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

Multiprobe Photoproximity Labeling of the EGFR Interactome in Glioblastoma Using Red-Light

Photocatalytic proximity labeling has emerged as a valuable technique for studying interactions between biomolecules in a cellular context, providing precise spatiotemporal control over protein labeling. One significant advantage of these methods is their modularity, allowing the use of a single photocatalyst with different reactive probes to expand interactome coverage and capture diverse protein interactions. Despite these advances, fewer methods have been developed using red-light excitation, limiting the use of photoproximity labeling in more complex media such as tissues and animal models. Herein, we develop a platform for proximity labeling under red-light excitation, utilizing a single catalyst and two distinct probe types. We first design a carbene based labeling system that utilizes sulfonium diazo probes. This system is successfully applied on A549 cells to capture the interactome of epidermal growth factor receptor (EGFR) using a Cetuximab-Chlorin e6 conjugate. Benchmarking against established techniques indicates that this approach performs comparably to leading carbene-based proximity labeling methods. Next, we leverage the strong singlet oxygen generation (SOG) ability of Chlorin e6 to establish an alternative labeling system using aniline and hydrazide probes. EGFR directed chemoproteomics experiments reveal significant overlap with the carbene system, with the carbene approach capturing a subset of interactions identified by the SOG system. Finally, we deploy our approach for the characterization of EGFR in resected human glioblastoma (GBM) tissue samples removed from distinct locations in the same tumor, representing the tumor's infiltrating edge and its viable center, identifying several GBM specific interacting proteins that may serve as a launch point for future therapeutic campaigns.

Two-Level Spatially Localized Proximity Labeling for Cross-Biological-Hierarchy Measurement and Manipulation

Proximity labeling (PL) has emerged as a powerful technique for the in situ elucidation of biomolecular interaction networks. However, PL methods generally rely on single-biological-hierarchy control of spatial localization at the labeling site, which limits their application in multi-tiered biological systems. Here, we introduced another enzymatic reaction upstream of an enzyme-based PL reaction and targeted the two enzymes to markers indicating different biological hierarchies, establishing a two-level spatially localized proximity labeling (P2L) platform for in situ molecular measurement and manipulation. Using the cellular- and glycan-level as the hierarchical models, we demonstrated the ability of P2L to efficiently execute a two-step logic operation and to discriminate target cells with different levels of glycosylation within mixed cell populations. By mounting clickable handles via P2L, we reprogrammed the robust covalent assembly of cells at designated sites. The combination of P2L with proteomics led to the profiling of the protein microenvironment of specific glycans on target cells, revealing changes in tumor-cell-surface interactions under immune pressure from a glycan perspective. P2L provides not only a solution for revealing the heterogeneity of biological systems, but also new insights in the fields of intelligent logic computation, enzyme engineering, tissue engineering, etc.

Microtubule-Targeting NAP Peptide-Ru(II)-polypyridyl Conjugate As a Bimodal Therapeutic Agent for Triple Negative Breast Carcinoma

Triple-negative breast cancer (TNBC) poses significant treatment challenges due to its high metastasis, heterogeneity, and poor biomarker expression. The N-terminus of an octapeptide NAPVSIPQ (NAP) was covalently coupled to a carboxylic acid derivative of Ru(2,2'-bipy)32+ (Rubpy) to synthesize an N-stapled short peptide-Rubpy conjugate (Ru-NAP). This photosensitizer (PS) was utilized to treat TNBC through microtubule (MT) targeted chemotherapy and photodynamic therapy (PDT). Ru-NAP formed more elaborate molecular aggregates with fibrillar morphology as compared to NAP. A much higher binding affinity of Ru-NAP over NAP toward β-tubulin (KRu-NAP: (6.8 ± 0.55) × 106 M-1; KNAP: (8.2 ± 1.1) × 104 M-1) was observed due to stronger electrostatic interactions between the MT with an average linear charge density of ∼85 e/nm and the cationic Rubpy part of Ru-NAP. This was also supported by docking, simulation, and appropriate imaging studies. Ru-NAP promoted serum stability, specific binding of NAP to the E-site of the βIII-tubulin followed by the disruption of the MT network, and effective singlet oxygen generation in TNBC cells (MDA-MB-231), causing cell cycle arrest in the G2/M phase and triggering apoptosis. Remarkably, MDA-MB-231 cells were more sensitive to Ru-NAP compared to noncancerous human embryonic kidney (HEK293 cells) when exposed to light (LightIC50Ru-NAP[HEK293]: 17.2 ± 2.5 μM, compared to LightIC50Ru-NAP[MDA-MB-231]: 32.5 ± 7.8 nM, DarkIC50Ru-NAP[HEK293]: > 80 μM, compared to DarkIC50Ru-NAP[MDA-MB-231]: 2.9 ± 0.5 μM). Ru-NAP also effectively inhibited tumor growth in MDA-MB-231 xenograft models in nude mice. Our findings provide strong evidence that Ru-NAP has a potential therapeutic role in TNBC treatment.

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.

DNA-modulated dimerization and oligomerization of cell membrane receptors

DNA-based nanostructures and nanodevices have recently been employed for a broad range of applications in modulating the assemblies and interaction patterns of different cell membrane receptors. These versatile nanodevices can be rationally designed with modular structures, easily programmed and tweaked such that they may act as smart chemical biology and cell biology tools to reveal insights into complicated cellular signaling processes. Their outstanding in vitro and cellular features have also begun to be further validated for some in vivo applications and demonstrated their great biomedical potential. In this review, we will highlight some key current advances in the molecular engineering and biological applications of DNA-based functional nanodevices, with a focus on how these tools have been used to respond and modulate membrane receptor dimerizations and/or oligomerizations, as a way to control cellular signaling processes. Some current challenges and future directions to further develop and apply these DNA nanodevices will also be discussed.

Proximity labeling-assisted click conjugation for electrochemical analysis of specific subpopulations in circulating extracellular vesicles

Sensitive and accurate analysis of specific subpopulations in circulating extracellular vesicles (EVs) can provide a wealth of information for cancer diagnosis and management. Thus, we propose herein a new electrochemical biosensing method based on a proximity labeling-assisted click conjugation strategy. The method's core design is use of antibody-guided proximity labeling to equip target EVs with a large amount of alkyne groups, so that azide-tagged silver nanoparticles can be accurately loaded onto target EV surfaces, via click conjugation, to generate significant electrochemical responses. Adopting CD44-positive EVs as the model, the electrochemical method was demonstrated by analyzing target EVs across a wide linear range (103-109 particles/mL) with acceptable sensitivity and specificity. Satisfactory utility in clinical blood samples, and versatility with human epidermal growth factor receptor-2-positive EVs as alternative targets, were also shown. This method may thus provide a novel approach to specific subgroup analyses of circulating EVs, and is expected to offer reliable guidance for cancer diagnoses and management strategies.

Current advances in photocatalytic proximity labeling

Understanding the intricate network of biomolecular interactions that govern cellular processes is a fundamental pursuit in biology. Over the past decade, photocatalytic proximity labeling has emerged as one of the most powerful and versatile techniques for studying these interactions as well as uncovering subcellular trafficking patterns, drug mechanisms of action, and basic cellular physiology. In this article, we review the basic principles, methodologies, and applications of photocatalytic proximity labeling as well as examine its modern development into currently available platforms. We also discuss recent key studies that have successfully leveraged these technologies and importantly highlight current challenges faced by the field. Together, this review seeks to underscore the potential of photocatalysis in proximity labeling for enhancing our understanding of cell biology while also providing perspective on technological advances needed for future discovery.