Sa Cai

All Publications

• Programmable control of spatial transcriptome in live cells and neurons. Nature Han, M., Fu, M. L., Zhu, Y., Choi, A. A., Li, E., Bezney, J., Cai, S., Miles, L., Ma, Y., Qi, L. S. 2025

  Abstract

  Spatial RNA organization has a pivotal role in diverse cellular processes and diseases1-4. However, functional implications of the spatial transcriptome remain largely unexplored due to limited technologies for perturbing endogenous RNA within specific subcellular regions1,5. Here we present CRISPR-mediated transcriptome organization (CRISPR-TO), a system that harnesses RNA-guided, nuclease-dead dCas13 for programmable control of endogenous RNA localization in live cells. CRISPR-TO enables targeted localization of endogenous RNAs to diverse subcellular compartments, including the outer mitochondrial membrane, p-bodies, stress granules, telomeres and nuclear stress bodies, across various cell types. It allows for inducible and reversible bidirectional RNA transport along microtubules via motor proteins, facilitating real-time manipulation and monitoring of RNA localization dynamics in living cells. In primary cortical neurons, we demonstrate that repositioned mRNAs undergo local translation along neurites and at neurite tips, and co-transport with ribosomes, with β-actin mRNA localization enhancing the formation of dynamic filopodial protrusions and inhibiting axonal regeneration. CRISPR-TO-enabled screening in primary neurons identifies Stmn2 mRNA localization as a driver of neurite outgrowth. By enabling large-scale perturbation of the spatial transcriptome, CRISPR-TO bridges a critical gap left by sequencing and imaging technologies, offering a versatile platform for high-throughput functional interrogation of RNA localization in living cells and organisms.

  View details for DOI 10.1038/s41586-025-09020-z

  View details for PubMedID 40399675

  View details for PubMedCentralID 9346928

• High-resolution dynamic imaging of chromatin DNA communication using Oligo-LiveFISH. Cell Zhu, Y., Balaji, A., Han, M., Andronov, L., Roy, A. R., Wei, Z., Chen, C., Miles, L., Cai, S., Gu, Z., Tse, A., Yu, B. C., Uenaka, T., Lin, X., Spakowitz, A. J., Moerner, W. E., Qi, L. S. 2025

  Abstract

  Three-dimensional (3D) genome dynamics are crucial for cellular functions and disease. However, real-time, live-cell DNA visualization remains challenging, as existing methods are often confined to repetitive regions, suffer from low resolution, or require complex genome engineering. Here, we present Oligo-LiveFISH, a high-resolution, reagent-based platform for dynamically tracking non-repetitive genomic loci in diverse cell types, including primary cells. Oligo-LiveFISH utilizes fluorescent guide RNA (gRNA) oligo pools generated by computational design, in vitro transcription, and chemical labeling, delivered as ribonucleoproteins. Utilizing machine learning, we characterized the impact of gRNA design and chromatin features on imaging efficiency. Multi-color Oligo-LiveFISH achieved 20-nm spatial resolution and 50-ms temporal resolution in 3D, capturing real-time enhancer and promoter dynamics. Our measurements and dynamic modeling revealed two distinct modes of chromatin communication, and active transcription slows enhancer-promoter dynamics at endogenous genes like FOS. Oligo-LiveFISH offers a versatile platform for studying 3D genome dynamics and their links to cellular processes and disease.

  View details for DOI 10.1016/j.cell.2025.03.032

  View details for PubMedID 40239646

• Color-neutral and reversible tissue transparency enables longitudinal deep-tissue imaging in live mice. bioRxiv : the preprint server for biology Keck, C. H., Schmidt, E. L., Roth, R. H., Floyd, B. M., Tsai, A. P., Garcia, H. B., Cui, M., Chen, X., Wang, C., Park, A., Zhao, S., Liao, P. A., Casey, K. M., Reineking, W., Cai, S., Zhang, L., Yang, Q., Yuan, L., Baghdasaryan, A., Lopez, E. R., Cooper, L., Cui, H., Esquivel, D., Brinson, K., Chen, X., Wyss-Coray, T., Coleman, T. P., Brongersma, M. L., Bertozzi, C. R., Wang, G. X., Ding, J. B., Hong, G. 2025

  Abstract

  Light scattering in biological tissue presents a significant challenge for deep in vivo imaging. Our previous work demonstrated the ability to achieve optical transparency in live mice using intensely absorbing dye molecules, which created transparency in the red spectrum while blocking shorter-wavelength photons. In this paper, we extend this capability to achieve optical transparency across the entire visible spectrum by employing molecules with strong absorption in the ultraviolet spectrum and sharp absorption edges that rapidly decline upon entering the visible spectrum. This new color-neutral and reversible tissue transparency method enables optical transparency for imaging commonly used fluorophores in the green and yellow spectra. Notably, this approach facilitates tissue transparency for structural and functional imaging of the live mouse brain labeled with yellow fluorescent protein and GCaMP through the scalp and skull. We show that this method enables longitudinal imaging of the same brain regions in awake mice over multiple days during development. Histological analyses of the skin and systemic toxicology studies indicate minimal acute or chronic damage to the skin or body using this approach. This color-neutral and reversible tissue transparency technique opens new opportunities for noninvasive deep-tissue optical imaging, enabling long-term visualization of cellular structures and dynamic activity with high spatiotemporal resolution and chronic tracking capabilities.

  View details for DOI 10.1101/2025.02.20.639185

  View details for PubMedID 40060493

• A frugal CRISPR kit for equitable and accessible education in gene editing and synthetic biology. Nature communications Collins, M., Lau, M. B., Ma, W., Shen, A., Wang, B., Cai, S., La Russa, M., Jewett, M. C., Qi, L. S. 2024; 15 (1): 6563

  Abstract

  Equitable and accessible education in life sciences, bioengineering, and synthetic biology is crucial for training the next generation of scientists, fostering transparency in public decision-making, and ensuring biotechnology can benefit a wide-ranging population. As a groundbreaking technology for genome engineering, CRISPR has transformed research and therapeutics. However, hands-on exposure to this technology in educational settings remains limited due to the extensive resources required for CRISPR experiments. Here, we develop CRISPRkit, an affordable kit designed for gene editing and regulation in high school education. CRISPRkit eliminates the need for specialized equipment, prioritizes biosafety, and utilizes cost-effective reagents. By integrating CRISPRi gene regulation, colorful chromoproteins, cell-free transcription-translation systems, smartphone-based quantification, and an in-house automated algorithm (CRISPectra), our kit offers an inexpensive (~$2) and user-friendly approach to performing and analyzing CRISPR experiments, without the need for a traditional laboratory setup. Experiments conducted by high school students in classroom settings highlight the kit's utility for reliable CRISPRkit experiments. Furthermore, CRISPRkit provides a modular and expandable platform for genome engineering, and we demonstrate its applications for controlling fluorescent proteins and metabolic pathways such as melanin production. We envision CRISPRkit will facilitate biotechnology education for communities of diverse socioeconomic and geographic backgrounds.

  View details for DOI 10.1038/s41467-024-50767-2

  View details for PubMedID 39095367

• Bioinspired nanotransducers for neuromodulation NANO RESEARCH Yang, F., Wu, X., Cai, S., Hong, G. 2023

  View details for DOI 10.1007/s12274-023-6136-6

  View details for Web of Science ID 001076987400003

• Nanotransducer-Enabled Deep-Brain Neuromodulation with NIR-II Light. ACS nano Wu, X., Yang, F., Cai, S., Pu, K., Hong, G. 2023

  Abstract

  The second near-infrared window (NIR-II window), which ranges from 1000 to 1700 nm in wavelength, exhibits distinctive advantages of reduced light scattering and thus deep penetration in biological tissues in comparison to the visible spectrum. The NIR-II window has been widely employed for deep-tissue fluorescence imaging in the past decade. More recently, deep-brain neuromodulation has been demonstrated in the NIR-II window by leveraging nanotransducers that can efficiently convert brain-penetrant NIR-II light into heat. In this Perspective, we discuss the principles and potential applications of this NIR-II deep-brain neuromodulation technique, together with its advantages and limitations compared with other existing optical methods for deep-brain neuromodulation. We also point out a few future directions where the advances in materials science and bioengineering can expand the capability and utility of NIR-II neuromodulation methods.

  View details for DOI 10.1021/acsnano.2c12068

  View details for PubMedID 37079455

• Systemically Delivered, Deep-Tissue Nanoscopic Light Sources PROGRESS IN ELECTROMAGNETICS RESEARCH-PIER Wu, X., Yang, F., Cai, S., Hong, G. 2023; 177: 33-42

  View details for Web of Science ID 000968675700001

• Palette of Rechargeable Mechanoluminescent Fluids Produced by a Biomineral-Inspired Suppressed Dissolution Approach. Journal of the American Chemical Society Yang, F., Wu, X., Cui, H., Jiang, S., Ou, Z., Cai, S., Hong, G. 2022

  Abstract

  Mechanoluminescent materials, which emit light in response to mechanical stimuli, have recently been explored as promising candidates for photonic skins, remote optogenetics, and stress sensing. All mechanoluminescent materials reported thus far are bulk solids with micron-sized grains, and their light emission is only produced when fractured or deformed in bulk form. In contrast, mechanoluminescence has never been observed in liquids and colloidal solutions, thus limiting its biological application in living organisms. Here, we report the synthesis of mechanoluminescent fluids via a suppressed dissolution approach. We demonstrate that this approach yields stable colloidal solutions comprising mechanoluminescent nanocrystals with bright emissions in the range of 470-610 nm and diameters down to 20 nm. These colloidal solutions can be recharged and discharged repeatedly under photoexcitation and hydrodynamically focused ultrasound, respectively, thus yielding rechargeable mechanoluminescent fluids that can store photon energy in a reversible manner. This rechargeable fluid can facilitate a systemically delivered light source gated by tissue-penetrant ultrasound for biological applications that require light in the tissue, such as optogenetic stimulation in the brain.

  View details for DOI 10.1021/jacs.2c06724

  View details for PubMedID 36190898

• A biomineral-inspired approach of synthesizing colloidal persistent phosphors as a multicolor, intravital light source. Science advances Yang, F., Wu, X., Cui, H., Ou, Z., Jiang, S., Cai, S., Zhou, Q., Wong, B. G., Huang, H., Hong, G. 2022; 8 (30): eabo6743

  Abstract

  Many in vivo biological techniques, such as fluorescence imaging, photodynamic therapy, and optogenetics, require light delivery into biological tissues. The limited tissue penetration of visible light discourages the use of external light sources and calls for the development of light sources that can be delivered in vivo. A promising material for internal light delivery is persistent phosphors; however, there is a scarcity of materials with strong persistent luminescence of visible light in a stable colloid to facilitate systemic delivery in vivo. Here, we used a bioinspired demineralization (BID) strategy to synthesize stable colloidal solutions of solid-state phosphors in the range of 470 to 650 nm and diameters down to 20 nm. The exceptional brightness of BID-produced colloids enables their utility as multicolor luminescent tags in vivo with favorable biocompatibility. Because of their stable dispersion in water, BID-produced nanophosphors can be delivered systemically, acting as an intravascular colloidal light source to internally excite genetically encoded fluorescent reporters within the mouse brain.

  View details for DOI 10.1126/sciadv.abo6743

  View details for PubMedID 35905189

• Tether-free photothermal deep-brain stimulation in freely behaving mice via wide-field illumination in the near-infrared-II window. Nature biomedical engineering Wu, X., Jiang, Y., Rommelfanger, N. J., Yang, F., Zhou, Q., Yin, R., Liu, J., Cai, S., Ren, W., Shin, A., Ong, K. S., Pu, K., Hong, G. 2022

  Abstract

  Neural circuitry is typically modulated via invasive brain implants and tethered optical fibres in restrained animals. Here we show that wide-field illumination in the second near-infrared spectral window (NIR-II) enables implant-and-tether-free deep-brain stimulation in freely behaving mice with stereotactically injected macromolecular photothermal transducers activating neurons ectopically expressing the temperature-sensitive transient receptor potential cation channel subfamily V member 1 (TRPV1). The macromolecular transducers, ~40 nm in size and consisting of a semiconducting polymer core and an amphiphilic polymer shell, have a photothermal conversion efficiency of 71% at 1,064 nm, the wavelength at which light attenuation by brain tissue is minimized (within the 400-1,800 nm spectral window). TRPV1-expressing neurons in the hippocampus, motor cortex and ventral tegmental area of mice can be activated with minimal thermal damage on wide-field NIR-II illumination from a light source placed at distances higher than 50 cm above the animal's head and at an incident power density of 10 mW mm-2. Deep-brain stimulation via wide-field NIR-II illumination may open up opportunities for social behavioural studies in small animals.

  View details for DOI 10.1038/s41551-022-00862-w

  View details for PubMedID 35314800