Dingchang Lin

Genomic recording enables transient biological signals to be indelibly captured through DNA alterations, creating a permanent record of cellular history retrievable by sequencing. However, current methods are limited by scarce writing space, typically targeting only one or a few amenable genomic sites and requiring large cell populations for signal reconstruction. Here, we establish Repeats for Genomic Recording (RGRs): sequences with up to 400 copies targetable by a single CRISPR guide RNA, readable with a common primer pair, and predicted to have minimal functional impact. We demonstrate that RGRs enable both signal deconvolution in single cells and high-resolution recording in cell populations. Individual RGR sites exhibit distinct response kinetics; thus, combining them improves recording resolution beyond what redundancy alone provides, analogous to diversity reception in wireless communication. We develop a computational pipeline for systematic RGR identification, revealing 15,000 to 25,000 candidates per species across human, mouse, and zebrafish, thereby markedly expanding recording capacity and enabling cell-type-specific applications. Finally, we validate RGRs in live mice by recording long-term immediate early gene activity across the brain following epilepsy induction. This work establishes genomic repeats as a high-capacity platform for single-cell molecular recording in vivo.

Protein crystals are naturally derived mesoporous materials with versatile structures and physicochemical properties. Here we introduce an intracellular synthesis platform that enables controllable and programmable protein crystallization. In live cells, we show that, after initial nucleation, steady protein expression governs crystal growth, yielding predictable, tunable dynamics in live cells. Exploiting this feature, we combined HaloTag and click chemistries to achieve modular, programmable immobilization of diverse guest materials with spatial patterning down to ~100 nm resolution. We further demonstrated the sequential release of immobilized materials in physiologically relevant fluids. As a proof of concept, we programmed particles to carry human fibroblast growth factors in distinct layers, which elicited designed oscillatory Akt signalling patterns in cell culture. This work outlines a programmable method for producing mesoporous materials, with possible applications in catalysis and biomedicine.

In cellulo protein assemblies, spanning protein cages, filaments, crystals, and biomolecular condensates, provide cells with modular strategies to package, organize, and regulate biomolecules and biochemical reactions. Their genetic encodability, structural diversity, and tunable material properties have also made them attractive biomaterials, where in cellulo fabrication has underpinned their precise assembly and broad applicability. This review surveys major classes of natural and engineered assemblies fabricated in cellulo, with particular emphasis on how their structure, chemistry, and material state shape functions. We compare diverse cellular reactors and outline how intracellular milieu, post-translational modifications, and folding/assembly machinery influence assembly outcomes. Engineering strategies for modifying the assemblies are summarized and mapped onto broad applications across fundamental biology, biomedicine, and nonbiological fields. Lastly, we highlight existing opportunities for engineering and designing in cellulo protein assemblies. Through this review, we hope to give a comprehensive overview of this exciting and rapidly growing field and share our perspective on the possible future directions.

Cells constantly change their molecular state in response to internal and external cues ¹ . Mapping cellular activity in tissues with spatiotemporal precision is essential for understanding organ physiology, pathology and regenerative processes. Current cell-sensing modalities primarily rely on either end point analysis that takes static snapshots ² or real-time sensing that monitors a small subset of cells ^3,4 . Here we introduce granularly expanding memory for intracellular narrative integration (GEMINI), an in cellulo recording platform that leverages a computationally designed protein assembly as an intracellular memory device to record the history of individual cells. GEMINI grows predictably within live cells, capturing cellular events as tree-ring-like fluorescent patterns for imaging-based retrospective readout. Absolute chronological information of activity histories is attainable with hour-level accuracy. GEMINI effectively maps differential NF-κB-mediated transcriptional changes, resolving fast dynamics of 15 min and providing quantifiable signal amplitudes. In a xenograft model, GEMINI records inflammation-induced signalling dynamics across tissue, revealing spatial heterogeneity linked to vascular density. When expressed in the mouse brain, GEMINI minimally impacts neuronal functions and can resolve both transcriptional changes and activity patterns of neurons. Together, GEMINI provides a robust and generalizable means for spatiotemporal mapping of cell dynamics underlying physiological and pathological processes in both culture and intact tissues.

1 The membrane potential of eukaryotic cells, classically described by the Goldman-Hodgkin-Katz model, is conventionally attributed to the steady-state balance of transmembrane ionic fluxes. Here, we demonstrate that non-excitable cells maintain stable, spatially heterogeneous membrane voltage gradients. Using the ratiometric voltage indicator JEDI-2P-cyOFP1, we quantitatively map membrane potential in live cells and find that cellular protrusions are consistently depolarized, whereas lateral membrane regions are hyperpolarized. These voltage gradients strongly correlate with anisotropic distributions of anionic lipids, including phosphatidylserine (PS) and phosphatidylinositol 3,4,5-trisphosphate (PIP ₃ ). Perturbation of cytoskeletal integrity, the ion exchanger NHE1, or vesicular trafficking disrupts both voltage anisotropy and lipid polarization, revealing an uncharacterized electromechanical regulatory mechanism. Moreover, membrane potential dynamically responds to cell shape, substrate stiffness, external electric fields, and cell cycle progression. To account for these phenomena, we develop a quantitative model that integrates ionic fluxes and lipid charge distributions, thereby explaining the emergence of voltage gradients. This framework establishes that membrane potential is governed not solely by ionic currents but also by lipid dynamics and mechanical signaling. Collectively, these findings identify membrane voltage as a global integrator of electrochemical and mechanical cues in eukaryotic cells.

Protein crystals are mesoporous materials derived from nature, known for their versatility in structure and physicochemical properties. Conventional in vitro synthesis relies on metastable crystallization and often lacks controllability and programmability. Here, we present an in cellulo synthesis platform for controllable and programmable protein crystallization. We showed that, following initial nucleation, crystal growth is governed by the steady protein expression, enabling predictable and tunable growth dynamics. Leveraging this property, we integrated HaloTag and click chemistries to achieve modular and programmable immobilization of diverse guest materials with precise nanoscale spatial patterns. Furthermore, we demonstrated the sequential release of immobilized materials in physiologically relevant fluids. As a proof-of-concept, we programmed particles to carry human fibroblast growth factors in distinct layers, which induced oscillatory Akt signaling of designed patterns in cell culture. This platform opens new avenues for the programmable production of mesoporous materials, with promising applications in catalysis, biomedicine, and beyond.

Electrophysiological recording technologies can provide valuable insights into the functioning of the central and peripheral nervous systems. Surface electrode arrays made of soft materials or implantable multi-electrode arrays with high electrode density have been widely utilized as neural probes. However, neither of these probe types can simultaneously achieve minimal invasiveness and robust neural signal detection. Here, we present an ultra-thin, minimally invasive neural probe (the “NeuroWeb”) consisting of hexagonal boron nitride and graphene, which leverages the strengths of both surface electrode array and implantable multi-electrode array. The NeuroWeb open lattice structure with a total thickness of 100 nm demonstrates high flexibility and strong adhesion, establishing a conformal and tight interface with the uneven mouse brain surface. In vivo electrophysiological recordings show that NeuroWeb detects stable single-unit activity of neurons with high signal-to-noise ratios. Furthermore, we investigate neural interactions between the somatosensory cortex and the cerebellum using transparent dual NeuroWebs and optical stimulation, and measure the times of neural signal transmission between the brain regions depending on the pathway. Therefore, NeuroWeb can be expected to pave the way for understanding complex brain networks with optical and electrophysiological mapping of the brain.

Spinal cord neuromodulation can restore partial to complete loss of motor functions associated with neuromotor disease and trauma. Current technologies have made substantial progress but have limitations as dorsal epidural or intraspinal devices that are either remote to ventral motor neurons or subject to surgical intervention in the spinal tissue. Here, we describe a flexible and stretchable spinal stimulator design with nanoscale thickness that can be implanted by minimally invasive injection through a polymeric catheter to target the ventral spinal space of mice. Ventrolaterally implanted devices exhibited substantially lower stimulation threshold currents and more precise recruitment of motor pools than did comparable dorsal epidural implants. Functionally relevant and novel hindlimb movements were achieved via specific stimulation patterns of the electrodes. This approach holds translational potential for improving controllable limb function following spinal cord injury or neuromotor disease.

Spinal cord neuromodulation can restore partial to complete loss of motor functions associated with neuromotor disease and trauma. Current technologies have made substantial progress, but have limitations as dorsal epidural or intraspinal devices that are either remote to ventral motor neurons or subject to surgical intervention in the spinal tissue. Here, we describe a flexible and stretchable spinal stimulator design with nanoscale thickness that can be implanted by minimally-invasive injection through a polymeric catheter to target the ventral spinal space of mice. Ventrolaterally implanted devices exhibited substantially lower stimulation threshold currents and more precise recruitment of motor pools than comparable dorsal epidural implants. Functionally relevant and novel hindlimb movements were achieved via specific stimulation patterns of the electrodes. This approach holds translational potential for improving controllable limb function following spinal cord injury or neuromotor disease.

Recording transcriptional histories of a cell would enable deeper understanding of cellular developmental trajectories and responses to external perturbations. Here we describe an engineered protein fiber that incorporates diverse fluorescent marks during its growth to store a ticker tape-like history. An embedded HaloTag reporter incorporates user-supplied dyes, leading to colored stripes that map the growth of each individual fiber to wall clock time. A co-expressed eGFP tag driven by a promoter of interest records a history of transcriptional activation. High-resolution multi-spectral imaging on fixed samples reads the cellular histories, and interpolation of eGFP marks relative to HaloTag timestamps provides accurate absolute timing. We demonstrate recordings of doxycycline-induced transcription in HEK cells and cFos promoter activation in cultured neurons, with a single-cell absolute accuracy of 30–40 minutes over a 12-hour recording. The protein-based ticker tape design we present here could be generalized to achieve massively parallel single-cell recordings of diverse physiological modalities.