Induction of Siglec-G by RNA viruses inhibits the innate immune response by promoting RIG-I degradation.

RIG-I is a critical RNA virus sensor that serves to initiate antiviral innate immunity. However, posttranslational regulation of RIG-I signaling remains to be fully understood. We report here that RNA viruses, but not DNA viruses or bacteria, specifically upregulate lectin family member Siglecg expression in macrophages by RIG-I- or NF-κB-dependent mechanisms. Siglec-G-induced recruitment of SHP2 and the E3 ubiquitin ligase c-Cbl to RIG-I leads to RIG-I degradation via K48-linked ubiquitination at Lys813 by c-Cbl. By increasing type I interferon production, targeted inactivation of Siglecg protects mice against lethal RNA virus infection. Taken together, our data reveal a negative feedback loop of RIG-I signaling and identify a Siglec-G-mediated immune evasion pathway exploited by RNA viruses with implication in antiviral applications. These findings also provide insights into the functions and crosstalk of Siglec-G, a known adaptive response regulator, in innate immunity.

Controllable Assembly of a Quantum Dot-Based Aptasensor Guided by CRISPR/Cas12a for Direct Measurement of Circulating Tumor Cells in Human Blood.

Accurate and sensitive analysis of circulating tumor cells (CTCs) in human blood provides a non-invasive approach for the evaluation of cancer metastasis and early cancer diagnosis. Herein, we demonstrate the controllable assembly of a quantum dot (QD)-based aptasensor guided by CRISPR/Cas12a for direct measurement of CTCs in human blood. We introduce a magnetic bead@activator/recognizer duplex core-shell structure to construct a multifunctional platform for the capture and direct detection of CTCs in human blood, without the need for additional CTC release and re-identification steps. Notably, the introduction of magnetic separation ensures that only a target-induced free activator can initiate the downstream catalysis, efficiently avoiding the undesired catalysis triggered by inappropriate recognition of the activator/recognizer duplex structure by crRNAs. This aptasensor achieves high CTC-capture efficiency (82.72%) and sensitive detection of CTCs with a limit of detection of 2 cells mL-1 in human blood, holding great promise for the liquid biopsy of cancers.

Integration of Demethylation-Activated DNAzyme with a Single Quantum Dot Nanosensor for Sensitive Detection of O6-Methylguanine DNA Methyltransferase in Breast Tissues.

O6-Methylguanine-DNA-methyltransferase (MGMT) is a demethylation protein that dynamically regulates the O6-methylguanine modification (O6 MeG), and dysregulated MGMT is implicated in various malignant tumors. Herein, we integrate demethylation-activated DNAzyme with a single quantum dot nanosensor to sensitively detect MGMT in breast tissues. The presence of MGMT induces the demethylation of the O6 MeG-caged DNAzyme and the restoration of catalytic activity. The activated DNAzyme then specifically cleaves the ribonucleic acid site of hairpin DNA to expose toehold sequences. The liberated toehold sequence may act as a primer to trigger a cyclic exponential amplification reaction for the generation of enormous signal strands that bind with the Cy5/biotin-labeled probes to form sandwich hybrids. The assembly of sandwich hybrids onto 605QD obtains 605QD-dsDNA-Cy5 nanostructures, inducing efficient FRET between the 605QD donor and Cy5 acceptor. Notably, the introduction of a mismatched base in hairpin DNA can greatly minimize the background and improve the signal-to-noise ratio. This nanosensor achieves a dynamic range of 1.0 × 10-8 to 0.1 ng/µL and a detection limit of 155.78 aM, and it can screen MGMT inhibitors and monitor cellular MGMT activity with single-cell sensitivity. Moreover, it can distinguish the MGMT level in tissues of breast cancer patients and healthy persons, holding great potential in clinical diagnostics and epigenetic research studies.

Construction of a 3D Quantum Dot Nanoassembly with Two-Step FRET for One-Step Sensing of Human Telomerase RNA in Breast Cancer Cells and Tissues.

Telomerase is an important biomarker for early diagnosis of cancers, but current telomerase assays usually rely on measuring the extension products of telomerase substrates, which increases the assay complexity. More evidence indicates that human telomerase RNA (hTR), as a core component of telomerase, is positively correlated with the telomerase activity. Herein, we demonstrate the development of a duplex-specific nuclease (DSN)-propelled 3D quantum dot (QD) nanoassembly with two-step Föster resonance energy transfer (FRET) for the one-step sensing of hTR in breast cancer cells and tissues. This assay involves only one hairpin probe modified with a Cy5 at the sixth base from the 5'-biotin end and a BHQ2 at the 3'-terminus, which integrates three functions of target recognition, target recycling amplification, and signal readout. The anchoring of the hairpin probe on the 605QD surface results in the formation of a 3D 605QD-Cy5-probe-BHQ2 nanoassembly in which two-step FRET occurs among the 605QD, Cy5, and BHQ2 quencher. Notably, the formation of 605QD-Cy5-probe-BHQ2 nanoassembly facilitates the reduction of background signal and the increase of signal-to-background ratio due to its dense, highly oriented nucleic acid shell-induced steric hindrance effect. This assay can achieve one-step and rapid detection of hTR with a detection limit of 2.10 fM, which is the simplest and most rapid hTR assay reported so far. Moreover, this assay can efficiently distinguish single-base mismatched sequences, and it can discriminate the hTR level between breast cancer patients and healthy donors with a high accuracy of 100%, with great prospects for early diagnosis of cancers.

Elongation and Ligation-Mediated Differential Coding for Label-Free and Locus-Specific Analysis of 8-Oxo-7,8-dihydroguanine in DNA.

Oxidative DNA damage is closely associated with the occurrence of numerous human diseases and cancers. 8-Oxo-7,8-dihydroguanine (8-oxoG) is the most prevalent form of DNA damage, and it has become not only an oxidative stress biomarker but also a new epigenetic-like biomarker. However, few approaches are available for the locus-specific detection of 8-oxoG because of the low abundance of 8-oxoG damage in DNA and the limited sensitivity of existing assays. Herein, we demonstrate the elongation and ligation-mediated differential coding for label-free and locus-specific analysis of 8-oxoG in DNA. This assay is very simple without the involvement of any specific labeled probes, complicated steps, and large sample consumption. The utilization of Bsu DNA polymerase can specifically initiate a single-base extension reaction to incorporate dATP into the opposite position of 8-oxoG, endowing this assay with excellent selectivity. The introduction of cascade amplification reaction significantly enhances the sensitivity. The proposed method can monitor 8-oxoG with a limit of detection of 8.21 × 10-19 M (0.82 aM), and it can identify as low as 0.001% 8-oxoG damage from a complex mixture with excessive undamaged DNAs. This method can be further applied to measure 8-oxoG levels in the genomic DNA of human cells under diverse oxidative stress, holding prospect potential in the dynamic monitoring of critical 8-oxoG sites, early clinical diagnosis, and gene damage-related biomedical research.

Construction of an Enzymatically Controlled DNA Nanomachine for One-Step Imaging of Telomerase in Living Cells.

Telomerase is a basic reverse transcriptase that maintains the telomere length in cells, and accurate and specific sensing of telomerase in living cells is critical for medical diagnostics and disease therapeutics. Herein, we demonstrate for the first time the construction of an enzymatically controlled DNA nanomachine with endogenous apurinic/apyrimidinic endonuclease 1 (APE1) as a driving force for one-step imaging of telomerase in living cells. The DNA nanomachine is designed by rational engineering of substrate probes and reporter probes embedded with an enzyme-activatable site (i.e., AP site) and their subsequent assembly on a gold nanoparticle (AuNP). Upon recognition and cleavage of the AP site in the substrate probe by APE1, the loop of the substrate probe unfolds, exposing telomeric primer (TP) with the 3'-OH end. Subsequently, the TP is elongated by telomerase at the 3'-OH end to generate a long telomeric product. The resultant telomeric product acts as a swing arm that can hybridize with a reporter probe to initiate the APE1-powered walking reaction, ultimately generating a significantly enhanced fluorescence signal. Notably, endogenous APE1 is used as the driving force of the DNA nanomachine, avoiding the introduction of exogenous auxiliary cofactors into the cellular microenvironment. Owing to the high kinetics and high amplification efficiency of the APE1-powered DNA nanomachine, this strategy enables one-step sensitive sensing of telomerase in vitro and in vivo. It can successfully discriminate telomerase activity between cancer cells and normal cells, screen telomerase inhibitors, and monitor the variations of telomerase activity in living cells, offering a prospective platform for molecular diagnostics and drug discovery.

A major gene for chilling tolerance variation in Indica rice codes for a kinase OsCTK1 that phosphorylates multiple substrates under cold.

Rice is susceptible to chilling stress. Identifying chilling tolerance genes and their mechanisms are key to improve rice performance. Here, we performed a genome-wide association study to identify regulatory genes for chilling tolerance in rice. One major gene for chilling tolerance variation in Indica rice was identified as a casein kinase gene OsCTK1. Its function and natural variation are investigated at the physiological and molecular level by its mutants and transgenic plants. Potential substrates of OsCTK1 were identified by phosphoproteomic analysis, protein-protein interaction assay, in vitro kinase assay, and mutant characterization. OsCTK1 positively regulates rice chilling tolerance. Three of its putative substrates, acidic ribosomal protein OsP3B, cyclic nucleotide-gated ion channel OsCNGC9, and dual-specific mitogen-activated protein kinase phosphatase OsMKP1, are each involved in chilling tolerance. In addition, a natural OsCTK1 chilling-tolerant (CT) variant exhibited a higher kinase activity and conferred greater chilling tolerance compared with a chilling-sensitive (CS) variant. The CT variant is more prevalent in CT accessions and is distributed more frequently in higher latitude compared with the CS variant. This study thus enables a better understanding of chilling tolerance mechanisms and provides gene variants for genetic improvement of chilling tolerance in rice.

Cholinergic drugs reduce metabolic inflammation and diabetic myocardial injury by regulating the gut bacterial component lipopolysaccharide-induced ERK/Egr-1 pathway.

Autonomic imbalance and metabolic inflammation are important pathological processes in diabetic cardiomyopathy. Gut microbiota dysbiosis and increased levels of bacterial component lipopolysaccharide (LPS) are associated with diabetic myocardial injury, but the mechanism by which gut microbes affect metabolic inflammation and cardiac injury remains unclear. We determined whether pyridostigmine (PYR), which inhibits cholinesterase to improve vagal activity, could regulate the disordered gut microbiota and attenuate gut barrier dysfunction, metabolic endotoxemia, and inflammation in diabetes. Db/db mice exhibited high blood glucose levels, insulin resistance, low vagal activity, and diabetic myocardial injury. Db/db mice also exhibited gut microbiota perturbations and subsequent disruption of gut barrier function, resulting in an influx of LPS, metabolic endotoxemia, and inflammation. PYR ameliorated the dysregulated glucose and lipid metabolism, modulated the overall structure of the gut microbiota, selectively enhanced the abundance of anti-inflammatory bacteria, and reduced the abundance of proinflammatory and potentially pathogenic bacteria in db/db mice. Importantly, PYR enhanced vagal activity, restored gut microbiota homeostasis, and alleviated gut barrier dysfunction. Therefore, the LPS-induced extracellular signal-regulated kinase (ERK)/early growth response-1 (Egr-1) pathway and consequent metabolic inflammation were inhibited, and eventually, cardiac hypertrophy, fibrosis, oxidative stress, and dysfunction were ameliorated in db/db mice. In vitro cardiomyocyte injury was induced by exposing primary neonatal rat ventricular cardiomyocytes to high glucose (HG) and LPS. In vitro analyses showed that HG + LPS induced ERK1/2 phosphorylation, Egr-1 expression, inflammation, and cell apoptosis, which were inhibited by acetylcholine (ACh). Alpha 7 nicotinic ACh receptor but not muscarinic 2 ACh receptor plays an important role in ACh-mediated anti-inflammatory effects and inhibiting the ERK/Egr-1 pathway in HG + LPS-administered neonatal rat ventricular cardiomyocytes. PYR and ACh ameliorated diabetic myocardial injury by inhibiting the LPS-induced ERK/Egr-1 pathway and metabolic inflammation. The vagus-gut-heart axis has provided new insights into the complex mechanisms of diabetes and offers novel therapeutic targets.

Friend or foe: role of pathological tau in neuronal death.

Neuronal death is one of the most common pathological hallmarks of diverse neurological diseases, which manifest varying degrees of cognitive or motor dysfunction. Neuronal death can be classified into multiple forms with complicated and unique regulatory signaling pathways. Tau is a key microtubule-associated protein that is predominantly expressed in neurons to stabilize microtubules under physiological conditions. In contrast, pathological tau always detaches from microtubules and is implicated in a series of neurological disorders that are characterized by irreversible neuronal death, such as necrosis, apoptosis, necroptosis, pyroptosis, ferroptosis, autophagy-dependent neuronal death and phagocytosis by microglia. However, recent studies have also revealed that pathological tau can facilitate neuron escape from acute apoptosis, delay necroptosis through its action on granulovacuolar degeneration bodies (GVBs), and facilitate iron export from neurons to block ferroptosis. In this review, we briefly describe the current understanding of how pathological tau exerts dual effects on neuronal death by acting as a double-edged sword in different neurological diseases. We propose that elucidating the mechanism by which pathological tau affects neuronal death is critical for exploring novel and precise therapeutic strategies for neurological disorders.

The association between monocyte to high-density lipoprotein cholesterol ratio and chronic kidney disease in a Chinese adult population: a cross-sectional study.

BACKGROUND: Monocyte to high-density lipoprotein cholesterol ratio (MHR) was confirmed as a novel inflammatory marker and strongly associated with the risk of several diseases. This study aimed to investigate the relationship between MHR and chronic kidney disease (CKD) in a Chinese adult population. METHODS: In this cross-sectional study, 232,775 community-dwelling adults in Binhai who completed health checkups in 2021 were enrolled. Participants were categorized based on the MHR quartiles. Clinical characteristics of participants across different groups were compared using one-way ANOVA, Kruskal-Wallis h-test, and Chi-squared test as appropriate. Univariate and multivariable logistic regression analyses were taken to assess the relationship between MHR and the presence of CKD, as well as its association with low estimated glomerular filtration rate (eGFR) and proteinuria. Subgroup analyses were further executed to confirm the reliability of this relationship. RESULTS: A total of 21,014 (9.0%) individuals were diagnosed with CKD. Characteristic indicators including waist circumference, body mass index (BMI), blood pressure (BP), serum uric acid (SUA), triglyceride, and fasting blood glucose (FBG) showed a gradual increase with higher MHR quartiles, whereas parameters such as age, total cholesterol, high-density lipoprotein cholesterol (HDL-C), and eGFR decreased (p < .001). In the multivariable logistic regression analysis, we observed independent associations between MHR (per 1 SD increase) and CKD, as well as low eGFR and proteinuria, with odds ratio (ORs) and 95% confidence intervals (95%CIs) of 1.206 (1.186-1.225), 1.289 (1.260-1.319), and 1.150 (1.129-1.171), respectively (p < .001). Similar conclusions were confirmed in subgroup analysis stratified by gender, age, BMI, central obesity, hypertension, and diabetes mellitus, after justification for confounding factors. CONCLUSION: Elevated MHR level was independently associated with the presence of CKD, suggesting that it might serve as a useful clinical tool for risk stratification, offering valuable insights to inform preventive and therapeutic approaches for clinicians in their routine medical practice.

Wavelength sensitivity reconfigurable SPR photodetector with a blazed grating profile.

Surface plasmonic detectors based on one-dimensional half-wavelength gratings have attracted attention due to their wavelength- or polarization-specific photodetection. Although the effect of a grating period and a grating depth on the photoelectric conversion of 1D half-wavelength grating-based surface plasmon resonance (SPR) detectors has been discussed thoroughly in recent years, the effect of different grating profiles on device performance is still limited to the rectangular shape. In this article, we proposed a wavelength sensitivity reconfigurable photodetector enhanced by SPR with a blazed grating profile. The gold layer was fabricated on a silicon-based blazed grating to form a Schottky barrier and act as an SPR coupler. By measuring the photocurrent in the range of -58° to -48°of an incident angle, the peak shifts of a photocurrent signal waveform are found to depend on the wavelength over 800-1000 nm.

Endovascular Treatment of Superior Mesenteric Artery Pseudoaneurysm Due to Infective Endocarditis With Stent-Graft.

PURPOSE: To report a successful case of pseudoaneurysm of the superior mesenteric artery (SMA) caused by infected endocarditis treated with a covered stent. CASE REPORT: A patient was diagnosed with infective endocarditis and 2 months later a proximal SMA pseudoaneurysm was identified on computed tomography. Daptomycin was started on admission and continued for approximately 4 months until the inflammatory markers normalized, and then the SMA pseudoaneurysm was successfully excluded with a stent-graft and antibiotics were continued for 1 year after the procedure. There were no associated complications or recurrences at the 3-year follow-up. CONCLUSION: Placing a covered stent with a full course of antibiotics before and after surgery may be a successful alternative to open surgery in the treatment of pseudoaneurysms of the SMA due to infective endocarditis. CLINICAL IMPACT: This case report reports a rare case of pseudoaneurysm of the superior mesenteric artery due to infective endocarditis, which was successfully treated with an overlapping stent and confirmed by complete imaging data at a three-year follow-up. This report suggests that endovascular treatment may be an alternative to open surgery in the treatment of pseudoaneurysms of the superior mesenteric artery caused by infective endocarditis.

RNF150 suppresses papillary thyroid carcinoma with ASK1 ubiquitination presenting a direct target via inactivating p38 signaling axis.

Papillary thyroid carcinoma (PTC) is the most prevalent cancer in endocrine system. However, the pathogenic mechanism underlying tumor recurrence remains unclear. RING finger protein (RNF) family plays a crucial role in cancers whereas the role of RNF150 in PTC requires investigation. Our study aimed to explore the function and molecular mechanism of RNF150 in PTC. Here, we extracted data from The Cancer Genome Atlas-THCA (TCGA-THCA) data set to investigate the expression and prognostic value of RNF150 in THCA. We found that RNF150 was lowly expressed in THCA and its high expression indicated favorable prognosis in THCA patients. RNF150 could inhibit the proliferation of PTC cells and suppress p38 phosphorylation both in vitro and in vivo. Meanwhile, the knockdown of RNF150 significantly promoted the proliferation of PTC cells and the phosphorylation of p38, which could be reversed by p38 inhibitor. Besides, RNF150 could interact with ASK1 and promoted its ubiquitination. The overexpression of ASK1 exerted opposite effects against RNF150 in PTC cells. In PTC specimens, RNF150 and ASK1 shared reversed expression pattern. In conclusion, our study revealed that RNF150 could suppress the proliferation of PTC by inactivating p38 pathway and promoting ASK1 ubiquitination, which provided novel targets for PTC treatment.

Association between gut microbiota and influenza: a bidirectional two-sample mendelian randomization study.

BACKGROUND: Previous observational studies have indicated a correlation between the gut microbiota and influenza; however, the exact nature of the bidirectional causal connection remains uncertain. METHOD: A two-way, two-sample Mendelian randomization (MR) study was conducted to evaluate the possible causal connection between the gut microbiota and the two outcomes of influenza (pneumonia without influenza and influenza pneumonia). The statistical analysis of gut microbiota is derived from the information of the most extensive meta-analysis (GWAS) conducted by the MiBioGen Alliance, encompassing a sample size of 18,340.The summary statistical data for influenza (not pneumonia, n = 291,090) and influenza pneumonia (n = 342,499) are from GWAS data published by FinnGen consortium R8.Estimate and summarize Single-nucleotide polymorphisms (SNPs) using Inverse variance weighted (IVW), MR Egger, and Weighted median (WM) in bidirectional MR analysis. To assess the heterogeneity, horizontal pleiotropy, and stability of SNPs, we employed Cochran's Q test, MR Egger intercept test, and sensitivity analysis. RESULT: The IVW analysis indicated that there was a significant association between influenza infection and five bacterial taxa. Additionally, the abundance changes of seven gut microbiota were found to be causally related to influenza infection. In addition, seven bacterial taxa showed a significant association with the occurrence of influenza pneumonia. The findings from the WM analysis largely support the outcomes of IVW, however, the results of MR egger analysis do not align with IVW. Furthermore, there is no proof to substantiate the cause-and-effect relationship between influenza pneumonia and the composition of gut microbiota. CONCLUSION: This analysis demonstrates a possible bidirectional causal connection between the prevalence of particular gut microbiota and the occurrence of influenza infection. The presence of certain gut microbiota may potentially contribute to the development of pneumonia caused by influenza. Additional investigation into the interaction between particular bacterial communities and influenza can enhance efforts in preventing, monitoring, and treating influenza.

Joint learning-based causal relation extraction from biomedical literature.

Causal relation extraction of biomedical entities is one of the most complex tasks in biomedical text mining, which involves two kinds of information: entity relations and entity functions. One feasible approach is to take relation extraction and function detection as two independent sub-tasks. However, this separate learning method ignores the intrinsic correlation between them and leads to unsatisfactory performance. In this paper, we propose a joint learning model, which combines entity relation extraction and entity function detection to exploit their commonality and capture their inter-relationship, so as to improve the performance of biomedical causal relation extraction. Experimental results on the BioCreative-V Track 4 corpus show that our joint learning model outperforms the separate models in BEL statement extraction, achieving the F1 scores of 57.0% and 37.3% on the test set in Stage 2 and Stage 1 evaluations, respectively. This demonstrates that our joint learning system reaches the state-of-the-art performance in Stage 2 compared with other systems.

First report of Epicoccum latusicollum causing leaf spot on Lophatherum gracile in Jiangsu Province of China.

Lophatherum gracile Brongn. is an important Chinese herbal medicine. Since 2016, a leaf spot disease has appeared on L. gracile seedlings in the traditional Chinese medicine resource garden of the Institute of Botany, Chinese Academy of Sciences, Jiangsu Province (32.06°N, 118.83°E). About approximately 80% of the seedlings suffered from the disease. The disease spot usually starts from the leaf margin, round or irregular, with yellow halo at the edge of the lesion. To isolate the pathogen, four diseased leaves were collected from four different seedlings and there are 6 sections from each diseased leaf. The leaf sections were surface sterilized in 75% alcohol for 30 s and 1.5% NaClO for 90 s, rinsed three times in sterilized distilled water, plated on potato dextrose agar (PDA). Pure cultures were obtained by monosporic isolation. Eleven isolates were obtained (isolate rate of 55%) and identified as Epicoccum sp.. Thus, a representative isolate, DZY3-3 was used for the further study. After 7 days of culture, the colony produced white aerial hyphae, and reddish orange pigment on the underside. The chlamydospores were produced, either multicellular or unicellular. The colony produced pycnidia and conidia after nearly three weeks of cultivation on oatmeal ager OA. Conidia were unicellular, hyaline, oval, and were 4.9 to 6.4 x 2.0 to 3.3 µm (n=35). In addition, a brown discoloration was produced on malt extract agar (MEA) after using the 1 mol/L NaOH solution for 1 h. These characteristics were consistent with the description of Epicoccum sp. (Chen et al. 2017). To comfirm this identification, the internal transcribed spacer (ITS), large subunit ribosomal RNA (LSU), beta-tubulin (TUB) and RNA polymerase II second largest subunit (RPB2) regions were amplified using the detailed primer pairs described by White et al., Rehner and Samuels, Woudenberg et al. and Liu et al., respectively. They had 99.8-100% homology to the ITS (GenBank no. MN215613, 504/505 bp), LSU (MN533800, 809/809 bp), TUB (MN329871, 333/333 bp), and RPB2 (MG787263, 596/596 bp) sequences of E. latusicollum in the GenBank database. A neighbor-joining phylogenetic tree was generated based on the concatenated sequences of all the above regions in MEGA7. The DZY3-3 clustered in the E. latusicollum clade with 100% bootstrap support. Koch's postulates were performed by spray inoculation (1×106 spores/mL) on the left sides of leaves of three healthy L. gracile seedlings and detached leaves, using isolate DZY3-3, while sterilized water served as the control was sprayed on the right sides of leaves. All plants and detached leaves were covered with clear polyethylene bags to maintain about 80% relative humidity at 25℃. Whether in vivo or in vitro pathogenicity test showed similar symptoms to those occurred in the field after 5 days post inoculation. No symptoms occurred on controls. The experiment was repeated three times. Subsequently, the same fungus was reisolated and identified from leaves of three inoculated seedlings. The E. latusicollum has a very wide host range. For example, it has been reported to cause stalk rot on Maize (Xu et al. 2022) and cause leaf spot on Tobacco in China (Guo et al. 2020). To our knowledge, it is the first report of E. latusicollum causing leaf spot on L. gracile in the world. This study will provide an important reference for the biology of E. latusicollum and the distribution of the disease.

Identification of autophagy-related genes in diabetic foot ulcer based on bioinformatic analysis.

Diabetic foot ulcer (DFU) complications involve autophagy dysregulation. This study aimed to identify autophagy-related bioindicators in DFU. Differentially expressed genes (DEGs) between DFU and healthy samples were analysed from the Gene Expression Omnibus (GEO) datasets, GSE7014 and GSE29221. The roles of autophagy-related DEGs were investigated using protein-protein interaction (PPI) networks, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, Gene Ontology (GO) enrichment, and Gene Set Enrichment Analysis (GSEA). Immune cell infiltration's correlation with these DEGs was also assessed. From the Human Autophagy Database (HADB), 232 autophagy-related genes (ARGs) were identified, with an intersection of 17 key DEGs between GSE7014 and GSE29221. These genes are involved in pathways like autophagy-animal, NOD-like receptor signalling, and apoptosis. In the protein network, epidermal growth factor receptor (EGFR) and phosphatase and tensin homologue (PTEN) showed significant interactions with ARGs. Survival analysis indicated the prognostic importance of calpain 2 (CAPN2), integrin subunit beta 1 (ITGB1), and vesicle-associated membrane protein 3 (VAMP3). Lower immune scores were observed in the type 2 diabetes mellitus (DM2) group than in controls. Autophagy and ARGs significantly influence DFU pathophysiology.

Single-Molecule Counting of FTO in Human Breast Tissues Based on a Rolling Circle Transcription Amplification-Driven Clustered Regularly Interspaced Short Palindromic Repeat─Cas12a.

N6-methyladenosine modification as an mRNA modification in mammalian cells is dynamically reversible, regulated by RNA demethylase [e.g., fat mass and obesity-associated protein (FTO)]. The abnormal expression of FTO is closely related to numerous diseases (e.g., various cancers and obesity). Herein, we demonstrate the single-molecule counting of FTO in human cancer cells and breast tissues based on a T7 RNA polymerase-mediated rolling circle transcription (RCT) amplification-driven clustered regularly interspaced short palindromic repeat (CRISPR)─Cas12a. When FTO is present, it demethylates the DNA substrate, initiating the DpnII-mediated cleavage reaction. After magnetic separation, the cleaved DNA fragments trigger the T7 RNA polymerase-mediated RCT amplification, activating CRISPR-/Cas12a-mediated cleavage of signal probes and releasing abundant FAM molecules that are simply counted via single-molecule detection. In this assay, only target FTO can generate CRISPR RNAs, efficiently improving detection specificity. Moreover, the integration of single-molecule detection with magnetic separation achieves zero background and effectively enhances detection sensitivity. This method can specifically and sensitively monitor FTO activity with a limit of detection of 1.20 × 10-13 M, and it may measure FTO at the single-cell level. Furthermore, it may accurately discriminate the FTO expression level in breast tissues between healthy persons and breast cancer patients and screen the FTO inhibitors as well, with great potential in clinical diagnosis and drug discovery.

Hydroxymethylation-Specific Ligation-Mediated Single Quantum Dot-Based Nanosensors for Sensitive Detection of 5-Hydroxymethylcytosine in Cancer Cells.

5-Hydroxymethylcytosine (5hmC) modification is a key epigenetic regulator of cellular processes in mammalian cells, and its misregulation may lead to various diseases. Herein, we develop a hydroxymethylation-specific ligation-mediated single quantum dot (QD)-based fluorescence resonance energy transfer (FRET) nanosensor for sensitive quantification of 5hmC modification in cancer cells. We design a Cy5-modified signal probe and a biotinylated capture probe for the recognition of specific 5hmC-containing genes. 5hmC in target DNA can be selectively converted by T4 ß-glucosyltransferase to produce a glycosyl-modified 5hmC, which cannot be cleaved by methylation-insensitive restriction enzyme MspI. The glycosylated 5hmC DNA may act as a template to ligate a signal probe and a capture probe, initiating hydroxymethylation-specific ligation to generate large amounts of biotin-/Cy5-modified single-stranded DNAs (ssDNAs). The assembly of biotin-/Cy5-modified ssDNAs onto a single QD through streptavidin-biotin interaction results in FRET and consequently the generation of a Cy5 signal. The nanosensor is very simple without the need for bisulfite treatment, radioactive reagents, and 5hmC-specific antibodies. Owing to excellent specificity and high amplification efficiency of hydroxymethylation-specific ligation and near-zero background of a single QD-based FRET, this nanosensor can quantify 5hmC DNA with a limit of detection of 33.61 aM and a wider linear range of 7 orders of magnitude, and it may discriminate the single-nucleotide difference among 5hmC, 5-methylcytosine, and unmodified cytosine. Moreover, this nanosensor can distinguish as low as a 0.001% 5hmC DNA in complex mixtures, and it can monitor the cellular 5hmC level and discriminate cancer cells from normal cells, holding great potential in biomedical research and clinical diagnostics.

A sandwich SERS detection system based on optical convergence and synergistic enhancement effects.

In this research, we propose a novel microlens surface-enhanced Raman spectroscopy (SERS) substrate @ Au film detection system, which is shown to have excellent attributes. This scheme involves the construction of a PDMS plano-convex microlens SERS-active substrate in combination with an Au film. Due to the optical convergence from the microlens, the synergistic enhancement effects due to the Au film, and the "Au film-molecules-AgNPs" sandwich structure, an outstanding SERS performance is achieved. Multiple tests using a portable Raman spectrometer show that the optical convergence due to the microlens and the coupling effects contribute around 1.85× and 26.18× enhancement of the Raman signal, respectively. Even for objective lenses with different numerical apertures, simulations show that the microlens SERS substrate can further enhance the signal collection efficiency; this indicates that the detection scheme is universally applicable. Moreover, the microlens SERS substrate @ Au film system shows excellent time stability, and its Raman enhancement performance remains consistently above 98% of the original signal, even one week later. Our proposed system is simple to prepare, is low cost and has many potential practical applications, which include the detection of biochemical samples.