Identifying spatial domain by adapting transcriptomics with histology through contrastive learning.

Recent advances in spatial transcriptomics have enabled measurements of gene expression at cell/spot resolution meanwhile retaining both the spatial information and the histology images of the tissues. Accurately identifying the spatial domains of spots is a vital step for various downstream tasks in spatial transcriptomics analysis. To remove noises in gene expression, several methods have been developed to combine histopathological images for data analysis of spatial transcriptomics. However, these methods either use the image only for the spatial relations for spots, or individually learn the embeddings of the gene expression and image without fully coupling the information. Here, we propose a novel method ConGI to accurately exploit spatial domains by adapting gene expression with histopathological images through contrastive learning. Specifically, we designed three contrastive loss functions within and between two modalities (the gene expression and image data) to learn the common representations. The learned representations are then used to cluster the spatial domains on both tumor and normal spatial transcriptomics datasets. ConGI was shown to outperform existing methods for the spatial domain identification. In addition, the learned representations have also been shown powerful for various downstream tasks, including trajectory inference, clustering, and visualization.

Anti-DNA antibody-targeted D-peptide nanoparticles ameliorate lupus nephritis in MRL/lpr mice.

Peptide ALW (ALWPPNLHAWVP) targeting anti-dsDNA antibodies has shown promising therapeutic effects in alleviating lupus nephritis, but is potentially limited by poor stability and non-kidney targeting. We recently developed a D-form modified ALW, called D-ALW, which has the capacity to widely inhibit pathogenic polyclonal anti-dsDNA antibody reactions. Further modification of D-ALW using PEG-PLGA nanoparticles to enhance good kidney-targeting ability and extend half-life. Here, we demonstrate that the D-form modified ALW maintains higher binding and inhibition efficiencies and achieves higher stability. Most importantly, D-ALW nanoparticles exhibit excellent kidney-targeting ability and prolong the half-life of the peptides in BALB/c mice. Additionally, compared to D-ALW, D-ALW nanoparticles significantly reduce the glomerular deposition of IgG and C3, improve renal histopathologies, such as glomerular proliferation and inflammatory cells infiltration, and markedly prolong lifespan in MRL/lpr lupus-prone mice. Overall, these results establish that the D-ALW nanoparticles offer synergistic benefits in both safety and efficacy, providing long-term renal preservation and treatment advantages in lupus nephritis.

Fluorescent noble metal nanoclusters for contaminants analysis in food matrix.

Recently, food safety issues caused by contaminants have aroused great public concern. The development of innovative and efficient sensing techniques for contaminants detection in food matrix is in urgent demand. As fluorescent nanomaterials, noble metal nanoclusters have attracted much attention because of their ease of synthesis, enhanced catalytic activity and biocompatibility, and most importantly, excellent photoluminescence property that provides promising analytical applications. This review comprehensively introduced the synthesis method of noble metal nanoclusters, and summarized the application of metal nanoclusters as fluorescent sensing materials in the detection of pollutants, including pesticides, heavy metal, mycotoxin, food additives, and other contaminants in food. The detection mechanism of pesticide residues mostly relies on the inhibition of natural enzymes. For heavy metals, the detection mechanism is mainly related to the interaction between metal ions and nanoclusters or ligands. It is evidenced that metal nanoclusters have great potential application in the field of food safety monitoring. Moreover, challenges and future trends of nanoclusters were discussed. We hope that this review can provide insights and directions for the application of nanoclusters in contaminants detection.

A two-step strategy for simultaneous dual-mode detection of methyl-paraoxon and Ni (â ¡).

Exogenous pollution of Chinese medicinal materials by pesticide residues and heavy metal ions has attracted great attention. Relying on the rapid development of nanotechnology and multidisciplinary fields, fluorescent techniques have been widely applied in contaminant detection and pollution monitoring due to their advantages of simple preparation, low cost, high throughput and others. Most importantly, synchronous detection of multi-targets has always been pursued as one of the major goals in the design of fluorescent probes. Herein, we firstly develop a simultaneous sensing method for methyl-paraoxon (MP) and Nickel ion (Ni, Ⅱ) by using carbon based fluorescent nanocomposite with ratiometric signal readout and nanozyme. Notably, the designed system showed excellent effectiveness even when the two pollutants co-exist. Under the optimum conditions, this method provides low limits of detection of 1.25 µM for methyl-paraoxon and 0.01 µM for Ni (Ⅱ). To further verify the reliability, recovery studies of these two analytes were performed on ginseng radix et rhizoma, nelumbinis semen, and water samples. In addition, smartphone-based visual analysis has been introduced to expand its applicability in point of care detection. This work not only expands the application of the dual-mode approach to pollutant detection, but also provides insights into the analysis of multiple pollutants in a single assay.

Fibroblast growth factor inducible 14 signaling facilitates anti-dsDNA IgG penetration into mesangial cells.

Anti-double-stranded DNA (dsDNA) antibodies induce renal damage in patients with systemic lupus erythematosus by triggering fibrotic processes in kidney cells. However, the precise mechanism underlying penetration of anti-dsDNA immunoglubolin G (IgG) into cells remains unclear. This study was designed to investigate the effect of tumor necrosis factor-like weak inducer of apoptosis (TWEAK)/fibroblast growth factor inducible 14 (Fn14) signaling on anti-dsDNA IgG penetration into cells. Mesangial cells were cultured in vitro, and stimulated with TWEAK and anti-dsDNA IgG. The results revealed that TWEAK dose-dependently enhanced cellular internalization of anti-dsDNA IgG and the expression of high-mobility group box 1 (HMGB1). In addition, TWEAK and anti-dsDNA IgG synthetically downregulate suppressor of cytokine signaling 1, and induce the expression of various fibrotic factors. Furthermore, inhibition of HMGB1 attenuates the enhancement effect of TWEAK on anti-dsDNA IgG internalization. The TWEAK upregulation of HMGB1 involves the nuclear factor-κB and phosphatidylinositide 3-kinase/protein kinase B pathways. Therefore, TWEAK/Fn14 signaling contributes to the penetration of anti-dsDNA IgG and relevant fibrotic processes in mesangial cells.

Conjugated Polymers: Optical Toolbox for Bioimaging and Cancer Therapy.

Conjugated polymers (CPs) are capable of coordinating the electron coupling phenomenon to bestow powerful optoelectronic features. The light-harvesting and light-amplifying properties of CPs are extensively used in figuring out the biomedical issues with special emphasis on accurate diagnosis, effective treatment, and precise theranostics. This review summarizes the recent progress of CP materials in bioimaging, cancer therapeutics, and introduces the design strategies by rationally tuning the optical properties. The recent advances of CPs in bioimaging applications are first summarized and the challenges to clear the future directions of CPs in the respective area are discussed. In the following sections, the focus is on the burgeoning applications of CPs in phototherapy of the tumor, and illustrates the underlying photo-transforming mechanism for further molecular designing. Besides, the recent progress in the CPs-assistant drug therapy, mainly including drug delivery, gene therapeutic, the optical-activated reversion of tumor resistance, and synergistic therapy has also been discussed elaborately. In the end, the potential challenges and future developments of CPs on cancer diagnosis and therapy are also illuminated for the improvement of optical functionalization and the promotion of clinical translation.

Inhibition of fibroblast growth factor-inducible 14 attenuates experimental tubulointerstitial fibrosis and profibrotic factor expression of proximal tubular epithelial cells.

BACKGROUND AND AIM: As a proinflammatory cytokine, tumor necrosis factor-like weak inducer of apoptosis (TWEAK) participates in the progression of renal fibrosis by binding to its receptor, fibroblast growth factor-inducible 14 (Fn14). However, the effect of Fn14 inhibition on tubular epithelial cell-mediated tubulointerstitial fibrosis remains unclear. This study aimed to elucidate the role of TWEAK/Fn14 interaction in the development of experimental tubulointerstitial fibrosis as well as the protective effect of Fn14 knockdown on proximal tubular epithelial cells. METHODS: A murine model of unilateral ureteral obstruction was constructed in both wild-type and Fn14-deficient BALB/c mice, followed by observation of the tubulointerstitial pathologies. RESULTS: Fn14 deficiency ameliorated the pathological changes, including inflammatory cell infiltration and cell proliferation, accompanied by reduced production of profibrotic factors and extracellular matrix deposition. In vitro experiments showed that TWEAK dose-dependently enhanced the expression of collagen I, fibronectin, and α-smooth muscle actin in proximal tubular epithelial cells. Interestingly, TWEAK also upregulated the expression levels of Notch1/Jagged1. Fn14 knockdown and Notch1/Jagged1 inhibition also mitigated the effect of TWEAK on these cells. CONCLUSIONS: In conclusion, TWEAK/Fn14 signals contributed to tubulointerstitial fibrosis by acting on proximal tubular epithelial cells. Fn14 inhibition might be a therapeutic strategy for protecting against renal interstitial fibrosis.

Peptidome profiles in melamine diet-induced bladder stones in C57BL/6 mice.

The aim of this research was to detect potential serum biomarkers of melamine diet-induced bladder stones in C57BL/6 mice. Magnetic bead-based weak cationexchange chromatography (MB-WCX) and matrix-assisted laser desorption ionization-time of flight-mass spectrometry (MALDI-TOF-MS) were employed to detect serum biomarkers in 10 mice fed a melamine diet and 10 control mice. Seventeen peaks (fold change>1.5) with a mass to charge (m/z) value of 1000-10,000 Da were detected in the two groups. Among the significant peaks, five were upregulated and the other 12 were downregulated in the model group. Among the upregulated peaks, 2954.49 and 1710.49 were found to correspond to the peptide regions of NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8(Ndufα8) and basigin, respectively, by liquid chromatography with electrospray ionization and tandem triple quadrupole mass spectrometry(LC-ESI-MS/MS). Western blot analysis was used to detect the expression of Ndufα8 and basigin in another 10 model mice and 10 control mice. The western blot results confirmed the LC-ESI-MS/MS data. The expression of serum basigin and Ndufα8 was partly dependent the concentration of melamine, but no time dependence. In conclusion, Ndufα8 and basigin may be potential serum biomarkers for the detection of melamine diet-induced bladder stones in C57BL/6 mice.

Nanozyme-assisted technique for dual mode detection of organophosphorus pesticide.

A novel dual-mode analytical method by employing nanozyme was developed for the detection of organophosphorus pesticides (OPP) for the first time. The detection principle is that the pesticide could be hydrolyzed to para-nitrophenol (p-NP) in the presence of nanoceria as nanozyme. p-NP exhibits the bright yellow color, and its color intensity has a positive correlation with the pesticide concentration. Meanwhile, the characteristic absorption peak at 400 nm of p-NP increases gradually with the raised concentration of pesticide. Therefore, a dual-mode method including smartphone-based colorimetric and spectroscopic strategies was rationally developed. Herein, methyl-paraoxon was selected as the representative compound. Under the optimum conditions, the detection limits of both two strategies were calculated to be 0.42 µmol L-1. Finally, the present method was successfully applied in three edible medicinal plants (Semen nelumbinis, Semen Armeniacae Amarum, Rhizoma Dioscoreae). The present work offers a reliable and convenient approach for routine detection of pesticide based on two different detection mechanisms.

Music intervention improves spatial learning and memory and alters serum proteomics profiling in rats.

Music has a long history of healing or mitigating physical and mental illness in the clinical setting. We aimed to test changes in behavioral cognition and serum proteomics in rats undergoing music intervention (MI). The Morris water maze (MWM) was used to evaluate spatial learning and memory in rats. Serum protein expression profiling was examined using magnetic bead-based matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF-MS). MI improved spatial learning and memory in both male and female rats. Peak 1708.61 (m/z values) was significantly increased in MI females vs. female controls. Peak 3925.09 (m/z values) was significantly reduced in MI males versus male controls. The two differential serum peptide peaks (m/z values: 1708.61, 3925.09) were further sequence identified as regions of proteins Desmin and Acsm1. Western blot and immunofluorescence testing of Desmin expression showed consistent results on proteomics analysis. MI plays an important role in behavioral cognition and protein expression in rats. This study provides a foundation in proteomics that suggests that MI might improve spatial learning and memory ability.

Nonoccupational Exposure to Pyrethroids and Risk of Coronary Heart Disease in the Chinese Population.

Pyrethroids and the metabolites have been frequently observed in the environment. Animal data suggests that pyrethroids can induce adverse effect on the cardiovascular system but there are no human studies examining pyrethoids exposure as a risk for coronary heart disease (CHD). We analyzed three nonspecific pyrethroids metabolites in urine and studied the association with CHD risk. A total of 72 CHD patients and 136 healthy subjects were recruited in Shanxi province in China from 2013 to 2014 by matching age and gender. The median concentrations of urinary cis-CDDA (cis-3-(2,2-dichlorovinyl)-2,2-dimethyl cyclopropane carboxylic acid), trans-CDDA (trans-3-(2,2-dichlorovinyl)-2,2-dimethyl cyclopropane carboxylic acid) and 3-PBA (3-phenoxybenzoic acid) among healthy subjects were 1.03, 0.42, 0.74 µg/L respectively, while the median concentrations of the three metabolites among CHD patients were 1.93, 1.07, 1.09 µg/L respectively, significantly higher than healthy subjects. Upper tertile of urinary pyrethroid metabolites were associated with an increased risk of CHD compared with the lowest tertile (cis-CDDA: ORT3vsT1 = 6.86, 95% CI: 2.76-17.06, p-trend = 0.000; trans-CDDA: ORT3vsT1 = 6.94; 95% CI: 2.80-17.19; p-trend =0.000; 3-PBA: ORT3vsT1 = 3.62; 95% CI: 1.48-8.88; p-trend = 0.009; total pyrethroid metabolites: ORT3vsT1 = 4.55; 95% CI: 1.80-11.54; p-trend = 0.002). This study provides information on pyrethroids exposure in China and reveals a possible positive association between pyrethroids exposure and the risk of coronary heart disease.

Identification of novel serum peptides biomarkers for female breast cancer patients in Western China.

This study aimed to identify novel serum peptides biomarkers for female breast cancer (BC) patients. We analyzed the serum proteomic profiling of 247 serum samples from 96 BC patients, 48 additional paired pre- and postoperative BC patients, 39 fibroadenoma patients as benign disease controls, and 64 healthy controls, using magnetic-bead-based separation followed by MALDI-TOF MS. ClinProTools software identified 78 m/z peaks that differed among all analyzed groups, ten peaks were significantly different (P < 0.0001), with Peaks 1-6 upregulated and Peaks 7-10 downregulated in BC. Moreover, three peaks of ten (Peak 1, m/z: 2660.11; Peak 2, m/z: 1061.09; Peak 10, m/z: 1041.25) showed a tendency to return to healthy control values after surgery. And these three peptide biomarkers were identified as FGA605-629, ITIH4 347-356, and APOA2 43-52. Methods used in this study could generate serum peptidome profiles of BC, and provide a new approach to identify potential biomarkers for diagnosis as well as prognosis of this malignancy.

Deciphering cell types by integrating scATAC-seq data with genome sequences.

The single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) technology provides insight into gene regulation and epigenetic heterogeneity at single-cell resolution, but cell annotation from scATAC-seq remains challenging due to high dimensionality and extreme sparsity within the data. Existing cell annotation methods mostly focus on the cell peak matrix without fully utilizing the underlying genomic sequence. Here we propose a method, SANGO, for accurate single-cell annotation by integrating genome sequences around the accessibility peaks within scATAC data. The genome sequences of peaks are encoded into low-dimensional embeddings, and then iteratively used to reconstruct the peak statistics of cells through a fully connected network. The learned weights are considered as regulatory modes to represent cells, and utilized to align the query cells and the annotated cells in the reference data through a graph transformer network for cell annotations. SANGO was demonstrated to consistently outperform competing methods on 55 paired scATAC-seq datasets across samples, platforms and tissues. SANGO was also shown to be able to detect unknown tumor cells through attention edge weights learned by the graph transformer. Moreover, from the annotated cells, we found cell-type-specific peaks that provide functional insights/biological signals through expression enrichment analysis, cis-regulatory chromatin interaction analysis and motif enrichment analysis.

A new chiral residue analysis method for triazole fungicides in water using dispersive liquid-liquid microextraction (DLLME).

A rapid, simple, reliable, and environment-friendly method for the residue analysis of the enantiomers of four chiral fungicides including hexaconazole, triadimefon, tebuconazole, and penconazole in water samples was developed by dispersive liquid-liquid microextraction (DLLME) pretreatment followed by chiral high-performance liquid chromatography (HPLC)-DAD detection. The enantiomers were separated on a Chiralpak IC column by HPLC applying n-hexane or petroleum ether as mobile phase and ethanol or isopropanol as modifier. The influences of mobile phase composition and temperature on the resolution were investigated and most of the enantiomers could be completely separated in 20 min under optimized conditions. The thermodynamic parameters indicated that the separation was enthalpy-driven. The elution orders were detected by both circular dichroism detector (CD) and optical rotatory dispersion detector (ORD). Parameters affecting the DLLME performance for pretreatment of the chiral fungicides residue in water samples, such as the extraction and dispersive solvents and their volume, were studied and optimized. Under the optimum microextraction condition the enrichment factors were over 121 and the linearities were 30-1500 µg L(-1) with the correlation coefficients (R(2)) over 0.9988 and the recoveries were between 88.7% and 103.7% at the spiking levels of 0.5, 0.25, and 0.05 mg L(-1) (for each enantiomer) with relative standard deviations varying from 1.38% to 6.70% (n = 6) The limits of detection (LODs) ranged from 8.5 to 29.0 µg L(-1) (S/N = 3).

Conjugation of the Fn14 Ligand to a SMAC Mimetic Selectively Suppresses Experimental Squamous Cell Carcinoma in Mice.

The mimetic of SMAC induced cell death in cancers by depleting the inhibitor of apoptosis proteins. Recent studies showed that Fn14 is overexpressed in the cells of squamous cell carcinoma (SCC), providing a promising candidate target for selective antitumor therapy. In this study, we conjugated a small-molecule SMAC mimetic MV1 to the ligand of Fn14, TWEAK. Our results showed that TWEAK‒MV1 conjugate retained adequate binding specificity to Fn14-positive SCC cells in vitro and accumulated selectively in tumor tissue of cutaneous SCC xenografts mice after intraperitoneal administration. This conjugation compound exhibited remarkable effectiveness in suppressing tumor growth and extending overall survival without causing significant side effects in SCC xenograft mice. Moreover, TWEAK‒MV1 conjugate greatly enhanced both apoptotic and necroptotic cell death both in vitro and in vivo, accompanied by a cellular inhibitor of apoptosis proteins degradation as well as activation of receptor-interacting protein kinase. Taken together, our preclinical data suggested that the designed conjugation compound of TWEAK and MV1 might provide a potential therapeutic strategy for cutaneous SCC with improved antitumor efficacy and negligible toxicity.

Semi-wrapped gold nanoparticles for surface-enhanced Raman scattering detection.

Researchers have struggled to develop highly reliable and sensitive surface-enhanced Raman scattering (SERS) substrates for detecting compounds in complicated systems. In this work, a strategy by constructing Au cores with incompletely wrapped Prussian blue (PB) for highly reliable and sensitive SERS substrate is proposed. The wrapped PB layers can provide the internal standard (IS) to calibrate the SERS signal floatation, whereas the exposed surface of Au cores offers the enhancement effect. The balance between the signal self-calibration and enhancement (hence the trade-off between SERS reliability and sensitivity) is obtained by the approximate semi-wrapping configuration of PB layers on Au cores (i.e., SW-Au@PB). The proposed SW-Au@PB nanoparticles (NPs) exhibit the similar enhancement factor as the pristine Au NPs and contribute to the ultralow RSD (8.55%) of calibrated SERS signals using R6G as probe molecules. The simultaneously realized reliability and sensitivity of SW-Au@PB NPs also enables the detection of hazardous pesticide residues such as paraquat and thiram in herbal plants, with the average detection accuracy up to 92%. Overall, this work mainly provides a controllable synthetic strategy for incompletely wrapped NPs, and most importantly, explores the potential with a proof-of-concept practical application in accurate and sensitive Raman detection of hazardous substances with varying solubility.

Copper ions assisted fluorescent detection of some dithiocarbamates based on nickel nanocluster with aggregation-induced emission enhancement behavior.

Pesticide residue contamination has become an urgent issue since it threatens both the natural environment and public health. In this study, a fluorescent method for detecting dithiocarbamate (DTC) compounds was constructed based on novel nickel nanoclusters (Ni NCs) and copper ions (Cu2+). The water-soluble fluorescent Ni NCs were synthesized for the first time through a one-pot method using glutathione as stabilizer and ascorbic acid as reducing agent. The as-prepared Ni NCs exhibited a maximum fluorescence emission at 445 nm when excited by 380 nm. And they displayed aggregation-induced emission enhancement when ethylene glycol was introduced into the nanocluster aqueous solution. Based on the Ni NCs, a label-free fluorescence quenching sensor was established for sensitive and selective detection of DTC compounds with the assistance of Cu2+. The complex formed by DTC and Cu2+ led to fluorescence quenching of Ni NCs through inner filter effect. The sensing method was successfully applied to two typical DTC compounds, thiram and disulfiram, with good linearity over a wide linear range and a low detection limit. Moreover, the proposed approach was capable of thiram detection in real samples, which confirms the potential of this sensing method as a platform for DTC compound detection.

A ratiometric fluorescent sensing system for the selective and ultrasensitive detection of pesticide residues via the synergetic effects of copper nanoclusters and carbon quantum dots.

Agricultural products, such as foodstuffs and herbal medicines, may be contaminated by pesticides. Therefore, developing sensitive methods for pesticide detection are urgently needed for the assurance of food safety. In this study, a ratiometric fluorescent sensing system based on blue-emitted nitrogen-doped carbon quantum dots (N-CQDs) and red-emitted copper nanoclusters (CuNCs) complex was fabricated for pesticide detection. The selective detection of thiram and paraquat, two typical widely used pesticides, can be easily realized by changing the solvent environment. The detection limit can be reached as low as 7.49 nM and 3.03 nM, respectively. A good linear correlation was found over the concentration range from 10 to 500 nM for thiram and 5 to 100 nM for paraquat. More interestingly, fast and visual detection of thiram and paraquat can be achieved via smartphone-based colorimetric analysis, which has provided an effective implementation for on-site monitoring of the levels of pesticide residues in food.

Synthesis of Copper Nanocluster and Its Application in Pollutant Analysis.

Copper nanoclusters (Cu NCs) with their inherent optical and chemical advantages have gained increasing attention as a kind of novel material that possesses great potential, primarily in the use of contaminants sensing and bio-imaging. With a focus on environmental safety, this article comprehensively reviews the recent advances of Cu NCs in the application of various contaminants, including pesticide residues, heavy metal ions, sulfide ions and nitroaromatics. The common preparation methods and sensing mechanisms are summarized. The typical high-quality sensing probes based on Cu NCs towards various target contaminants are presented; additionally, the challenges and future perspectives in the development and application of Cu NCs in monitoring and analyzing environmental pollutants are discussed.

Chemoproteomics-enabled discovery of covalent RNF114-based degraders that mimic natural product function.

The translation of functionally active natural products into fully synthetic small-molecule mimetics has remained an important process in medicinal chemistry. We recently discovered that the terpene natural product nimbolide can be utilized as a covalent recruiter of the E3 ubiquitin ligase RNF114 for use in targeted protein degradation-a powerful therapeutic modality within modern-day drug discovery. Using activity-based protein profiling-enabled covalent ligand-screening approaches, here we report the discovery of fully synthetic RNF114-based recruiter molecules that can also be exploited for PROTAC applications, and demonstrate their utility in degrading therapeutically relevant targets, such as BRD4 and BCR-ABL, in cells. The identification of simple and easily manipulated drug-like scaffolds that can mimic the function of a complex natural product is beneficial in further expanding the toolbox of E3 ligase recruiters, an area of great importance in drug discovery and chemical biology.