Proximity ligation assay mediated rolling circle amplification strategy for in situ amplified imaging of glycosylated PD-L1

Robust visualization of membrane protein by aptamer mediated proximity ligation assay and Förster resonance energy transfer

In situ cell imaging plays a crucial role in studying physiological and pathological processes of cells. Proximity ligation assay (PLA) and rolling circle amplification (RCA) are commonly used to study the abundance and interactions of biological macromolecules. The most frequently applied strategy to visualize the RCA products is with single-fluorophore probe, however, cellular auto-fluorescence and unbound fluorescent probes could interfere with RCA products, leading to non-specific signals. Here, we present a novel approach combining aptamer mediated PLA, RCA, and Förster Resonance Energy Transfer (FRET), namely Apt-PLA-RCA-FRET, for sensitive in situ imaging and analysis of the abundances and interactions of membrane proteins such as tetraspanin CD63 and human epidermal growth factor receptor 2 (HER2). Apt-RCA-FRET was initially designed to show its ability to assess the abundance of target proteins on different cells. Dual functional oligonucleotides served as both the aptamer for recognizing specific membrane proteins and the primer of circular DNA for following RCA process, and the resulting RCA products were subsequently imaged by FRET signals from Cy3 to Cy5 probes which hybridized sequentially on them. FRET was demonstrated to show its great potential to resist the interferences of nonspecific fluorescence compared to single-fluorophore strategies. PLA was then introduced to Apt-RCA-FRET to investigate the spatial localization of different proteins on cell membrane and their interactions. Our approach utilizing aptamer as membrane proteins recognition element simply converted the abundance of proteins into nucleic acid signals and facilitated the following signal amplification, thus it serves as an important alternative to methods typically based on antibody and presents a more robust and sensitive method for analyzing the abundances of different cell membrane proteins and their spatial localization, which offers valuable insights into physiological and pathological processes of cells.

Aptamer-Proximity Ligation Coupled with Rolling Circle Amplification Strategy for an Ultrasensitive Analysis of Tumor-Derived Extracellular Vesicles PD-L1

Tumor-derived extracellular vesicles (T-EVs) PD-L1 are an important biomarker for predicting immunotherapy response and can help us understand the mechanism of resistance to immunotherapy. However, this is due to the interference from a large proportion of nontumor-derived EVs. It is still challenging to accurately analyze T-EVs PD-L1 in complex human fluids. Herein, a simple and ultrasensitive method based on the dual-aptamer-proximity ligation assay (PLA)-guided rolling circle amplification (RCA) for the analysis of T-EVs PD-L1 was developed. First, dual aptamers with strong binding affinity were utilized for the recognition of EpCAM and PD-L1 on EVs, and then the aptamer-based PLA occurred. With the aid of the high signal amplification ability of RCA guided by the dual-aptamer-based PLA and efficient magnetic separation, the biosensor could realize highly sensitive quantification of EpCAM and PD-L1 dual-positive EVs with a low detection limit of 7.5 particles/μL. In addition, this method based on the aptamer-PLA-guided RCA was used to discriminate cancer patients from healthy donors with 100% accuracy without additional purification. Overall, this strategy might provide a practical tool for the analysis of multiple proteins on EVs, exhibiting great potential in early cancer diagnosis and treatment.

A PLA-mediated transistor biosensor enables specific identification of tumor-derived exosomal PD-L1

The expression of programmed death ligand 1 (PD-L1) on tumor-derived exosomes (tExos) forecasts the efficacy of immunotherapy and tumor diagnosis. Due to the heterogeneity of exosomes, current detection methods face challenges in distinguishing between tumor-derived and non-tumor-derived exosome PD-L1. To address this challenge, we introduce a novel field effect transistor (FET) biosensor based on proximity ligation assay (PLA) technology. This approach uses a single probe to simultaneously recognize two biomarkers on exosomes to identify tumor-derived exosome PD-L1 (tExo-PD-L1). This method, for the first time, integrates the PLA strategy with FET technology, allowing for tracking of exosomes that co-express multiple biomarkers. In clinical diagnostics, this strategy not only significantly improves the sensitivity and specificity, but also enhances the precision and accuracy, compared to conventional approaches that identify total Exo-PD-L1 or Exo-EpCAM using a single biomarker. This technology holds promise for enhancing the reliability of using exosomes as biomarkers in clinical diagnostics and further exploring the biological functions of exosomes more effectively.

Immuno-Rolling Circle Amplification (Immuno-RCA): Biosensing Strategies, Practical Applications, and Future Perspectives

In the rapidly evolving field of life sciences and biomedicine, detecting low-abundance biomolecules, and ultraweak biosignals presents significant challenges. This has spurred a rapid development of analytical techniques aiming for increased sensitivity and specificity. These advancements, including signal amplification strategies and the integration of biorecognition events, mark a transformative era in bioanalytical precision and accuracy. A prominent method among these innovations is immuno-rolling circle amplification (immuno-RCA) technology, which effectively combines immunoassays with signal amplification via RCA. This process starts when a targeted biomolecule, such as a protein or cell, binds to an immobilized antibody or probe on a substrate. The introduction of a circular DNA template triggers RCA, leading to exponential amplification and significantly enhanced signal intensity, thus the target molecule is detectable and quantifiable even at the single-molecule level. This review provides an overview of the biosensing strategy and extensive practical applications of immuno-RCA in detecting biomarkers. Furthermore, it scrutinizes the limitations inherent to these sensors and sets forth expectations for their future trajectory. This review serves as a valuable reference for advancing immuno-RCA in various domains, such as diagnostics, biomarker discovery, and molecular imaging.

Harnessing CRISPR/Cas12a Activity and DNA-Based Ultrabright FluoroCube for In Situ Imaging of Metabolically Labeled Cell Membrane Glycoproteins

Fluorescence imaging of cell membrane glycoproteins based on metabolic labeling faces challenges including the sensitivity and spatial specificity and the use of a high concentration of unnatural sugars. To overcome these limitations, we developed a method for in situ imaging of cell membrane glycoproteins by operating Cas12a activity, and employing the ultrabright DNA nanostructure, FluoroCube (FC), as a signal reporter. Following Cas12a activation, we observed stable and intense fluorescence signals within 15 min. The combination of bright FC and Cas12a's amplification capability allows for effective imaging with only 5 μM of unnatural sugars and a brief 24-h incubation. Computational modeling demonstrates that Cas12a specifically cleaves FC in the 11-17 nm range of the glycosylation site, enabling spatially precise imaging. This approach successfully enabled fluorescence imaging of glycoproteins across various cell lines and the detection of changes in glycoprotein levels induced by drugs.

Aptamers combined with immune checkpoints for cancer detection and targeted therapy: A review

In recent years, remarkable strides have been made in the field of immunotherapy, which has emerged as a standard treatment for many cancers. As a kind of immunotherapy drug, monoclonal antibodies employed in immune checkpoint therapy have proven beneficial for patients with diverse cancer types. However, owing to the extensive heterogeneity of clinical responses and the complexity and variability of the immune system and tumor microenvironment (TME), accurately predicting its efficacy remains a challenge. Recent advances in aptamers provide a promising approach for monitoring alterations within the immune system and TME, thereby facilitating targeted immunotherapy, particularly focused on immune checkpoint blockade, with enhanced antitumor efficiency. Aptamers have been widely used in tumor cell detection, biosensors, drug discovery, and biomarker screening due to their high specificity and high affinity with their targets. This review aims to comprehensively examine the research status and progress of aptamers in cancer diagnosis and immunotherapy, with a specific emphasis on those related to immune checkpoints. Additionally, we will discuss the future research directions and potential therapeutic targets for aptamer-based immune checkpoint therapy, aiming to provide a theoretical basis for targeting immunotherapy molecules and blocking tumor immune escape.

Smart Tumor Cell-Derived DNA Nano-Tree Assembly for On-Demand Macrophages Reprogramming

Without coordinated strategies to balance the population and activity of tumor cells and polarized macrophages, antitumor immunotherapy generally offers limited clinical benefits. Inspired by the "eat me" signal, a smart tumor cell-derived proximity anchored non-linear hybridization chain reaction (Panel-HCR) strategy is established for on-demand regulation of tumor-associated macrophages (TAMs). The Panel-HCR is composed of a recognition-then-assembly module and a release-then-regulation module. Upon recognizing tumor cells, a DNA nano-tree is assembled on the tumor cell surface and byproduct strands loaded with CpG oligodeoxynucleotides (CpG-ODNs) are released depending on the tumor cell concentration. The on-demand release of CpG-ODNs can achieve efficient regulation of M2 TAMs into the M1 phenotype. Throughout the recognition-then-assembly process, tumor cell-targeted bioimaging is implemented in single cells, fixed tissues, and living mice. Afterward, the on-demand release of CpG-ODNs regulate the transformation of M2 TAMs into the M1 phenotype by stimulating toll-like receptor 9 to activate the NF-κB pathway and increasing inflammatory cytokines. This release-then-regulation process is verified to induce strong antitumor immune responses both in vitro and in vivo. Altogether, this proposed strategy holds tremendous promise for on-demand antitumor immunotherapy.

In Situ Glycan Analysis and Editing in Living Systems

Besides proteins and nucleic acids, carbohydrates are also ubiquitous building blocks of living systems. Approximately 70% of mammalian proteins are glycosylated. Glycans not only provide structural support for living systems but also act as crucial regulators of cellular functions. As a result, they are considered essential pieces of the life science puzzle. However, research on glycans has lagged far behind that on proteins and nucleic acids. The main reason is that glycans are not direct products of gene coding, and their synthesis is nontemplated. In addition, the diversity of monosaccharide species and their linkage patterns contribute to the complexity of the glycan structures, which is the molecular basis for their diverse functions. Research in glycobiology is extremely challenging, especially for the in situ elucidation of glycan structures and functions. There is an urgent need to develop highly specific glycan labeling tools and imaging methods and devise glycan editing strategies. This Perspective focuses on the challenges of in situ analysis of glycans in living systems at three spatial levels (i.e., cell, tissue, and in vivo) and highlights recent advances and directions in glycan labeling, imaging, and editing tools. We believe that examining the current development landscape and the existing bottlenecks can drive the evolution of in situ glycan analysis and intervention strategies and provide glycan-based insights for clinical diagnosis and therapeutics.

Harnessing aptamers for the biosensing of cell surface glycans - A review

Cell surface glycans (CSGs) are essential for cell recognition, adhesion, and invasion, and they also serve as disease biomarkers. Traditional CSG recognition using lectins has limitations such as limited specificity, low stability, high cytotoxicity, and multivalent binding. Aptamers, known for their specific binding capacity to target molecules, are increasingly being employed in the biosensing of CSGs. Aptamers offer the advantage of high flexibility, small size, straightforward modification, and monovalent recognition, enabling their integration into the profiling of CSGs on living cells. In this review, we summarize representative examples of aptamer-based CSG biosensing and identify two strategies for harnessing aptamers in CSG detection: direct recognition based on aptamer-CSG binding and indirect recognition through protein localization. These strategies enable the generation of diverse signals including fluorescence, electrochemical, photoacoustic, and electrochemiluminescence signals for CSG detection. The advantages, challenges, and future perspectives of using aptamers for CSG biosensing are also discussed.

Assay methods based on proximity-enhanced reactions for detecting non-nucleic acid molecules

Accurate and reliable detection of biological molecules such as nucleic acids, proteins, and small molecules is essential for the diagnosis and treatment of diseases. While simple homogeneous assays have been developed and are widely used for detecting nucleic acids, non-nucleic acid molecules such as proteins and small molecules are usually analyzed using methods that require time-consuming procedures and highly trained personnel. Recently, methods using proximity-enhanced reactions (PERs) have been developed for detecting non-nucleic acids. These reactions can be conducted in a homogeneous liquid phase via a single-step procedure. Herein, we review three assays based on PERs for the detection of non-nucleic acid molecules: proximity ligation assay, proximity extension assay, and proximity proteolysis assay.

Molecular probes for cellular imaging of post-translational proteoforms

Specific post-translational modification (PTM) states of a protein affect its property and function; understanding their dynamics in cells would provide deep insight into diverse signaling pathways and biological processes. However, it is not trivial to visualize post-translational modifications in a protein- and site-specific manner, especially in a living-cell context. Herein, we review recent advances in the development of molecular imaging tools to detect diverse classes of post-translational proteoforms in individual cells, and their applications in studying precise roles of PTMs in regulating the function of cellular proteins.