Aptamer Probes Labeled with Lanthanide-Doped Carbon Nanodots Permit Dual-Modal Fluorescence and Mass Cytometric Imaging

Luminescent Metal-Organic Framework Probes with Metallic and Fluorescent Dual-Properties for Mass Cytometry and Imaging

Mass cytometry (CyTOF) and imaging mass cytometry (IMC), as cutting-edge technologies in single-cell analysis, are capable of detecting more than 40 biomarkers simultaneously on a single cell. However, their sensitivity and multiparameter detection capabilities have been long constrained by the development of metal labeling materials. Meanwhile, as an imaging technique, IMC has suffered from a rather slow data acquisition rate. Here, we present a luminescent PCN-224-OH material that exhibits both fluorescent and mass dual-functionality and is enriched with Zr-OH-/H2O active sites. Without the additional need for complex postmodification or chemical coupling reactions, PCN-224-OH can be directly functionalized with antibodies/aptamers and poly(ethylene glycol) (PEG), resulting in the production of PCN-224-Ab-PEG or PCN-224-Apt-PEG probes. We demonstrated that PCN-224-Ab-PEG was compatible with commercial polymer-based probes but with superior sensitivity and specificity. Meanwhile, since PCN-224-Apt-PEG expressed both fluorescence and mass signals, we could adopt fluorescence signals for rapid tissue section scanning to swiftly identify the regions of interest (ROIs), and then adopt IMC for multiparameter imaging at the specific ROIs. The application of the PCN-224-Apt-PEG probe could significantly reduce the blind IMC scanning time by up to 90% and effectively compensate for IMC's low resolution. This study not only broadens the application scope of luminescent metal-organic frameworks but also offers a potentially novel toolbox for single-cell multiparameter detection.

Solution-Gated Thin Film Transistor Biosensor-Based SnO2 Amorphous Film for Label-Free Detection of Epithelial Cell Adhesion Molecules

Epithelial cell adhesion molecule (EpCAM) was considered to be an important marker of multiple tumors, and its high expression is closely related to the early diagnosis and treatment of tumors. At present, metal oxide semiconductors have become a key component of biosensor and bioelectronics technology. Tin oxide shows great potential for development because of its nontoxic, nonpolluting, low price, and excellent electrical properties. In this study, a novel SnO2 solution-gated thin film transistor (SGTFT) biosensor for the specific detection of EpCAM was successfully developed using SnO2 film prepared by the sol-gel method as the channel material. By selecting the optimal thickness of 100 nm SnO2 film as the channel material, the transconductance value (gm) reached 1432 μS, and the threshold voltage (Vth) remained stable at 0.288 V. In order to achieve qualitative and quantitative detection of EpCAM, SnO2 films were subjected to a specific chemical treatment to fix the aptamer. Through a specific recognition between the aptamer and EpCAM, the gate voltage changes were triggered to regulate the channel current of the device. FE-SEM, EIS, XPS, and electrical performance tests were employed to track and measure the modification process. Based on the optimizations described above, the prepared SGTFT exhibited high detection sensitivity (14.6 mV·dec-1), the limit of detection (LOD) down to 24.4 pg/mL, and the calibration curves in the range of 0.02 ng/mL-500 ng/mL for EpCAM sensing. The developed SnO2-SGTFT biosensor is anticipated to provide a new highly sensitive and specific detection platform for health monitoring and disease diagnosis.

Derivative Technologies of Expansion Microscopy and Applications in Biomedicine

Expansion microscopy (ExM) is an innovative super-resolution imaging technique that utilizes physical expansion to magnify biological samples, facilitating the visualization of cellular structures that are challenging to observe using traditional optical microscopes. The fundamental principle of ExM revolves around employing a specialized hydrogel to uniformly expand biological samples, thereby achieving super-resolution imaging under conventional optical imaging conditions. This technology finds application not only in various biological samples such as cells and tissue sections, but also enables super-resolution imaging of large biological molecules including proteins, nucleic acids, and metabolite molecules. In recent years, numerous researchers have delved into ExM, resulting in the continuous development of a range of derivative technologies that optimize experimental protocols and broaden practical application fields. This article presents a comprehensive review of these derivative technologies, highlighting the utilization of ExM for anchoring nucleic acids, proteins, and other biological molecules, as well as its applications in biomedicine. Furthermore, this review offers insights into the future development prospects of ExM technology.

A two-dimensional fluorescence and chemiluminescence orthogonal probe for discriminating and quantifying similar proteins

Given that proteins with minor variations in amino acid sequences cause distinct functional outcomes, identifying and quantifying similar proteins is crucial, but remains a long-standing challenge. Herein, we present a two-dimensional orthogonal fluorescence and chemiluminescence design strategy for the probe DCM-SA, which is sequentially activated by albumin-mediated hydrolysis, exhibiting light-up fluorescence and photo-induced cycloaddition generating chemiluminescence, enabling orthogonal signal amplification for discrimination of subtle differences between similar proteins. By orthogonalizing these dual-mode signals, a two-dimensional work curve of fluorescence and chemiluminescence is established to distinguish and quantify similar proteins HSA and BSA. Importantly, the dual-mode signals of DCM-SA exhibit contrary incremental trends towards HSA and BSA. Molecular docking and femtosecond transient absorbance spectroscopy reveal that the lower K D value of DCM-SA with HSA and the longer excited-state lifetime of DCM-SA with BSA underlie the distinct dual-mode responses. Using two-dimensional orthogonal signals, for the first time, we precisely measure the HSA/BSA ratio in mixed serum. This method facilitates rapid blood source identification and trace HSA quantitation in human urine. Our two-dimensional orthogonal amplification approach offers a powerful tool for distinguishing and quantifying subtle differences among highly similar proteins, demonstrating great potential for both basic life science research and clinical applications.

Visualizing DNA/RNA, Proteins, and Small Molecule Metabolites within Live Cells

Live cell imaging is essential for obtaining spatial and temporal insights into dynamic molecular events within heterogeneous individual cells, in situ intracellular networks, and in vivo organisms. Molecular tracking in live cells is also a critical and general requirement for studying dynamic physiological processes in cell biology, cancer, developmental biology, and neuroscience. Alongside this context, this review provides a comprehensive overview of recent research progress in live-cell imaging of RNAs, DNAs, proteins, and small-molecule metabolites, as well as their applications in molecular diagnosis, immunodiagnosis, and biochemical diagnosis. A series of advanced live-cell imaging techniques have been introduced and summarized, including high-precision live-cell imaging, high-resolution imaging, low-abundance imaging, multidimensional imaging, multipath imaging, rapid imaging, and computationally driven live-cell imaging methods, all of which offer valuable insights for disease prevention, diagnosis, and treatment. This review article also addresses the current challenges, potential solutions, and future development prospects in this field.

The investigation of the interaction between fluorescent carbon dots labeling silk fibroin using a fluorescence microscope-surface plasmon resonance system

The use of fluorescent carbon dots (CDs) as highly precise biolabeling probes has been widespread in the fields of live cell imaging and protein labeling due to their small size and excellent photoluminescence ability to accurately target specific molecules with surface chemical properties. However, there was a lack of research on the interaction between CDs and labeled molecules. In this work, we presented a novel investigation strategy, the fluorescence microscopy-surface plasmon resonance (FM-SPR) system, which combined the use of fluorescence microscopy and wavelength modulation surface plasmon resonance to study the interaction between CDs and labeled molecules in real-time. Using this system, simultaneously recorded the SPR signals and the fluorescence images on the surface of the FM-SPR sensor chip. We observed the dynamic curve and fluorescence images of the interaction between green emissive nitrogen-doped carbon dots (N-CDs) and silk fibroin (SF) in real-time. The kinetic parameters, the quantitative analysis, and the investigation of the binding could be achieved. The results showed a strong linear relationship between the change in SPR signals and the concentration of N-CDs, with a linear coefficient of 0.99913. The linear detection range was 2.5 μg/mL-100 μg/mL, and the real lowest detection limit reached 0.5 μg/mL. Additionally, the green fluorescence points in the imaging region on the FM-SPR sensor chip increased with the concentration of N-CDs, which was consistent with the change in SPR signals. Using this system we also acquired the association rate and dissociation rate of N-CDs to SF which were 2.65 × 10-5/s and 1.52 × 10-5/s, respectively. This demonstrated the effectiveness of our method in quantitatively analyzing SF labeled with N-CDs.

Negatively Charged Carbon Dots Employed Symplastic and Apoplastic Pathways to Enable Better Plant Delivery than Positively Charged Carbon Dots

Efficient delivery of nanoparticles (NPs) to plants is important for agricultural application. However, to date, we still lack knowledge about how NPs' charge matters for its translocation pathway, i.e., symplastic and apoplastic pathways, in plants. In this study, we synthesized and used negatively charged citrate sourced carbon dots (C-CDs, -37.97 ± 1.89 mV), Cy5 coated C-CDs (Cy5-C-CDs, -41.90 ± 2.55 mV), positively charged PEI coated carbon dots (P-CDs, +43.03 ± 1.71 mV), and Cy5 coated P-CDs (Cy5-P-CDs, +48.80 ± 1.21 mV) to investigate the role of surface charges and coatings on the employed translocation pathways (symplastic and apoplastic pathways) of charged NPs in plants. Our results showed that, different from the higher fluorescence intensity of P-CDs and Cy5-P-CDs in extracellular than intracellular space, the fluorescence intensity of C-CDs and Cy5-C-CDs was similar between intracellular and extracellular space in cucumber and cotton roots. It suggests that the negatively charged CDs were translocated via both symplastic and apoplastic pathways, but the positively charged CDs were mainly translocated via the apoplastic pathway. Furthermore, our results showed that root applied negatively charged C-CDs demonstrated higher leaf fluorescence than did positively charged P-CDs in both cucumber (8.09 ± 0.99 vs 3.75 ± 0.23) and cotton (7.27 ± 1.06 vs 3.23 ± 0.22), indicating that negatively charged CDs have a higher translocation efficiency from root to leaf than do positively charged CDs. It should be noted that CDs do not affect root cell activities, ROS level, and photosynthetic performance in cucumber and cotton, showing its good biocompatibility. Overall, this study not only figured out that root applied negatively charged CDs employed both symplastic and apoplastic pathways to do the transportation in roots compared with mainly the employment of apoplastic pathway for positively charge CDs, but also found that negatively charge CDs could be more efficiently translocated from root to leaf than positively charged CDs, indicating that imparting negative charge to NPs, at least CDs, matters for its efficient delivery in crops.

Metal-detection based techniques and their applications in metallobiology

Metals are essential for human health and play a crucial role in numerous biological processes and pathways. Gaining a deeper insight into these biological events will facilitate novel strategies for disease prevention, early detection, and personalized treatment. In recent years, there has been significant progress in the development of metal-detection based techniques from single cell metallome and proteome profiling to multiplex imaging, which greatly enhance our comprehension of the intricate roles played by metals in complex biological systems. This perspective summarizes the recent progress in advanced metal-detection based techniques and highlights successful applications in elucidating the roles of metals in biology and medicine. Technologies including machine learning that couple with single-cell analysis such as mass cytometry and their application in metallobiology, cancer biology and immunology are also emphasized. Finally, we provide insights into future prospects and challenges involved in metal-detection based techniques, with the aim of inspiring further methodological advancements and applications that are accessible to chemists, biologists, and clinicians.

Integrating aptasensor with an explosive mass-tag signal amplification strategy for ultrasensitive and multiplexed analysis using a miniature mass spectrometer

Mass probes attached with aptamers and mass tags offer excellent specificity and sensitivity for multiplexed detection, wherein the dissociation of mass tags from the mass probes is as important as their labeling. Herein, aggregation-induced emission luminogen (AIEgen)-tagged mass probes (AIEMPs) were established to analyze estrogens, which integrated aptasensor with an explosive mass-tag signal amplification strategy via a simple ultrasound-assisted emulsification of nanoliposomes. The AIEMPs were assembled by the hybridization of aptamer-modified Fe3O4 nanoparticles (Fe NPs@Apt) and nanoliposomes loaded with massive AIEgen mass tags and partially complementary DNA strands (AIE NLs@cDNA). The aptamer was preferentially and specifically bound to estrogen, resulting in the detachment of AIE NLs from AIEMPs. Subsequently, the AIEMPs were deposited with electrospray solvents for explosive release of mass tags. Using nanoelectrospray ionization mass spectrometry (nanoESI-MS), the AIEMP-based aptasensor achieved ultrasensitive analysis of estrogens with limits of detection of 0.168-0.543 pg/mL and accuracies in the range of 87.9-114.0%. Compared to direct nanoESI-MS detection, the AIEMP-based aptasensor provides a signal amplification of four orders of magnitude. Furthermore, the utilization of different AIEMPs enables multiplexed detection of three estrogens with a miniature mass spectrometer, showing promising potential for on-site detection. This work expands the diversity of mass-tagging strategy and provides a versatile mass probe-based aptasensor platform for routine MS detection of trace analytes.

Platinum-Chimeric Carrier Cells for Ultratrace Cell Analysis in Mass Cytometry

Mass cytometry by time-of-flight (CyTOF), a high-dimensional single-cell analysis platform, detects up to 50 biomarkers at single-cell resolution. However, CyTOF analysis of biological samples with a minimal number of available cells or rare cell subsets remains a major technical challenge due to the extensive loss of cells during cell recovery, staining, and acquisition. Here, we introduce a platinum-chimeric carrier cell strategy for mass cytometry profiling of ultratrace cell samples. Cisplatin can rapidly enter broken plasma membranes of dead cells and form a chimeric interaction with cellular proteins, peptides, and amino acids. Thus, 198Pt-cisplatin is adopted to tag carrier cells in the pretreatment stage. We investigated 8 cell lines that are commonly accessible in laboratories for their potential as carrier cells to preserve rare target cells for CyTOF analysis. We designed a panel of 35 protein biomarkers to evaluate the comprehensive single-cell subtype classification capability with or without the carrier cell strategy. We further demonstrated the detection and analysis of as few as 1 × 104 immune cells using our method. The proposed method thus allows CyTOF analysis on precious clinical samples with less abundant cells.

A universal mass tag based on polystyrene nanoparticles for single-cell multiplexing with mass cytometry

Mass cytometry (MC) is an emerging bioanalytical technique for high-dimensional biomarkers interrogation simultaneously on individual cells. However, the sensitivity and multiplexed analysis ability of MC was highly restricted by the current metal chelating polymer (MCP) mass tags. Herein, a new design strategy for MC mass tags by using a commercial available and low cost classical material, polystyrene nanoparticle (PS-NP) to carry metals was reported. Unlike inorganic materials, sub-micron-grade metal-loaded polystyrene can be easily detected by MC, thus it is not essential to pursue extremely small particle size in this mass tag design strategy. An altered cell staining buffer can significantly lower the nonspecific binding (NSB) of non-functionalized PS-NPs, revealing another method to lower NSB beside surface modification. The metal doped PS-NP_Abs mass tags showed high compatibility with MCP mass tags and 5-fold higher sensitivity. By using Hf doped PS-NP_Abs as mass tags, four new MC detection channels (¹⁷⁷Hf, ¹⁷⁸Hf, ¹⁷⁹Hf and ¹⁸⁰Hf) were developed. In general, this work provides a new strategy in designing MC mass tags and lowering NSB, opening up possibility of introducing more potential MC mass tag candidates.

Recent progress of emitting long-wavelength carbon dots and their merits for visualization tracking, target delivery and theranostics

As a novel strategy for in vivo visualization tracking and monitoring, carbon dots (CDs) emitting long wavelengths (LW, 600-950 nm) have received tremendous attention due to their deep tissue penetration, low photon scattering, satisfactory contrast resolution and high signal-to-background ratios. Although, the mechanism of CDs emitting LW remains controversial and what properties are best for in vivo visualization have not been specifically elucidated, it is more conducive to the in vivo application of LW-CDs through rational design and ingenious synthesis based on the appreciation of the luminescence mechanism. Therefore, this review analyzes the current tracer technologies applied in vivo and their advantages and disadvantages, with emphasis on the physical mechanism of emitting LW fluorescence for in vivo imaging. Subsequently, the general properties and merits of LW-CDs for tracking and imaging are summarized. More importantly, the factors affecting the synthesis of LW-CDs and its luminescence mechanism are highlighted. Simultaneously, the application of LW-CDs for disease diagnosis, integration of diagnosis and therapy are summarized. Finally, the bottlenecks and possible future directions of LW-CDs in visualization tracking and imaging in vivo are detailly discussed.

Nucleolin recognizing silica nanoparticles inhibit cell proliferation by activating the Bax/Bcl-2/caspase-3 signalling pathway to induce apoptosis in liver cancer

Multifunctional nanocarrier platforms have shown great potential for the diagnosis and treatment of liver cancer. Here, a novel nucleolin-responsive nanoparticle platform was constructed for the concurrent detection of nucleolin and treatment of liver cancer. The incorporation of AS1411 aptamer, icaritin (ICT) and FITC into mesoporous silica nanoparticles, labelled as Atp-MSN (ICT@FITC) NPs, was the key to offer functionalities. The specific combination of the target nucleolin and AS1411 aptamer caused AS1411 to separate from mesoporous silica nanoparticles surface, allowing FITC and ICT to be released. Subsequently, nucleolin could be detected by monitoring the fluorescence intensity. In addition, Atp-MSN (ICT@FITC) NPs can not only inhibit cell proliferation but also improve the level of ROS while activating the Bax/Bcl-2/caspase-3 signalling pathway to induce apoptosis in vitro and in vivo. Moreover, our results demonstrated that Atp-MSN (ICT@FITC) NPs had low toxicity and could induce CD3⁺ T-cell infiltration. As a result, Atp-MSN (ICT@FITC) NPs may provide a reliable and secure platform for the simultaneous identification and treatment of liver cancer.

Reagents for Mass Cytometry

Mass cytometry (cytometry by time-of-flight detection [CyTOF]) is a bioanalytical technique that enables the identification and quantification of diverse features of cellular systems with single-cell resolution. In suspension mass cytometry, cells are stained with stable heavy-atom isotope-tagged reagents, and then the cells are nebulized into an inductively coupled plasma time-of-flight mass spectrometry (ICP-TOF-MS) instrument. In imaging mass cytometry, a pulsed laser is used to ablate ca. 1 μm² spots of a tissue section. The plume is then transferred to the CyTOF, generating an image of biomarker expression. Similar measurements are possible with multiplexed ion bean imaging (MIBI). The unit mass resolution of the ICP-TOF-MS detector allows for multiparametric analysis of (in principle) up to 130 different parameters. Currently available reagents, however, allow simultaneous measurement of up to 50 biomarkers. As new reagents are developed, the scope of information that can be obtained by mass cytometry continues to increase, particularly due to the development of new small molecule reagents which enable monitoring of active biochemistry at the cellular level. This review summarizes the history and current state of mass cytometry reagent development and elaborates on areas where there is a need for new reagents. Additionally, this review provides guidelines on how new reagents should be tested and how the data should be presented to make them most meaningful to the mass cytometry user community.

Dual-emission carbon dots for sensitive fluorescence detection of metal ions and ethanol in water

Carbon dots (CDs) have been widely used in biomedical fields because of their superior optical properties, high sensitivity and high selectivity to specific substances. However, there are few studies on trace detection of the ethanol content in aqueous solution using CDs. Herein, novel red fluorescent CDs with dual emission are synthesized and show good dispersibility in various solvents and excitation independence of photoluminescence (PL). After investigating the structure and properties of the red CDs, a multifunctional fluorescent nanoprobe based on the red CDs with high-sensitivity detection for dual-ion trace detection of Fe³⁺ and Cu²⁺ can be successfully constructed. The limit of detection of Fe³⁺ and Cu²⁺ can be up to 0.024 μM and 0.036 μM, respectively, which is superior to that in previous reports. Meanwhile, in view of the specific solvent effect on their PL, the red CDs are able to be applied for trace detection of the ethanol content in aqueous solution. The methods of colorimetry and fluorescence spectrometry are utilized to perform the threshold test and high-sensitivity quantitative analysis of the ethanol content in aqueous solution. Based on this, a multifunctional fluorescent nanoprobe based on the dual-emission red CDs can be obtained, which provides a promising way for their applications in detection and sensing fields.

Regulation of multi-color fluorescence of carbonized polymer dots by multiple contributions of effective conjugate size, surface state, and molecular fluorescence

Fluorescent carbon dots (CDs)-based nanomaterials exhibited promising potential in the fields of biomedicine, bioanalysis, and biosensors. In this work, multi-colored fluorescent carbonized polymer dots (CPDs) ranging from blue to red are obtained using different synthesis methods using citric acid and urea as raw materials, and the controllable synthesis of CPDs with multi-color fluorescence is successfully realized. Then, the photoluminescence (PL) mechanism of CPDs is studied using multiple characterization methods, and the key factors affecting the fluorescence emission wavelength of CPDs are discussed. It is shown that the fluorescence of the CPDs originates from three main components: the carbon nuclei in the intrinsic state, the functional groups in the surface state, and the molecular fluorophores adsorbed on the surface of the CPDs. The reaction temperature and reaction time affect the effective conjugation size of the carbon nuclei, which in turn affects the fluorescence redshift of CPDs; the reaction solvent greatly alters the surface state of CPDs (e.g. surface defects and functional groups), which leads to a significant redshift in the fluorescence of CPDs; the presence of molecular fluorophores facilitates the fluorescence redshift of CPDs. Finally, we have successfully applied the prepared red fluorescent CPDs for in vitro cell imaging. The study on the color regulation mechanism of CPDs is of great significance for the controllable preparation of high-performance fluorescent CDs and their application in the field of biomedicine.

One-pot green preparation of deep-ultraviolet and dual-emission carbon nanodots for dual-channel ratiometric determination of polyphenol in tea sample

A novel deep-ultraviolet and dual-emission carbon nanodots (DUCDs)-based dual-channel ratiometric probe was prepared by a one-pot environmental-friendly hydrothermal process using guanidine as the only starting material for sensing polyphenol in tea sample (TPPs). Under the exposure to TPPs, the DUCDs not only provided a characteristic colorimetric response to TPPs, but also displayed TPPs-sensitive ratiometric fluorescence quenching. The detection mechanism was proved to be that enrichment-specific hydroxyl sites (e.g., -NH₂ and -COOH) of DUCDs can specifically react with phenolic hydroxyl groups of TPPs to generate dynamic amide and carboxylate bonds by dehydration and/or condensation reaction. As a result, a new carbon nanomaterial with decrement of surface passivation groups, inherent light-absorbing, and invalid fluorescence emission was generated. The ratio (FL_297nm/FL_395nm) of fluorescence intensity at 297 nm and 395 nm of DUCDs excited at 275 nm decreased with increasing TPPs concentration. The linearity range was 5.0 ng/mL to 100 µg/mL with a detection limit (DL) of 3.5 ± 0.04 ng/mL for TPPs (n = 3, 3σ/k). Colorimetry of DUCDs, best measured as absorbance at 320 nm, was increased linearly in the TPP concentration range 200 ng/mL-200 µg/mL with a DL of 94.7 ± 0.04 ng/mL (n = 3, 3σ/k). The probe was successfully applied to the determination of TPPs in real tea samples, showing potential application prospects in food analysis.