Dual-Modal Apoptosis Assay Enabling Dynamic Visualization of ATP and Reactive Oxygen Species in Living Cells

Simply Designed and Universal DNA Nanohydrogel for Stimuli-Responsive NIR-II Fluorescence Imaging of Early-Stage Tumor

The delayed detection and recurrence of cancer lead to disappointing cure rates, underscoring the imperative for exploring precise early tumor diagnosis techniques. Despite the superior biocompatibility and flexible programmability of DNA nanoprobes for tumor imaging, intricate designs with multiple oligonucleotide sequences are always indispensable, which significantly hinder their clinical application and commercial development. To construct a simply designed DNA nanoprobe, here, we constructed a universal stimuli-responsive nanohydrogel through the hybridization of the staple strand and skeleton strand. Through a simple substitution of the staple strand, this hydrogel can be adapted for the response to different targets without necessitating a series of subsequent revisions and synthesis optimization. To achieve near-infrared II region (NIR-II) fluorescence imaging, alkynyl-modified NIR-II fluorescent dyes are labeled at two ends of bent staple strands and display weak fluorescence because of the aggregation-caused quenching effect. The highly expressed ATP or cytokine in tumor cells activates the liberation of staples and collapse of the bent configuration, which generates fluorescence recovery for tumor imaging. Moreover, this nanohydrogel also allows for the targeted release of anticancer drugs intercalated in the DNA helix. By integration of NIR-II fluorescent dyes, this versatile nanohydrogel enables precise diagnosis and treatment of early tumors. The straightforward design demonstrates low cost and easy adaptability for multitarget detection, highlighting its significant implications for the advancement of DNA nanotechnology in clinical application and commercialization production.

A Fluorescence-SERS Dual-Mode Nanoprobe for Imaging of HSP90 mRNA and Peroxynitrite in Living Cells

The dysregulation of heat shock protein 90 mRNA (HSP90 mRNA) and reactive oxygen species (ROS) is implicated in stress response and various diseases. Visualizing HSP90 mRNA and ROS dynamics is important to studying their interactions and related physiopathological mechanisms. However, effective methods for detecting both remain lacking. Herein, a covalent organic framework-based (COF-based) dual-mode nanoprobe is designed to monitor HSP90 mRNA and ONOO- (ROS model). The nanoprobe is prepared by in situ assembly of a COF shell as the aptamer carrier on the gold nanorods (AuNRs), followed by conjugation of the ONOO--responsive molecule, 4-mercaptophenylboronic acid (4-MPBA), to the AuNRs and modification of the HSP90 mRNA aptamer (HSP90MB) onto the COF shell. The prepared nanoprobe enables sensitive and selective fluorescence (FL) and surface-enhanced Raman spectroscopy (SERS) detection of HSP90 mRNA and ONOO-, respectively. The dual-channel detection highlights the advantages of facilitating spectral analysis and eliminating mutual interference. In addition, the proposed strategy visualizes a positive interaction between HSP90 mRNA and ONOO- in living cells, revealing their cellular response mechanism under stress conditions and related diseases.

Hydrophobic SERS substrate for PFOA sensing and cooperative adsorption

The widespread use of perfluorinated organic compounds (PFOA) has posed significant threats to ecosystems and biological health. This study investigates a fluorinated metal-organic framework (F-MOF) for highly sensitive SERS detection and efficient adsorption of PFOA in aqueous environments. Au@MIL-4F, synthesized via a mild thermochemical method using tetrafluoroterephthalic acid and iron (Ⅲ), exhibits exceptional selectivity and sensitivity toward PFOA, achieving a broad detection range with a remarkably low detection limit of 38 pM. The SERS sensor demonstrates excellent reproducibility and stability. Furthermore, adsorption kinetics and thermodynamic studies reveal a maximum adsorption capacity of 254.25 mg/g for PFOA on Au@MIL-4F. The adsorption mechanism, elucidated through spectroscopic and structural analyses, provides critical theoretical insights for developing dual-functional systems that integrate detection and adsorption capabilities. This work not only advances material design for environmental remediation but also offers a practical strategy to address PFOA contamination with precision and sustainability.

Multifunctional Fluorescent Probe for Simultaneous Detection of ATP, Cys, Hcy, and GSH: Advancing Insights into Epilepsy and Liver Injury

Adenosine triphosphate (ATP) is a critical intracellular energy currency that plays a key role in various cellular processes and is closely associated with numerous diseases. Similarly, biothiols such as glutathione (GSH), cysteine (Cys), and homocysteine (Hcy) are integral to many physiological and pathological processes due to their strong redox properties. Simultaneous discrimination and detection of ATP and biothiols offer valuable insights into the pathogenesis of conditions such as epilepsy and liver injury. This study introduces the first fluorescent probe, BCR, designed for multifunctional detection of ATP, GSH, Hcy, and Cys. With outstanding optical properties, excellent biocompatibility, high selectivity, and superior sensitivity, probe BCR enables effective imaging of ATP and biothiol dynamics in vivo. Moreover, probe BCR successfully visualizes changes in ATP, GSH, Hcy, and Cys levels in a PTZ-induced epileptic zebrafish model and an APAP-induced mouse liver injury tissue section model. These findings underscore the significant potential of probe BCR for early disease diagnosis and therapeutic applications.

Reduced glutathione enhances adipose tissue-derived mesenchymal stem cell engraftment efficiency for liver fibrosis by targeting TGFβ1/SMAD3/NOX4 pathway

Reduced glutathione (GSH) could reduce oxidative stress to improve adipose tissue-derived mesenchymal stem cell (ADSC) engraftment efficiency in vivo. However, the underlying mechanisms remain unclear. Our goal is to investigate whether GSH enhances ADSC engraftment through targeting the TGFβ/SMAD3/NOX4 pathway. Liver fibrotic male mice were administrated GSH, setanaxib (STX), and SIS3 during ADSC transplantation. ADSC engraftment efficiency and reactive oxygen species (ROS) level were detected both in vivo and ex vivo. Biochemical analysis was used to analyze the content of superoxide and nicotinamide adenine dinucleotide phosphate oxidases (NOXs) in liver tissues. Immunohistochemistry and western blotting were used to examine the protein level of NOX1, NOX2, NOX4, transforming growth factor-β1 (TGFβ1), SMAD3, and p-SMAD3 in liver tissues. Additionally, the therapeutic efficacy of the ADSC transplantation was further investigated. We found that GSH significantly improved ADSC engraftment efficiency, which was closely related to the reduced ROS generation in liver tissues. However, the enhanced cell engraftment was abolished after the combined treatment with STX or SIS3. GSH could effectively reduce superoxide and NOXs content, and selectively inhibit NOX4 expression in liver tissues. The co-localization results showed that GSH could reduce NOX4 expressed in activated hepatic stellate cells. Mechanistically, GSH down-regulated TGFβ/SMAD3 signaling. More importantly, GSH enhanced the therapeutic efficacy of ADSC therapy in liver fibrotic mice. Taken together, GSH could improve the engraftment efficiency of ADSCs in liver fibrosis by targeting TGFβ1/SMAD3/NOX4 signaling pathway, which provides a new theoretical basis for GSH enhancing ADSC engraftment efficiency in liver diseases.

A chemically modified DNAzyme-based electrochemical sensor for binary and highly sensitive detection of reactive oxygen species

Reactive oxygen species (ROS) play a critical role in regulating various physiological processes. To gain a comprehensive understanding of their distinct functions in different physiological events, it is imperative to detect binary ROS simultaneously. However, the development of the sensing method capable of binary ROS detection remains a significant challenge. In this study, we address this challenge by integrating chemically modified DNAzyme probes with a functionalized metal-organic framework (MOF) to create an efficient electrochemical sensing platform for the binary detection of ROS. ROS targets would activate the DNAzyme cleavage activity by removing the phenylboronate (BO) and phosphorothioate (PS) modifications, leading to the controlled release of doxorubicin (DOX) and methylene blue (MB) enclosed within MOF nanocomposites. This process generates two distinct voltammetric current peaks, with their potentials and intensities reflecting the identity and concentration of the ROS targets. The sensor demonstrates simultaneous detection of multiple ROS (H2O2 and HClO) produced by cancer cells with high sensitivity across a broad linear range of 1 to 200 nM and a low detection limit in the sub-nanomolar range. The design strategies behind the developed ROS sensing system could also be exploited to create other biosensors with highly sensitive and binary detection to promote clinical research and revolutionize disease diagnostics.

Aqueous extract of Cornus officinalis alleviate NAFLD via protecting hepatocytes proliferation through regulation of the tricarboxylic acid cycle

ETHNOPHARMACOLOGICAL RELEVANCE

Cornus officinalis (CO) has been widely used as Chinese herbal medicine and has a good clinical efficacy in liver disease. In particular, it has a significant therapeutic effect on metabolic liver disease. However, systematic pharmacological studies on its hepatoprotective effect on non-alcoholic fatty liver disease (NAFLD) are lacking.

AIM OF THE STUDY

We investigated the impact of Cornus officinalis extract (COE) on two mouse models of NAFLD, screened the potential mechanisms of action by using metabolomics assays, and explored the protective effects on hepatocyte proliferation by regulating glutamate metabolism and tricarboxylic acid (TCA) cycle.

METHODS

The main components of COE were identified by high performance liquid chromatograph (HPLC). Male C57BL/6J mice were subjected to construct carbon tetrachloride (CCl4) or methionine choline deficient (MCD) induced NAFLD mice. Liver function and lipid biochemical indicators were detected using commercial assay kits. Masson staining, Western blot, and immunohistochemistry analyses were used for assessing hepatic injury and fibrosis. LC-MS non-targeted analysis was performed using the 1290 Ultra-High Performance Liquid Chromatograph System and the 6540 Q-TOF Mass Spectrometry. Palmitic acid (PA) induced L-02 cell model was established. The mediators in glutamate metabolism and TCA cycle were assessed by assay kits.

RESULTS

In vivo experiments validated that COE significantly improved liver function in NAFLD mice, reduced lipid accumulation, and alleviated pathological damage and liver fibrosis. The non-targeted metabolomics analysis combined with Ingenuity Pathway Analysis (IPA) located glutamate metabolism and the downstream TCA cycle as potential mechanisms of COE, which was further confirmed in NAFLD model mice and PA-induced L-02 cells. Finally, we confirmed that COE could promote mitochondrial energy supply by remodeling the homeostasis of the TCA cycle, thereby enhancing hepatocyte proliferation.

CONCLUSIONS

This study demonstrated that COE could significantly improve CCl4 or MCD-induced NAFLD by promoting hepatocyte proliferation. These results highlighted the potential of COE as leads for the development of innovative treatments for NAFLD.

Recent advances in fluorescent probes for ATP imaging

Adenosine-5'-triphosphate (ATP) is a critical biological molecule that functions as the primary energy currency within cells. ATP synthesis occurs in the mitochondria, and variations in its concentration can significantly influence mitochondrial and cellular performance. Prior studies have established a link between ATP levels and a variety of diseases, such as cancer, neurodegenerative conditions, ischemia, and hypoglycemia. Consequently, researchers have developed many fluorescent probes for ATP detection, recognizing the importance of monitoring intracellular ATP levels to understand cellular processes. These probes have been effectively utilized for visualizing ATP in living cells and biological samples. In this comprehensive review, we categorize fluorescent sensors developed in the last five years for ATP detection. We base our classification on fluorophores, structure, multi-response channels, and application. We also evaluate the challenges and potential for advancing new generations of fluorescence imaging probes for monitoring ATP in living cells. We hope this summary motivates researchers to design innovative and effective probes tailored to ATP sensing. We foresee imminent progress in the development of highly sophisticated ATP probes.

Metal-Organic Nanomaterials for Tumor Metabolic Blockade and Image to Increase Tumor Therapy

The abnormal energy metabolism level of a tumor reduces the efficiency of chemotherapy. Metal-organic nanomaterials (MONs) with high drug loading efficiency, easy processes of synthesis, and controlled drug release have shown great potential in metabolic blocking and enhancement of tumor therapy. These metal-organic nanomedicines have been reported to modulate glycolysis or oxidative phosphorylation to provide monotherapy or combined therapies in tumorous treatments. In addition, the encapsulation or coordination of fluorescent dyes into MONs endowed them with the imaging ability of tumor metabolism. Herein, this Perspective summarizes the progress of MONs as therapeutic agents or imaging probes for application during tumor metabolic blocking or imaging, providing solid inspiration for biomedical applications of effective biomaterials. In addition, the current drawbacks of MONs for further biological applications in the future were discussed, giving stimulation of innovation and development in biomedical applications of MONs.

Recent advances of MOF-based SERS substrates in quantitative analysis of food contaminants: a review

Advancements in food-contaminant detection technologies can significantly improve food safety and human health. Surface-enhanced Raman spectroscopy (SERS) has become the preferred analytical method for food-safety detection owing to its numerous advantages, which include unique 'molecular fingerprinting' features, high sensitivity, rapid responses, and non-invasive characteristics. Raman-signal enhancements rely heavily on high-performance SERS substrates. In recent years, metal-organic framework (MOF)-based SERS substrates have gained attention as promising candidates for developing SERS technologies owing to their distinctive structures and functions. This review comprehensively examines recent advances in MOF-based SERS substrates, focusing on the main role of MOFs in SERS substrates as well as their typical categories and structures, construction methods, and representative applications in food-contaminant detection. First, the primary roles of MOFs in SERS substrates are briefly introduced. Next, a comprehensive overview of the typical categories and structures of MOF-based SERS substrates is discussed. Subsequently, a fundamental view of the general construction methods for MOF-based SERS substrates is presented. Next, the main applications of MOF-based SERS substrates for food-contaminant detection are summarised. Finally, challenges and perspectives, including improvements in SERS performance and stability, and the unification of SERS mechanisms, are addressed and discussed.

The antisense lncRNA of TAB2 that prevents oxidative stress to enhance the follicular growth in mammals

LncRNAs are highly implicated in oxidative stress (OS) during the growth of mammalian follicles. TAK1 binding protein 2 gene (TAB2) has been suggested to involve in the normal apoptosis and proliferation of granulosa cells (GCs), the main supporting cells in ovarian follicles. In this study, we found that TAB2 increased the expressions of SOD1, P50, and P65 to suppress the OS, thereby inhibiting the apoptosis and promoting the proliferation in GCs. Notably, DNMTs appeared to mediate the expression of TAB2 without the changes of DNA methylation at TAB2's promoter. We identified an antisense lncRNA of TAB2, discovered that DNA methylation regulated the transcription of TAB2-AS in GCs, and found TAB2-AS medicated the follicular growth of ovaries in vivo. Mechanistically, the hypomethylation of the CpG site (-1759/-1760) activated the transcription of TAB2-AS, and the 1-155 nt and 156-241 nt of TAB2-AS were respectively complementary to 4368-4534 nt and 4215-4300 nt of TAB2's mRNA to increase the expression of TAB2. Moreover, TAB2-AS inhibited the OS and apoptosis of GCs, while promoted the proliferation of GCs to expedite the follicular growth, which was in line with that of TAB2. Collectively, these findings revealed the antisense lncRNA mechanism mediated by DNA methylation, and TAB2-AS might be the target to control OS during follicular growth in mammals.

High-Resolution and Dynamic Visualization of Intracellular Redox Potential Using a Metal-Organic Framework-Functionalized Nanopotentiometer

Redox potential plays a key role in regulating intracellular signaling pathways, with its quantitative analysis in individual cells benefiting our understanding of the underlying mechanism in the pathophysiological events. Here, a metal organic framework (MOF)-functionalized SERS nanopotentiometer has been developed for the dynamic monitoring of intracellular redox potential. The approach is based on the encapsulation of zirconium-based MOF (Uio-66-F4) on a surface of gold-silver nanorods (Au-Ag NRs) that is modified with the newly synthesized redox-sensitive probe ortho-mercaptohydroquinone (HQ). Thanks to size exclusion of MOF as the chemical protector, the nanopotentiometer can be adapted to long-term use and possess high anti-interference ability toward nonredox species. Combining the superior fingerprint identification of SERS with the electrochemical activity of the quinone/hydroquinone, the nanopotentiometer shows a reversible redox responsivity and can quantify redox potential with a relatively wide range of -250-100 mV. Furthermore, the nanopotentiometer allows for dynamic visualization of intracellular redox potential changes induced by drugs' stimulation in a high-resolution manner. The developed approach would be promising for offering new insights into the correlation between redox potential and tumor proliferation-involved processes such as oxidative stress and hypoxia.

Application of Aptamer-SERS Nanotags for Unveiling the PD-L1 Immunomarker Progression Correlated to the Cell Metabolic Bioprocess

In recent years, the expression and progression of programmed cell death ligand 1 (PD-L1) as an immunomarker in the context of a cell metabolic environment has gained significant attention in cancer research. However, intercellular bioprocesses that control the dynamics of PD-L1 have been largely unexplored. This study aimed to explore the cell metabolic states and conditions that govern dynamic variations of PD-L1 within the cell metabolic environment using an aptamer-based surface-enhanced Raman scattering (SERS) approach. The aptamer-SERS technique offers a sensitive, rapid, and powerful analytical tool for targeted and nondestructive detection of an immunomarker with high sensitivity and specificity. By combining aptamer-SERS with cell state profiling, we investigated the modulation in PD-L1 expression under different metabolic states, including glucose deprivation, metabolic coenzyme activity, and altered time/concentration-based cytokine availability. The most intriguing features in our findings include the cell-specific responses, cell differentiation by revealing distinct patterns, and dynamics of PD-L1 in different cell lines. Additionally, the time-dependent variations in PD-L1 expression, coupled with the dose-dependent relationship between glucose concentration and PD-L1 levels, underscore the complex interplay between immune checkpoint regulation and cellular metabolism. Therefore, this work demonstrates the advantages of using highly-sensitive and specific aptamer-SERS nanotags for investigating the immune checkpoint dynamics and related metabolic bioprocess.

Engineered aptamers for molecular imaging

Molecular imaging, including quantification and molecular interaction studies, plays a crucial role in visualizing and analysing molecular events occurring within cells or organisms, thus facilitating the understanding of biological processes. Moreover, molecular imaging offers promising applications for early disease diagnosis and therapeutic evaluation. Aptamers are oligonucleotides that can recognize targets with a high affinity and specificity by folding themselves into various three-dimensional structures, thus serving as ideal molecular recognition elements in molecular imaging. This review summarizes the commonly employed aptamers in molecular imaging and outlines the prevalent design approaches for their applications. Furthermore, it highlights the successful application of aptamers to a wide range of targets and imaging modalities. Finally, the review concludes with a forward-looking perspective on future advancements in aptamer-based molecular imaging.

Nanoporous Crystalline Materials for the Recognition and Applications of Nucleic Acids

Nucleic acid plays a crucial role in countless biological processes. Hence, there is great interest in its detection and analysis in various fields from chemistry, biology, to medicine. Nanoporous crystalline materials exhibit enormous potential as an effective platform for nucleic acid recognition and application. These materials have highly ordered and uniform pore structures, as well as adjustable surface chemistry and pore size, making them good carriers for nucleic acid extraction, detection, and delivery. In this review, the latest developments in nanoporous crystalline materials, including metal organic frameworks (MOFs), covalent organic frameworks (COFs), and supramolecular organic frameworks (SOFs) for nucleic acid recognition and applications are discussed. Different strategies for functionalizing these materials are explored to specifically identify nucleic acid targets. Their applications in selective separation and detection of nucleic acids are highlighted. They can also be used as DNA/RNA sensors, gene delivery agents, host DNAzymes, and in DNA-based computing. Other applications include catalysis, data storage, and biomimetics. The development of novel nanoporous crystalline materials with enhanced biocompatibility has opened up new avenues in the fields of nucleic acid analysis and therapy, paving the way for the development of sensitive, selective, and cost-effective diagnostic and therapeutic tools with widespread applications.

Universal Near-Infrared Fluorescent Nanoprobes for Detection and Real-Time Imaging of ATP in Real Food Samples, Living Cells, and Bacteria

Adenosine triphosphate (ATP), an essential metabolite for active microorganisms to maintain life activities, has been widely regarded as a marker of cell activity and an indicator of microbial contamination. Herein, we designed two near-infrared (NIR) fluorescent nanoprobes named CYA@ZIF-90 and CYQ@ZIF-90 by encapsulating the NIR dye CYA/CYQ in ZIF-90 for the rapid detection of ATP. Between them, nanoprobe CYA@ZIF-90 can achieve higher NIR emission (702 nm) and rapid detection (2 min). Based on the superior spatiotemporal resolution imaging of ATP fluctuations in living cells, the applicability of CYA@ZIF-90 for imaging and detection of ATP in living bacteria was explored for the first time. The nanoprobe indirectly realizes the quantitative detection of bacteria, and the detection limit can be as low as 74 CFU mL-1. Therefore, the prepared nanoprobe is expected to become a universal ATP sensing detection tool, which can be further applied to evaluate cell apoptosis, cell proliferation, and food-harmful microbial control.

ATP-triggered highly sensitive probes for super-resolution mitochondrial imaging and low-dose bioimaging

Adenosine triphosphate (ATP), mainly produced in mitochondria, plays an important role in various pathological processes such as inflammation and acute liver injury. Fluorescence imaging is a powerful tool for imaging tissue structure and function in vivo. To date, the lack of biocompatible ATP probes with bright fluorescence emission has hindered their application in basic research and clinical trials. Here, we report a method for preparing ATP probes using a ZIF-90 potting dye, which produces bright ATP probes by encapsulating a modified high fluorescence quantum yield dye into a ZIF-90 skeleton. The nanoprobe does not fluoresce due to the coating. ATP can cooperate with Zn²⁺ to decompose the nanoprobe structure, release the dye and restore the fluorescence. Both nanoprobes ORhBSO₂@ZIF-90 and SiRhBSO₂@ZIF-90 showed higher sensitivity than the reported ATP nanoprobes with detection limits of 7.56 μM and 6.6 μM, and with lower doses (10 μg mL^-1) of probes for cell imaging. In addition, SiRhBSO₂@ZIF-90 has also been successfully used in the liver injury model. The ZIF-90 encapsulation strategy can retain the high fluorescence quantum yield and improve the biocompatibility of the dye.

Machine Learning-Based Label-Free SERS Profiling of Exosomes for Accurate Fuzzy Diagnosis of Cancer and Dynamic Monitoring of Drug Therapeutic Processes

Exosomes are a class of extracellular vesicles secreted by cells, which can be used as promising noninvasive biomarkers for the early diagnosis and treatment of diseases, especially cancer. However, due to the heterogeneity of exosomes, it remains a grand challenge to distinguish accurately and reliably exosomes from clinical samples. Herein, we achieve accurate fuzzy discrimination of exosomes from human serum samples for accurate diagnosis of breast cancer and cervical cancer through machine learning-based label-free surface-enhanced Raman spectroscopy (SERS), by using "hot spot" rich 3D plasmonic AuNPs nanomembranes as substrates. Due to the existence of some weak distinguishable SERS fingerprint signals and the high sensitivity of the method, the machine learning-based SERS analysis can precisely identify three (normal and cancerous) cell lines, two of which are different types of cancer cells, without specific labeling of biomarkers. The prediction accuracy based on the machine learning algorithm was up to 91.1% for the discrimination of different cell lines (H8, HeLa, and MCF-7 cell)-derived exosomes. Our model trained with SERS spectra of cell-derived exosomes could reach 93.3% prediction accuracy for clinical samples. Furthermore, the action mechanism of the chemotherapeutic process of MCF-7 cells can be revealed by dynamic monitoring of SERS profiling of the exosomes secreted. The method would be useful for noninvasive and accurate diagnosis and postoperative assessment of cancer or other diseases in the future.