Ru(bpy)3 2+ -Enabled Cell-Surface Photocatalytic Proximity Labeling toward More Efficient Capture of Physically Interacting Cells

Engineered Proteins and Chemical Tools to Probe the Cell Surface Proteome

The cell surface proteome, or surfaceome, is the hub for cells to interact and communicate with the outside world. Many disease-associated changes are hard-wired within the surfaceome, yet approved drugs target less than 50 cell surface proteins. In the past decade, the proteomics community has made significant strides in developing new technologies tailored for studying the surfaceome in all its complexity. In this review, we first dive into the unique characteristics and functions of the surfaceome, emphasizing the necessity for specialized labeling, enrichment, and proteomic approaches. An overview of surfaceomics methods is provided, detailing techniques to measure changes in protein expression and how this leads to novel target discovery. Next, we highlight advances in proximity labeling proteomics (PLP), showcasing how various enzymatic and photoaffinity proximity labeling techniques can map protein-protein interactions and membrane protein complexes on the cell surface. We then review the role of extracellular post-translational modifications, focusing on cell surface glycosylation, proteolytic remodeling, and the secretome. Finally, we discuss methods for identifying tumor-specific peptide MHC complexes and how they have shaped therapeutic development. This emerging field of neo-protein epitopes is constantly evolving, where targets are identified at the proteome level and encompass defined disease-associated PTMs, complexes, and dysregulated cellular and tissue locations. Given the functional importance of the surfaceome for biology and therapy, we view surfaceomics as a critical piece of this quest for neo-epitope target discovery.

Clone-Resolved Chemical Depletion of T cells via Cellular Proximity Chemistry

T cells play a pivotal role in the development of autoimmune diseases. To mitigate autoimmune inflammation without inducing global immunosuppression, it is crucial to selectively eliminate autoreactive T cell clones while preserving the normal T cell repertoire. In this study, we applied cellular proximity chemistry to develop a T-cell depletion method with clonal precision. Using engineered dendritic cells (DCs) with surface-bound photosensitizers, we generated reactive oxygen species (ROS) at immune synapses, leading to the targeted death of antigen-specific T cells in close proximity. This process induces lipid oxidation in T cell membranes, triggering ferroptosis-like cell death. The method enables the selective elimination of specific T cell clones without affecting others, in which the clonal resolution was demonstrated by TCR sequencing. Finally, we demonstrated the efficacy of this approach in a type 1 diabetes model by selectively depleting the pathogenic 8.3 T cell clone, thereby protecting islet β cells and preserving overall T cell function. This strategy offers a promising avenue for immunosuppressive therapy that targets pathogenic T cells while maintaining overall immune integrity.

Deep-Red and Ultrafast Photocatalytic Proximity Labeling Empowered In Situ Dissection of Tumor-Immune Interactions in Primary Tissues

Immunotherapy efficacy in solid tumors varies greatly, influenced by the tumor microenvironment (TME) and the dynamic tumor-immune interactions within it. Decoding these interactions in situ with minimal interference with native tissue architecture and delicate immune responses is critical for understanding tumor progression and optimizing therapeutic strategies. Here, we introduce CAT-Tissue, a novel deep-red photocatalytic proximity labeling method that enables ultrafast, high-resolution profiling of tumor-immune interactions in primary tissues. By leveraging nanobody-Chlorin e6 as the photocatalyst and biotin-aniline as the probe, CAT-Tissue enabled the rapid and comprehensive detection of various tumor-immune interactions in both coculture systems and primary tumor sections. Coupled with bulk RNA-sequencing, CAT-Tissue revealed distinct gene expression patterns between tumor-neighboring and tumor-distal lymphocytes, highlighting the recognition and immune responses of tumor-neighboring CD8+ T cells, which exhibited activated, effector, and exhausted phenotypes. By leveraging a deep-red photocatalytic proximity cell labeling strategy with excellent tissue penetration and biocompatibility, CAT-Tissue offers a nongenetically encoded platform with high sensitivity and spatiotemporal controllability for rapid profiling tumor-immune interactions within complex tissue environments in situ, which may advance our understanding of tumor immunology and guide the development of more effective immunotherapies.

Near-Infrared Light-Mediated Living Cells Mitochondrial Proteome Proximity Labeling

Photocatalytic proximity labeling techniques enable significant advances in understanding the subcellular proteome. However, current methods primarily utilize visible light that suffers from low labeling efficiency and limited identification coverage due to absorption overlap with endogenous chromophores and scattering in biological samples. To address these issues, we reported the proximity labeling strategy using near-infrared excitation (PL-NIR) strategy, a proximity labeling platform that used a near-infrared-excited catalyst to activate labeling mediated by reactive oxygen species, which could avoid the disadvantages of visible light. Taking advantage of the near-infrared excitation and mitochondrial targeting properties of IR780, the mitochondrial proteome were selectively labeled by spatially limited reaction in the native environment. The PL-NIR strategy facilitated the plotting of the mitochondrial proteome in which up to 245 mitochondrial proteins were identified in living HeLa cells. Compared with the current methods, the PL-NIR strategy significantly increased identification coverage, especially for mitochondrial inner membrane proteins. Furthermore, mitochondrial proteome dynamics were deciphered in LPS stimulated HMC3 cells, which were hard to transfect. Overall, the PL-NIR strategy as a highly precise proteomic platform offered improved identification coverage for more knowledge of subcellular biology discovering.

Painting Cell-Cell Interactions by Horseradish Peroxidase and Endogenously Generated Hydrogen Peroxide

Cell-cell interactions are fundamental in biology for maintaining physiological conditions with direct contact being the most straightforward mode of interaction. Recent advancements have led to the development of various chemical tools for detecting or identifying these interactions. However, the use of exogenous cues, such as toxic reagents, bulky probes, and light irradiation, can disrupt normal cell physiology. For example, the toxicity of hydrogen peroxide (H2O2) limits the applications of peroxidases in the proximity labeling field. In this study, we aimed to address this limitation by demonstrating that membrane-localized horseradish peroxidase (HRP-TM) efficiently utilizes endogenously generated extracellular H2O2. By harnessing endogenous H2O2, we observed that HRP-TM-expressing cells can effectively label contacting cells without the need for exogenous H2O2 treatment. Furthermore, we confirmed that HRP-TM labels proximal cells in an interaction-dependent manner. These findings offer a novel approach for studying cell-cell interactions under more physiological conditions without the confounding effects of exogenous stimuli. Our study contributes to elucidating cell-cell interaction networks in various model organisms, providing valuable insights into the dynamic interplay between cells in their native network.

2D Nano-Photosensitizer Facilitates Proximity Labeling for Living Cells Surfaceome Deciphering

Photocatalytic proximity labeling has shown great promise for mapping the spatiotemporal dynamics of surfaceome. Although cell-surface targeting photosensitizers relying on antibodies, lipid molecules, and metabolic labeling have gained effects, the development of simpler and stable methods that avoid complex chemical synthesis and biosynthesis steps is still a huge challenge. Here, the study has introduced 2D nanomaterials with the ability of cell surface engineering to perform the in situ anchoring of photosensitizer on living cell surface. Photosensitizer can be stabilized on nanomaterials by coordination after one-step mixing, resulting in the nano-photosensitizer combining cell surface targeting ability and photosensitivity that allowing surface-specific proximity labeling. Nano-photosensitizer can be dispersed stably in aqueous solution, avoiding the defects of poor water solubility and aggregation of traditional organic photosensitizers. Singlet oxygen is generated locally under light irradiation, enabling spatiotemporally-resolved activating and labeling of cell surface proteome. Further application in the brain metastatic lung cancer has been found effective with numerous quantified differential cell surfaces proteins highly correlated with cancer metastasis and three potential players have been validated via immunoblotting and immunofluorescence, providing important insights for metastasis supported molecular mechanism.

Stressor-Actuated Proximity Labeling for Reporting Cellular Interaction

Cell-cell interactions determine the activation state and function of cells. When host cells are exposed to stressors such as microorganisms, immune defense machinery is activated to release H2O2, providing direct evidence of the relevant cellular physiological processes. Inspired by the fact that peroxidase can catalyze proximity labeling in the presence of exogenous H2O2, a stressor-actuated proximity labeling (SAPL) strategy is developed to report the process information on cell-cell interactions by recording stress levels. The stressors are covalently modified with horseradish peroxidase (HRP) and the H2O2 released by the host cells in response to the stressors triggers HRP-based proximity labeling. Using a fungal mimic or live fungi as stressors, the stress levels of different host cells are compared by in situ imaging of the labeling signals. The ability to accumulate stress signals allows SAPL to more sensitively differentiate between interactions involving different macrophage phenotypes. SAPL is also a powerful tool for real-time, in situ monitoring of the effects of surface modifications on cellular interactions. Thus, the SAPL strategy represents a new perspective in the monitoring of cell-cell interactions using endogenous effector molecules.

Single-cell sequencing to multi-omics: technologies and applications

Cells, as the fundamental units of life, contain multidimensional spatiotemporal information. Single-cell RNA sequencing (scRNA-seq) is revolutionizing biomedical science by analyzing cellular state and intercellular heterogeneity. Undoubtedly, single-cell transcriptomics has emerged as one of the most vibrant research fields today. With the optimization and innovation of single-cell sequencing technologies, the intricate multidimensional details concealed within cells are gradually unveiled. The combination of scRNA-seq and other multi-omics is at the forefront of the single-cell field. This involves simultaneously measuring various omics data within individual cells, expanding our understanding across a broader spectrum of dimensions. Single-cell multi-omics precisely captures the multidimensional aspects of single-cell transcriptomes, immune repertoire, spatial information, temporal information, epitopes, and other omics in diverse spatiotemporal contexts. In addition to depicting the cell atlas of normal or diseased tissues, it also provides a cornerstone for studying cell differentiation and development patterns, disease heterogeneity, drug resistance mechanisms, and treatment strategies. Herein, we review traditional single-cell sequencing technologies and outline the latest advancements in single-cell multi-omics. We summarize the current status and challenges of applying single-cell multi-omics technologies to biological research and clinical applications. Finally, we discuss the limitations and challenges of single-cell multi-omics and potential strategies to address them.

DNA-Directed Activation of Photocatalytic Labeling at Cell-Cell Contact Sites

Cell-cell interactions govern diverse biological activities, necessitating molecular tools for understanding and regulating these interactions. Photoredox chemistry can detect cell-cell interactions by anchoring photocatalysts on cellular membranes to generate reactive species that tag closely contacting cells. However, the activation of photocatalysts lacks precise spatial resolution for selectively labeling intercellular interfaces. Herein, we report a DNA-based approach to selectively activate photocatalytic reactions at cell-cell contacts. Two cell populations are coated with distinct DNA strands, which interact at intercellular contacts, mediating the site-specific turn-on of a Ru(bpy)3-type photocatalyst. We demonstrate high spatial specificity for intercellular chemical labeling in cultured mammalian cells. Furthermore, as a proof of concept, we activate the dynamic DNA catalyst at cell-cell contacts in response to customized DNA triggers. This study lays the foundation for designing versatile chemical tools with high spatial precision and programmable responsiveness, along with the temporal resolution afforded by photoirradiation, to investigate and manipulate cell-cell interactions.

Proximitomics by Reactive Species

The proximitome is defined as the entire collection of biomolecules spatially in the proximity of a biomolecule of interest. More broadly, the concept of the proximitome can be extended to the totality of cells proximal to a specific cell type. Since the spatial organization of biomolecules and cells is essential for almost all biological processes, proximitomics has recently emerged as an active area of scientific research. One of the growing strategies for proximitomics leverages reactive species-which are generated in situ and spatially confined, to chemically tag and capture proximal biomolecules and cells for systematic analysis. In this Outlook, we summarize different types of reactive species that have been exploited for proximitomics and discuss their pros and cons for specific applications. In addition, we discuss the current challenges and future directions of this exciting field.

A T-Cell Inspired Sonoporation System Enhances Low-Dose X-Ray-Mediated Pyroptosis and Radioimmunotherapy Efficacy by Restoring Gasdermin-E Expression

Genome editing has the potential to improve the unsatisfactory therapeutic effect of antitumor immunotherapy. However, the cell plasma membrane prevents the entry of almost all free genome-manipulation agents. Therefore, a system can be spatiotemporally controlled and can instantly open the cellular membrane to allow the entry of genome-editing agents into target cells is needed. Here, inspired by the ability of T cells to deliver cytotoxins to cancer cells by perforation, an ultrasound (US)-controlled perforation system (UPS) is established to enhance the delivery of free genome-manipulating agents. The UPS can perforate the tumor cell membrane while maintaining cell viability via a controllable lipid peroxidation reaction. In vitro, transmembrane-incapable plasmids can enter cells and perform genome editing with the assistance of UPS, achieving an efficiency of up to 90%. In vivo, the UPS is biodegradable, nonimmunogenic, and tumor-targeting, enabling the puncturing of tumor cells under US. With the application of UPS-assisted genome editing, gasdermin-E expression in 4T1 tumor-bearing mice is successfully restored, which leads to pyroptosis-mediated antitumor immunotherapy via low-dose X-ray irradiation. This study provides new insights for designing a sonoporation system for genome editing. Moreover, the results demonstrate that restoring gasdermin expression by genome editing significantly improves the efficacy of radioimmunotherapy.

Chemical immunology: Recent advances in tool development and applications

Immunology was one of the first biological fields to embrace chemical approaches. The development of new chemical approaches and techniques has provided immunologists with an impressive arsenal of tools to address challenges once considered insurmountable. This review focuses on advances at the interface of chemistry and immunobiology over the past two decades that have not only opened new avenues in basic immunological research, but also revolutionized drug development for the treatment of cancer and autoimmune diseases. These include chemical approaches to understand and manipulate antigen presentation and the T cell priming process, to facilitate immune cell trafficking and regulate immune cell functions, and therapeutic applications of chemical approaches to disease control and treatment.

Revealing protein trafficking by proximity labeling-based proteomics

Protein trafficking is a fundamental process with profound implications for both intracellular and intercellular functions. Proximity labeling (PL) technology has emerged as a powerful tool for capturing precise snapshots of subcellular proteomes by directing promiscuous enzymes to specific cellular locations. These enzymes generate reactive species that tag endogenous proteins, enabling their identification through mass spectrometry-based proteomics. In this comprehensive review, we delve into recent advancements in PL-based methodologies, placing particular emphasis on the label-and-fractionation approach and TransitID, for mapping proteome trafficking. These methodologies not only facilitate the exploration of dynamic intracellular protein trafficking between organelles but also illuminate the intricate web of intercellular and inter-organ protein communications.

Switchable DNA Catalysts for Proximity Labeling at Sites of Protein-Protein Interactions

Proximity labeling (PL) has emerged as a powerful approach to elucidate proteomes within a defined radius around a protein of interest (POI). In PL, a catalyst is attached to the POI and tags nearby endogenous proteins, which are then isolated by affinity purification and identified by mass spectrometry. Although existing PL methods have yielded numerous biological insights, proteomes with greater spatial resolution could be obtained if PL catalysts could be activated at more specific subcellular locations, such as sites where both the POI and a chemical stimulus are present or sites of protein-protein interactions (PPIs). Here, we report DNA-based switchable PL catalysts that are attached to a POI and become activated only when a secondary molecular trigger is present. The DNA catalysts consist of a photocatalyst and a spectral quencher tethered to a DNA oligomer. They are catalytically inactive by default but undergo a conformational change in response to a specific molecular trigger, thus activating PL. We designed a system in which the DNA catalyst becomes activated on living mammalian cells specifically at sites of Her2-Her3 heterodimers and c-Met homodimers, PPIs known to increase the invasion and growth of certain cancers. While this study employs a Ru(bpy)3-type complex for tagging proteins with biotin phenol, the switchable DNA catalyst design is compatible with diverse synthetic PL photocatalysts. Furthermore, the switchable DNA PL catalysts can be constructed from conformation-switching DNA aptamers that respond to small molecules, ions, and proteins, opening future opportunities for PL in highly specific subcellular locations.