #Neuroscience #QiLab #WuTsaiNeuroscienceInstitute neuroscience.stanford.edu/programs/pro...
neuroscience.stanford.edu
Pathways to Neurosciences
The Pathways to Neurosciences program fosters belonging, excellence, and leadership in the next
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Stanley Qi @stanleyqilab.bsky.social · 06/08/2025
Beyond maps to mechanisms, this new list of comprehensive aging signatures offers biomarkers of aging status and targets to engineer for better anti-aging therapies without altering core cell identity. #CellTherapy #Aging
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Stanley Qi @stanleyqilab.bsky.social · 06/08/2025
We integrated 405 GWAS datasets and found that CRISPRi-defined inflammaging genes are significantly enriched for heritability of aging traits across diverse organ systems. #GWAS #Aging
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Stanley Qi @stanleyqilab.bsky.social · 06/08/2025
We discovered and validated inflammaging-specific drivers including EIF2AK2, SERPING1, HMGCS2, CMKLR1. Inhibiting them blunts IL-6-associated senescence while maintaining cell identity.
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Stanley Qi @stanleyqilab.bsky.social · 06/08/2025
Mitochondrial pathway emerges as top hits: SAMM50 and AK2 act as pro-aging genes and CRISPRi knockdown reduces aging biomarkers on stem cells while preserving cell identity (CD29/CD44/CD73/CD90).
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Stanley Qi @stanleyqilab.bsky.social · 06/08/2025
Two screens for two aging states: replicative senescence (RSS) and IL-6–driven inflammaging (ISS). Positive-selection CRISPRi reveals novel regulators you can modulate without breaking MSC identity to alter their aging state.
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Stanley Qi @stanleyqilab.bsky.social · 06/08/2025
We’re happy to share our new paper in Genome Biology led by Lingling Wu and Xiang Wu, in collaboration with Xueqiu Lin lab at Fred Hutch. Parallel whole-genome CRISPRi screens in primary human MSCs map distinct regulators of aging processes across organs. #Aging #CRISPRi #Senescence
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Stanley Qi @stanleyqilab.bsky.social · 26/05/2025
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.
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Stanley Qi @stanleyqilab.bsky.social · 26/05/2025
CRISPR-TO-enabled screening in primary neurons identifies Stmn2 mRNA localization as a driver of neurite outgrowth.
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Stanley Qi @stanleyqilab.bsky.social · 26/05/2025
In primary cortical neurons, we demonstrate that repositioned mRNAs undergo local translation, which regulates neuronal morphology and axonal regeneration.
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Stanley Qi @stanleyqilab.bsky.social · 26/05/2025
CRISPR-TO effectively functions in primary neurons for ultra-long distance RNA transport, in which spatial transcriptomes are crucially linked to pathological processes.
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Stanley Qi @stanleyqilab.bsky.social · 26/05/2025
It allows for inducible and reversible bidirectional RNA transport along microtubules via motor proteins.
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Stanley Qi @stanleyqilab.bsky.social · 26/05/2025
CRISPR-TO enables targeted localization of endogenous RNAs to diverse subcellular compartments.
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Stanley Qi @stanleyqilab.bsky.social · 26/05/2025
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.
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Stanley Qi @stanleyqilab.bsky.social · 26/05/2025
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.
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Stanley Qi @stanleyqilab.bsky.social · 26/05/2025
www.nature.com/articles/s41...
nature.com
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.
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Stanley Qi @stanleyqilab.bsky.social · 26/05/2025
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
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Stanley Qi @stanleyqilab.bsky.social · 17/04/2025
We look forward to seeing further applications enabled by the technology! 🔬
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Stanley Qi @stanleyqilab.bsky.social · 17/04/2025
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.
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Stanley Qi @stanleyqilab.bsky.social · 17/04/2025
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).
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Stanley Qi @stanleyqilab.bsky.social · 17/04/2025
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.
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Stanley Qi @stanleyqilab.bsky.social · 17/04/2025
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.
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Stanley Qi @stanleyqilab.bsky.social · 17/04/2025
Utilizing machine learning, we characterized key parameters of chromatin and gRNA features on imaging efficiency and established gRNA design principles for live chromatin imaging.
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Stanley Qi @stanleyqilab.bsky.social · 17/04/2025
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.
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Stanley Qi @stanleyqilab.bsky.social · 17/04/2025
The 3D chromatin dynamics is crucial for gene transcription and cellular function. However, real-time, live-cell DNA visualization remains challenging.
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Stanley Qi @stanleyqilab.bsky.social · 17/04/2025
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...
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Stanley Qi @stanleyqilab.bsky.social · 17/04/2025
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
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Stanley Qi @stanleyqilab.bsky.social · 20/03/2025
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!
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Stanley Qi @stanleyqilab.bsky.social · 20/03/2025
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.
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Stanley Qi @stanleyqilab.bsky.social · 20/03/2025
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).
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Stanley Qi @stanleyqilab.bsky.social · 20/03/2025
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.
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Stanley Qi @stanleyqilab.bsky.social · 20/03/2025
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.
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Stanley Qi @stanleyqilab.bsky.social · 20/03/2025
www.biorxiv.org/content/10.1...
biorxiv.org
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...
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Stanley Qi @stanleyqilab.bsky.social · 20/03/2025
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.
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Stanley Qi @stanleyqilab.bsky.social · 20/03/2025
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
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Stanley Qi @stanleyqilab.bsky.social · 06/02/2025
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...
stanforddaily.com
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.
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