Poly(vinylpyrrolidone)-Enhanced CRISPR-Cas System for Robust Nucleic Acid Diagnostics.

Clustered regularly interspaced short palindromic repeats (CRISPR) technology has opened a new path for molecular diagnostics based on RNA programmed trans-cleavage activity. However, their accessibility for highly sensitive clinical diagnostics remains insufficient. In this study, we systematically investigated the impact of various surfactants on the CRISPR-Cas12a system and found that poly(vinylpyrrolidone) (PVP), a nonionic surfactant, showed the highest enhancement effect among these tested surfactants. Additionally, the enhancement effects of PVP are compatible and versatile to CRISPR-Cas12b and Cas13a systems, improving the sensitivity of these CRISPR-Cas systems toward synthetic targets by 1-2 orders of magnitude. By integrating the PVP-enhanced CRISPR system with isothermal nucleic acid amplification, both the two- and one-step assays exhibited comparable sensitivity and specificity to gold-standard quantitative polymerase chain reaction (qPCR) in the assay of clinical human papillomavirus (HPV) samples, thereby holding significant promise for advancing clinical diagnostics and biomedical research.

Fabrication of a Near-Infrared-Emissive Probe for Detecting Dipeptidyl Peptidase 4 in the Liver of Diabetic Mice and Clinical Serum.

Dipeptidyl peptidase 4 (DPP4) plays a key role in glucose metabolism, which has been a close target for diabetes pathology and treatment. It is significant for the evaluation of cellular DPP4 activity in various biological systems. Fluorescence imaging technology is currently a popular method for detecting enzymes in living cells due to its advantages of high selectivity, high sensitivity, high spatiotemporal resolution, and real-time visualization. Herein, a near-infrared (NIR)-emissive probe NEDP with a large Stokes shift (153 nm) was developed for the assay of DPP4 activity. Upon addition of DPP4, NEDP can emit a significant turn-on NIR fluorescence signal (673 nm) with high sensitivity and specificity. Moreover, NEDP can successfully be used for imaging of intracellular DPP4, confirming the regulation of DPP4 expression in hyperglucose and its treatment in living cells. Most importantly, NEDP can not only monitor the changes of DPP4 in vivo but also show that DPP4 in diabetes is mainly up-regulated in the liver, and the level of DPP4 is positively correlated with the pathological damage of the liver. In addition, NEDP can identify the serum of diabetic patients from healthy people through the fluorescence response to DPP4. These results demonstrated that the designed probe NEDP provides a prospective visual tool to explore the relationship between DPP4 and diabetes and would be applied for detecting serum of diabetes in the clinic.

Tight focusing through scattering media via a Bessel-basis transmission matrix.

The transmission matrix (TM) is a powerful tool for focusing light through scattering media. Here, we demonstrate a Bessel-basis TM that enables tight focusing through the scattering media and reduces the full width at half maximum of the focus by 23% on average, as compared to the normally used Hadamard-basis TM. To measure the Bessel-basis TM, we establish a common-path inter-mode interferometer (IMI), which can fully utilize the pixels of the spatial light modulator, leading to an enhancement in the peak-to-background intensity ratio (PBR) of the focus. Experimental results suggest that the Bessel-basis TM can achieve a tighter focus behind the scattering media, and the PBR of the focus obtained by the IMI is around 14.3% higher than that achieved using the normal peripheral reference interferometry.

3D spheroid HepaRG and fluorescent biphasic tracer for CYP3A4-mediated antibiotic interaction monitoring in sepsis.

Cytochrome P450 3A4 (CYP3A4) is a crucial enzyme in the metabolism of xenobiotics, particularly in drug metabolism interactions (DDIs), making it a significant factor in clinical drug use. However, current assay techniques are both laborious and costly, making it difficult to construct a high-throughput monitoring method that can be used in conjunction with the clinic. This poses certain safety hazards for drug combination. Therefore, it is crucial to develop a synchronized monitoring method for the inhibition and induction of CYP3A4. In this study, we utilized 3D culture technology to develop a HepaRG cells spheroid model. The CYP450 and transporter expression, the albumin secretion, and urea synthesis capacity characteristics were analyzed. The NEN probe was utilized as a tracer molecule for CYP3A4. The fluorescence intensity of metabolites was characterized by laser confocal technique to determine the inhibition and expression of CYP3A4 in the HepaRG cell spheroid model by the antibiotics for sepsis. The results indicate that the HepaRG sphere model successfully possessed the physiological phenotype of the liver, which could be used for drug interaction monitoring. Through positive drug testing, NEN probe was able to achieve bidirectional characterization of CYP3A4 induction and inhibition. The monitoring method described in this paper was successfully applied to drug interaction monitoring of commonly used antibiotics in sepsis patients, which is a convenient and rapid monitoring method. The proposed method offers a new strategy for monitoring CYP3A4-mediated drug-drug interactions with a high-throughput assay, which will help to improve the safety of clinical drug combination.

Universal crRNA Acylation Strategy for Robust Photo-Initiated One-Pot CRISPR-Cas12a Nucleic Acid Diagnostics.

Spatiotemporal regulation of clustered regularly interspaced short palindromic repeats (CRISPR) system is attractive for precise gene editing and accurate molecular diagnosis. Although many efforts have been made, versatile and efficient strategies to control CRISPR system are still desirable. Here, we proposed a universal and accessible acylation strategy to regulate the CRISPR-Cas12a system by efficient acylation of 2'-hydroxyls (2'-OH) on crRNA strand with photolabile agents (PLGs). The introduction of PLGs confers efficient suppression of crRNA function and rapid restoration of CRISPR-Cas12a reaction upon short light exposure regardless of crRNA sequences. Based on this strategy, we constructed a universal PhotO-Initiated CRISPR-Cas12a system for Robust One-pot Testing (POIROT) platform integrated with recombinase polymerase amplification (RPA), which showed two orders of magnitude more sensitive than the conventional one-step assay and comparable to the two-step assay. For clinical sample testing, POIROT achieved high-efficiency detection performance comparable to the gold-standard quantitative PCR (qPCR) in sensitivity and specificity, but faster than the qPCR method. Overall, we believe the proposed strategy will promote the development of many other universal photo-controlled CRISPR technologies for one-pot assay, and even expand applications in the fields of controllable CRISPR-based genomic editing, disease therapy, and cell imaging.

Enhancing the Selectivity of Leucine Aminopeptidase Near-Infrared Fluorescent Probes for Assisting in Surgical Tumor Resection.

Selective fluorescence imaging of analytes is a challenge for monitoring diseases as homologues interfere with the imaging agents. Leucine aminopeptidase (LAP), a kind of protease, is related to tumor pathogenesis. The known LAP fluorescent probes based on leucine recognition have limited selectivity. Herein, a selective t-butyl-alanine recognition unit for LAP through the ligand regulation strategy is prepared as a new near-infrared (NIR) fluorescent probe (DCM-LAP) having a large Stokes shift of 214 nm and a high sensitivity with a detection limit of 168 mU/L. DCM-LAP has an enhanced response toward LAP with NIR fluorescence at 656 nm based on intramolecular charge transfer. The probe is selective without being interfered with by biological enzymes including the aminopeptidase N (APN). DCM-LAP can image LAP activity in living cells. It can also visualize the cell invasion and migration processes. DCM-LAP is employed in the real-time imaging of LAP in tumor-bearing nude mice and guides in the accurate resection of breast tumors. It also distinguishes tumor tissues from normal with a high tumor-to-normal ratio (9.8). The DCM-LAP probe can thus assist in the investigations of LAP-associated clinical disease.

Ultrasensitive CRISPR/Cas13a-Mediated Photoelectrochemical Biosensors for Specific and Direct Assay of miRNA-21.

Sensitive and specific assay of microRNAs (miRNAs) is beneficial to early disease screening. Herein, we for the first time proposed clustered regularly interspaced short palindromic repeats (CRISPR)/Cas13a-mediated photoelectrochemical biosensors for the direct assay of miRNA-21. In this study, compared with traditional nucleic acid-based signal amplification strategies, the CRISPR/Cas13a system can greatly improve the specificity and sensitivity of target determination due to its accurate recognition and high-efficient trans-cleavage capability without complex nucleic acid sequence design. Moreover, compared with the CRISPR/Cas12a-based biosensing platform, the developed CRISPR/Cas13a-mediated biosensor can directly detect RNA targets without signal transduction from RNA to DNA, thereby avoiding signal leakage and distortion. Generally, the proposed biosensor reveals excellent analysis capability with a wider linear range from 1 fM to 5 nM and a lower detection limit of 1 fM. Additionally, it also shows satisfactory stability in the detection of human serum samples and cell lysates, manifesting that it has great application prospects in the areas of early disease diagnosis and biomedical research.

Advances in Multifunctional Chemotherapeutic Prodrugs for Near-infrared Fluorescence Imaging-guided Therapy.

Conventional chemotherapy (CT) is associated with severe side effects and inducible resistance, making it difficult to meet clinical requirements, forcing the development of new multifunctional prodrugs for precision medicine. In recent decades, researchers and clinicians have focused on developing of multifunctional chemotherapeutic prodrugs with tumor-targeting capability, activatable and traceable chemotherapeutic activity, as a powerful tool to improve theranostic outcomes in cancer treatment. The conjugates of near-infrared (NIR) organic fluorophores and chemotherapy reagents create an exciting avenue for real-time monitoring of drug delivery and distribution, as well as the combination of chemotherapy and photodynamic therapy (PDT). Therefore, there are great opportunities for researchers to conceive and exploit multifunctional prodrugs that can visualize chemo-drugs release and tumor treatment in vivo. In this review, the design strategy and the recent progress of multifunctional organic chemotherapeutic prodrugs for activating NIR fluorescence imaging-guided therapy are described and discussed in detail. Finally, the prospects and challenges of multifunctional chemotherapeutic prodrugs for NIR fluorescence imaging-guided therapy are provided.

A NIR-emissive probe with a remarkable Stokes shift for CO-releasing molecule-3 detection in cells and in vivo.

Carbon monoxide (CO) is regarded as one of the most important gaseous transmitters, playing a vital role in biological systems; meanwhile, abnormal levels of CO can be correlated with conditions such as lung disease, Alzheimer's disease, and cardiovascular disease. CO-releasing molecules (CORMs) are chemical agents used to release CO as an endogenous, biologically active molecule in order to treat diseases. CO-releasing molecule-3 (CORM-3), as a convenient and safe CO donor and therapeutic drug molecule, has been widely used to release exogenous CO in living cells to study the physiological and pathological roles of CO in living systems. Herein, we designed a NIR-emitting probe (NIR-CORM-3) with a large Stokes shift based on a 4-(dimethylamino)cinnamaldehyde lepidine derived fluorophore. A 4-nitrobenzyl group was selected as the CORM-3 recognizing moiety, and the probe is able to selectively and sensitively respond to CORM-3 (within only 15 min). Upon encountering CORM-3, NIR-CORM-3 releases a fluorophore with a response at 670 nm, and it shows a remarkable Stokes shift (up to 250 nm). In addition, NIR-CORM-3 has low cytotoxicity and exhibits outstanding NIR imaging abilities in living cells and mice.

Label-free detection of ssDNA base insertion and deletion mutations by surface-enhanced Raman spectroscopy.

Surface-enhanced Raman spectroscopy (SERS), as a label-free, highly sensitive analytical method, has become an important tool for providing substance fingerprints. In this study, silver nanoparticles containing thiosulfate ions and calcium ions (Ag@SCNPs) have been used as an enhanced substrate to eliminate the interference of impurities on DNA signals. Intrinsic structural information on single-strand DNA (ssDNA) was directly obtained through SERS. The improved enhancement system was used to explore the base-stacking rules of ssDNA in a solution environment. For the first time, single-base insertion mutations and deletion mutations, as well as their exact mutation sites, were identified, and Raman spectra with high stability, repeatability, and high signal-to-noise ratio were obtained. The method is simple, fast, and accurate, and the detection process is nondestructive. It has potential to be applied in the fields of medical diagnosis and genetics research.

A novel fluorescence ratio probe based on dual-emission carbon dots for highly selective and sensitive detection of chlortetracycline and cell imaging.

The novel dual-emission carbon dots (DECDs) for highly selective and sensitive recognition of chlortetracycline (CTC) and cell imaging were synthesized successfully by one-step synthesis. The obtained DECDs possessed two fluorescence peaks (345 nm and 450 nm) and showed specific response to CTC, resulting in a decrease in fluorescence intensity at 345 nm, a blue shift, and an increase in fluorescence intensity at 450 nm. The obtained DECDs exhibited highly selective response to CTC and not to its analogues, such as tetracycline, doxycycline, and oxytetracycline. Thus, an excellent ratiometric probe for the detection of CTC was fabricated successfully and used for the detection of CTC in real samples with the detection limit (LOD) of 16.45 nM. More importantly, the DECDs were used for quantitative detection of CTC in living cells, which demonstrated excellent biocompatibility and broad prospects in biomedicine application. Finally, the excellent selectivity of DECDs toward CTC was attributed to the FRET mechanism and the formation of complexes.

Roles of m6A modification in neurological diseases. / m6A ä¿®é¥°åœ¨ç¥žç»ç³»ç»Ÿç–¾ç— ä¸­çš„ä½œç”¨.

N6-methyladenosine (m6A) methylation modification is one of the most common epigenetic modifications for eukaryotic mRNA. Under the catalytic regulation of relevant enzymes, m6A participates in the body's pathophysiological processes via mediating RNA transcription, splicing, translation, and decay. In the past, we mainly focused on the regulation of m6A in tumors such as hematological tumors, cervical cancer, breast cancer. In recent years, it has been found that m6A is enriched in mRNAs of neurogenesis, cell cycle, and neuron differentiation. Its regulation in the nervous system is gradually being recognized. When the level of m6A modification and the expression levels of relevant enzyme proteins are changed, it will cause neurological dysfunction and participate in the occurrence and conversion of neurological diseases. Recent studies have found that the m6A modification and its associated enzymes were involved in major depressive disorder, Parkinson's disease, Alzheimer's disease, Fragile X syndrome, amyotrophic lateral sclerosis, and traumatic brain injury, and they also play a key role in the development of neurological diseases and many other neurological diseases. This paper mainly reviewed the recent progress of m6A modification-related enzymes, focusing on the impact of m6A modification and related enzyme-mediated regulation of gene expression on the central nervous system diseases, so as to provide potential targets for the prevention of neurological diseases.

Label-Free Detection of C-T Mutations by Surface-Enhanced Raman Spectroscopy Using Thiosulfate-Modified Nanoparticles.

Recent developments in molecular spectroscopy have widened the scope of surface-enhanced Raman spectroscopy (SERS) for detection of nucleic acids. In order to solve the interference of impurity signals in SERS analysis that hamper the reliable detection of DNA, Ag nanoparticles modified with thiosulfate ions were used to obtain SERS signals of DNA molecules in aqueous solutions, which showed good reproducibility. By using thiosulfate ions and calcium ions as aggregating agents, this method not only eliminated the influence of citrate on DNA signals completely but also obtained the signals for all bases indiscriminately, including the T base that was considered to have low Raman activity. Subsequently, the base stacking rule was used to identify mutations arising from C/T transition. It further identified the mutation sites of single-base C/T transition using this platform for the first time. This method has wide application prospects in DNA analysis, DNA sequencing, and genetic testing.

[Study on the application of aptamers in the screening of tumor serum markers].

The nucleic acid adapters of tumor serum markers are oligonucleotide molecules with high specificity and high affinity with tumor serum markers obtained by in vitro screening with systematic evolution of ligands by exponential enrichment (SELEX). Researchers take the advantage of the nucleic acid adapter to explore new tumor serum markers that have more diagnostic value for tumor diagnosis. Recently, some achievements have been achieved in the research of liver cancer and stomach cancer. This paper has reviewed nucleic acid adapter and its research in the serum tumor marker screening, and discussed the value of the nucleic acid adapter of serum tumor markers in the diagnosis, as well as current problems existing in the research. This paper is very useful to help people better understand the screening of nucleic acid adapters of tumor serum markers, and to provide help in discovering new tumor serum markers.

[Screening of nucleic acid aptamer of lung cancer cells based on cell exponential enrichment ligand system evolution and its application in tumor diagnosis and treatment].

Nucleic acid aptamer is an oligonucleotide sequence screened by the exponential enrichment ligand system evolution technology (SELEX). Previous studies have shown that nucleic acid aptamer has a good application prospect in tumor diagnosis and treatment. Therefore, we reviewed the selection and identification of nucleic acid aptamer of lung cancer cells in recent years, and discussed the effect of aptamer as targeting drugs and targeting vectors on the diagnosis of tumors, which provide a new idea for early diagnosis and treatment of tumor.

A single mitochondria-targetable fluorescent probe for visualizing cysteine and glutathione in ferroptosis of myocardial ischemia/reperfusion injury.

Ferroptosis plays an important role in the early stage of myocardial ischemia/reperfusion (MI/R) injury, which is closely associated with the antioxidant damage of mitochondrial cysteine (Cys)/glutathione (GSH)/glutathione peroxidase 4 (GPX4) axis. Visualization of Cys and GSH in mitochondria is meaningful to value ferroptosis and further contributes to understanding and preventing MI/R injury. Herein a mitochondria-targetable thiols fluorescent probe (MTTP) was designed and synthesized based on sulfonyl benzoxadiazole (SBD) chromophore with a triphenylphosphine unit as the mitochondria-targeted functional group. Cys and GSH can be differentiated by MTTP with two distinguishable emission bands (583 nm and 520 nm) through the controllable aromatic substitution-rearrangement reaction. Importantly, MTTP is capable of monitoring ferroptosis and its inhibition by measuring mitochondrial Cys and GSH. MTTP was also employed to non-invasively detect ferroptosis during oxygen and glucose deprivation/reoxygenation (OGD/R)-induced MI/R injury in H9C2 cells. In a word, MTTP provides a visual tool that can simultaneously detect Cys and GSH to monitor ferroptosis processes during MI/R injury, which helps for more deeper understanding of the role of ferroptosis in MI/R injury-related diseases.

Antibiotic combinations prediction based on machine learning to multicentre clinical data and drug interaction correlation.

BACKGROUND: With increasing antibiotic resistance and regulation, the issue of antibiotic combination has been emphasised. However, antibiotic combination prescribing lacks a rapid identification of feasibility, while its risk of drug interactions is unclear. METHODS: We conducted statistical descriptions on 16 101 antibiotic coprescriptions for inpatients with bacterial infections from 2015 to 2023. By integrating the frequency and effectiveness of prescriptions, we formulated recommendations for the feasibility of antibiotic combinations. Initially, a machine learning algorithm was utilised to optimise grading thresholds and habits for antibiotic combinations. A feedforward neural network (FNN) algorithm was employed to develop antibiotic combination recommendation model (ACRM). To enhance interpretability, we combined sequential methods and DrugBank to explore the correlation between antibiotic combinations and drug interactions. RESULTS: A total of 55 antibiotics, covering 657 empirical clinical antibiotic combinations were used for ACRM construction. Model performance on the test dataset showed AUROCs of 0.589-0.895 for various antibiotic recommendation classes. The ACRM showed satisfactory clinical relevance with 61.54-73.33% prediction accuracy in a new independent retrospective cohort. Antibiotic interaction detection showed that the risk of drug interactions was 29.2% for strongly recommended and 43.5% for not recommended. A positive correlation was identified between the level of clinical recommendation and the risk of drug interactions. CONCLUSIONS: Machine learning modelling of retrospective antibiotic prescriptions habits has the potential to predict antibiotic combination recommendations. The ACRM plays a supporting role in reducing the incidence of drug interactions. Clinicians are encouraged to adopt such systems to improve the management of antibiotic usage and medication safety.

The effects of dietary patterns and food groups on symptomatic osteoarthritis: A systematic review.

AIM: To systematically review current literature to determine the association between symptomatic osteoarthritis and dietary patterns, diet quality and food groups in adults aged ≥45 years. METHODS: The review was registered on PROSPERO (CRD42021270891). Cochrane Central Library, Cumulative Index of Nursing and Allied Health Literature, Embase, Medline and Web of Science databases were searched. A total of 3816 records were identified. Eligible articles involved populations aged ≥45 years with symptomatic osteoarthritis, assessing dietary patterns, diet quality or food groups, with pain in joints as outcomes. The Joanna Briggs Institute Critical Appraisal Checklists were used for quality assessment. Grading of Recommendations, Assessment, Development and Evaluation was used to assess the certainty of evidence. RESULTS: Six cohort studies were included. The Prudent dietary pattern and the Mediterranean dietary pattern reduced the progression of osteoarthritis symptoms. The Western dietary pattern increased symptomatic osteoarthritis progression. Increased total fibre consumption reduced symptomatic osteoarthritis progression and pain worsening, but the effects of fibre from each food group were inconclusive. Diet with high inflammatory potential increased risk of new onset symptomatic osteoarthritis, but the effects of overall diet quality were inconclusive. CONCLUSIONS: The Prudent dietary pattern showed the highest protection on symptomatic osteoarthritis in adults aged 45 years and over. The body of evidence is limited, suggesting that further research is needed to corroborate the estimated effect at a high certainty of evidence, and to incorporate previously unstudied dietary patterns and food groups. Identifying the most beneficial dietary pattern may inform future guidelines for reducing symptomatic osteoarthritis in middle aged and older adults.

Detection of simple proteins by direct surface-enhanced Raman scattering based on the Hofmeister ion-specific effect.

Surface-enhanced Raman scattering (SERS) spectroscopy has unique advantages in detecting biomolecules, but label-free determination of proteins with low scattering cross-sections remains challenging. In this study, such proteins' SERS signals have been optimized using the Hofmeister effect between protein molecules and CsI solution at physiological concentrations (A 100 mmol/L Cesium iodide, CsI). Cs+ as chaotro cation ion has a complex interaction mechanism with protein, can not only deprive hydrated water molecules on the surface of protein but also penetrate into the hydrophobic interior of protein. In addition to the above advantages, I- in excess CsI solution with appropriate concentration can removes the interference of citric acid-based impurities on the surface of silver nanoparticles, and Cs+ in excess CsI solution attracts the aggregation of negatively charged silver nanoparticles and cause local electromagnetic field enhancement to achieve high sensitivity in protein detection. This has been combined with principal component analysis to perform a comprehensive analysis of several proteins. Molecular dynamics simulations have been performed to study the mechanism of interaction between CsI and proteins. In addition, the vibrational peak of water has been used as an internal standard to quantify the protein content, and a good linear relationship between peak intensity and concentration was obtained.

Engineering a near-infrared LAP fluorescent probe with high sensitivity and selectivity for surgical resection of liver cancer.

Hepatocellular carcinoma (HCC) is a type of cancer associated with a high rate of mortality and morbidity. In order to achieve precise HCC theranostics, it is important to develop excellent fluorescent probes. However, the existing probes are not sensitive or specific enough to accurately identify HCC margins and contours. For diagnosing HCC and identifying tumors during surgery, it is urgent to engineer highly sensitive and selective fluorescent probes. Liver tumor progression is closely associated with leucine aminopeptidase (LAP) overexpression, a biomarker of liver cancer. Herein, we have rationally designed a NIR fluorescent probe, NLAP, which is specially activated by LAP. The probe exhibited high sensitivity (detection limit = 6.8 mU L-1) and superior affinity (Km = 2.98 µM) for LAP. With this probe, we distinguished cancer cells overexpressing LAP from normal cells and applied it intraoperatively to guide liver tumor excisions. Furthermore, NLAP was employed to successfully detect the LAP of intestinal and splenic metastatic tumors in orthotopic liver tumor mice by "in situ spraying" and good performances were demonstrated.