Multi-omics characterization of macrophage polarization-related features in osteoarthritis based on a machine learning computational framework.

Background: OA imposes a heavy burden on patients and society in that its mechanism is still unclear, and there is a lack of effective targeted therapy other than surgery. Methods: The osteoarthritis dataset GSE55235 was downloaded from the GEO database and analyzed for differential genes by limma package, followed by analysis of immune-related modules by xcell immune infiltration combined with the WGCNA method, and macrophage polarization-related genes were downloaded according to the Genecard database, and VennDiagram was used to determine their intersection. These genes were also subjected to gene ontology (GO), disease ontology (DO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analyses. Using machine learning, the key osteoarthritis genes were finally screened. Using single gene GSEA and GSVA, we examined the significance of these key gene functions in immune cell and macrophage pathways. Next, we confirmed the correctness of the hub gene expression profile using the GSE55457 dataset and the ROC curve. Finally, we projected TF, miRNA, and possible therapeutic drugs using the miRNet, TargetScanHuman, ENCOR, and NetworkAnalyst databases, as well as Enrichr. Results: VennDiagram obtained 71 crossover genes for DEGs, WGCNA-immune modules, and Genecards; functional enrichment demonstrated NF-κB, IL-17 signaling pathway play an important role in osteoarthritis-macrophage polarization genes; machine learning finally identified CSF1R, CX3CR1, CEBPB, and TLR7 as hub genes; GSVA analysis showed that CSF1R, CEBPB play essential roles in immune infiltration and macrophage pathway; validation dataset GSE55457 analyzed hub genes were statistically different between osteoarthritis and healthy controls, and the AUC values of ROC for CSF1R, CX3CR1, CEBPB and TLR7 were more outstanding than 0.65. Conclusions: CSF1R, CEBPB, CX3CR1, and TLR7 are potential diagnostic biomarkers for osteoarthritis, and CSF1R and CEBPB play an important role in regulating macrophage polarization in osteoarthritis progression and are expected to be new drug targets.

Modulating α-synuclein propagation and decomposition: Implications in Parkinson's disease therapy.

α-Synuclein (α-Syn) is closely related to the pathogenesis of Parkinson's disease (PD). Under pathological conditions, the conformation of α-syn changes and different forms of α-syn lead to neurotoxicity. According to Braak stages, α-syn can propagate in different brain regions, inducing neurodegeneration and corresponding clinical manifestations through abnormal aggregation of Lewy bodies (LBs) and lewy axons in different types of neurons in PD. So far, PD lacks early diagnosis biomarkers, and treatments are mainly targeted at some clinical symptoms. There is no effective therapy to delay the progression of PD. This review first summarized the role of α-syn in physiological and pathological states, and the relationship between α-syn and PD. Then, we focused on the origin, secretion, aggregation, propagation and degradation of α-syn as well as the important regulatory factors in these processes systematically. Finally, we reviewed some potential drug candidates for alleviating the abnormal aggregation of α-syn in order to provide valuable targets for the treatment of PD to cope with the occurrence and progression of this disease.

Fabrication of large-area photonic crystal-modified X-ray scintillator imager for optical coding imaging.

The limited pattern area of periodic nanostructures limits the development of practical devices. This study introduces an X-ray interference lithography (XIL) stitching technique to fabricate a large-area (1.5 cm × 1.5 cm) two-dimensional photonic crystal (PhC) on the YAG: Ce scintillator, which functions as an encoder in a high numerical aperture optical encoding imaging system to effectively capture high-frequency information. An X-ray imaging experiment revealed a substantial 7.64 dB improvement in the signal-to-noise ratio (SNR) across a large field of view (2.6 mm × 2.6 mm) and achieved comparable or superior image quality with half the exposure dose. These findings have significant implications for advancing practical applications of X-ray imaging.

MiRNA-100 ameliorates diabetes mellitus-induced erectile dysfunction by modulating autophagy, anti-inflammatory, and antifibrotic effects.

BACKGROUND: Diabetes mellitus-induced erectile dysfunction (DMED) has become a common disease in adult men that can seriously reduce the quality of life of patients, and new therapies are urgently needed. miRNA-100 has many targets and can induce autophagy and reduce fibrosis by inhibiting the mTOR pathway and the TGF-ß pathway. However, no research has been conducted with miR-100 in the field of DMED, and the specific mechanism of action is still unclear. OBJECTIVES: To ascertain the effects of miR-100 on corpus cavernosum tissue of DMED rats and vascular endothelial cells in a high glucose environment and to elucidate the relevant mechanisms in autophagy, fibrosis and inflammation to find a new approach for the DMED therapy. METHODS: Thirty rats were divided into three groups: the control group, the DMED group, and the DMED + miR-100 group. Using intraperitoneal injections of streptozotocin, all rats except the control group were modeled with diabetes mellitus, which was verified using the apomorphine (APO) test. For rats in the DMED + miR-100 group, rno-miR-100-5p agomir (50 nmol/kg, every 2 days, 6 times in total) was injected via the tail vein. After 13 weeks, the erectile function of each rat was assessed using cavernous manometry, and the corpus cavernosum tissue was harvested for subsequent experiments. For cellular experiments, human coronary microartery endothelial cells (HCMEC) were divided into four groups: the control group, the high-glucose (HG, 40 mM) group, the HG + mimic group, and the HG + inhibitor group. The cells were cultured for 6 days and collected for subsequent experiments 2 days after transfection. RESULTS: Diabetic modeling impaired the erectile function in rats, and miR-100 reversed this effect. By measuring autophagy-related proteins such as mTOR/Raptor/Beclin1/p62/LC3B, we found that miR-100 could suppress the expression of mTOR and induce autophagy. The analysis of the eNOS/NO/cGMP axis function indicated that impaired endothelial function was improved by miR-100. By evaluating the TGF-ß1/CTGF/Smad2/3 and NF-κB/TNF-α pathways, we found that miR-100 could lower the level of inflammation and fibrosis, which contributed to the improvement of the erectile function. Cellular experiments can be used as supporting evidence for these findings. CONCLUSION: MiR-100 can improve the erectile function by inhibiting mTOR and thus inducing autophagy, improving the endothelial function through the eNOS/NO/cGMP axis, and exerting antifibrotic and anti-inflammatory effects, which may provide new ideas and directions for the treatment of DMED.

STX4 as a potential biomarker for predicting prognosis and guiding clinical treatment decisions in clear cell renal cell carcinoma.

Clear cell renal cell carcinoma (ccRCC) represents a frequent subtype of kidney cancer, with the prognosis remaining poor for individuals with metastatic disease. Given its resistance to both radiation and chemotherapy, targeted therapies and immunotherapies have emerged as critical for effective ccRCC treatment. Within this context, the SNARE protein STX4, which is associated with malignant cancer cell migration, provides a promising focus. The underlying mechanism, however, requires further illumination. Furthermore, the influence of STX4 on the ccRCC tumor microenvironment remains to be determined. In our research, we utilized multiple databases and immunohistochemical staining to confirm differential STX4 expression and its prognostic implications. We evaluated the potential tumor-promoting function of STX4 in ccRCC cell lines through molecular studies. Additionally, we conducted functional enrichment analysis to delve deeper into the underlying mechanisms and performed immune infiltration and drug sensitivity analyses to assess the potential of STX4 as a prognostic biomarker and therapeutic target. Our study reveals that STX4 contributes to cancer progression by enhancing AKT expression and stimulating the activation of VEGF signaling pathways. Additionally, STX4 further fosters CD8+ T-cell infiltration and diminishes the percentage of CAFs and M2-TAMs. Our findings suggest that patients presenting higher STX4 levels may exhibit enhanced responsiveness to immunotherapy and higher sensitivity to the medications axitinib and everolimus. Finally, we propose STX4 expression assessment as a novel approach to predict patient response to respective immunotherapies and targeted treatments, hence potentially improving patient outcomes.

Additive Manufacturing of Transparent Multi-Component Nanoporous Glasses.

Fabrication of glass with complex geocd the low resolution of particle-based or fused glass technologies. Herein, a high-resolution 3D printing of transparent nanoporous glass is presented, by the combination of transparent photo-curable sol-gel printing compositions and digital light processing (DLP) technology. Multi-component glass, including binary (Al2 O3 -SiO2 ), ternary (ZnO-Al2 O3 -SiO2 , TiO2 -Al2 O3 -SiO2 ), and quaternary oxide (CaO-P2 O5 -Al2 O3 -SiO2 ) nanoporous glass objects with complex shapes, high spatial resolutions, and multi-oxide chemical compositions are fabricated, by DLP printing and subsequent sintering process. The uniform nanopores of Al2 O3 -SiO2 -based nanoporous glasses with the diameter (≈6.04 nm), which is much smaller than the visible light wavelength, result in high transmittance (>95%) at the visible range. The high surface area of printed glass objectives allows post-functionalization via the adsorption of functional guest molecules. The photoluminescence and hydrophobic modification of 3D printed glass objectives are successfully demonstrated. This work extends the scope of 3D printing to transparent nanoporous glasses with complex geometry and facile functionalization, making them available for a wide range of applications.

Integrating bioinformatic analysis and detailed experiments reveal an EMT-related biomarker for clear cell renal cell carcinoma.

BACKGROUND: Epithelial-mesenchymal transition (EMT) is associated with early recurrence and a poor prognosis in clear cell renal cell carcinoma (ccRCC). Studies have shown that EMT-related genes play an important regulatory role in tumor invasion, metastasis, and drug resistance, but the biological functions of EMT-related genes in ccRCC have not been specifically described. METHODS: The mRNA and clinicopathological data of 532 ccRCC and 72 normal samples were downloaded from The Cancer Genome Atlas as a training set. The gene expression matrix and survival data of 91 and 101 ccRCC samples were obtained from the International Cancer Genome Consortium and the ArrayExpress databases as validation sets, respectively. Univariate Cox analysis was used to identify and cluster prognostic genes, and multivariate Cox was performed to construct a prognostic signature. Moreover, CIBERSORT and CellMiner were used to assess immune cell infiltration and prognostic gene-drug sensitivity of the signature, respectively. Most importantly, we performed detailed experiments to verify the oncogenic function of a significant gene, OLFML2B, in vitro and in vivo. RESULTS: We constructed a prognostic signature including seven genes and divided patients into high-risk and low-risk groups. The prognosis of the high-risk group was significantly worse than that of the low-risk group through Kaplan-Meier survival analysis. Interestingly, significant differences were observed in clinical characteristics and immune cell infiltration between the two groups. In addition, a significant correlation was found between the expression of prognostic genes and the sensitivity of tumor cells to chemotherapeutics. Most importantly, OLFML2B was proved to contribute to the proliferation and metastasis of ccRCC through detailed functional experiments in vitro and in vivo, and its prognostic efficacy for ccRCC patients was affirmed. CONCLUSION: We identified the prognostic signature of seven genes based on EMT-related genes as prognostic biomarkers for ccRCC. Besides, OLFML2B was validated as a potential diagnostic and therapeutic target for ccRCC by our detailed experiments.

Effects of attapulgite on the growth status of submerged macrophytes Vallisneria spiralis and sediment microenvironment.

The effects of raw attapulgite clay and thermally modified attapulgite clay on the growth status of submerged plant Vallisneria Spiralis (V. spiralis) and the microenvironment of sediment were first explored. The results demonstrated that the attapulgite could effectively promote the development of V. spiralis and improve plant stress resistance by enhancing the activity of antioxidant enzymes. The 10% addition of attapulgite clay increased the biomass of V. spiralis by 27%∼174%, and the promoted rate of raw attapulgite clay was 2∼5 times of modified attapulgite clay. The attapulgite increased redox potential in sediment (P < 0.05) and provided proper niches for organism propagation, further promoting the degradation of organic matter and nutrient metabolism in sediment. The value of Shannon, Chao, and Ace was 9.98, 4865.15, 5029.08 in the 10% modified attapulgite group, and 10.12, 4856.85, 4947.78 in the 20% raw attapulgite group, respectively, indicating that the attapulgite could increase the microbial diversity and abundance in sediment. Additionally, the nutrient elements, such as Ca, Na, S, Mg, K, Zn, and Mo, that dissolved from attapulgite may also promote the V. spiralis growth. This study provided an environment-friendly approach to facilitating submerged macrophyte restoration in the eutrophic lake ecosystem.

A novel gene signature related to oxidative stress predicts the prognosis in clear cell renal cell carcinoma.

Clear cell renal cell carcinoma (ccRCC) is considered to be related to the worse prognosis, which might in part be attributed to the early recurrence and metastasis, compared with other type of kidney cancer. Oxidative stress refers to an imbalance between production of oxidants and antioxidant defense. Accumulative studies have indicated that oxidative stress genes contribute to the tumor invasion, metastasis and drug sensitivity. However, the biological functions of oxidative stress genes in ccRCC remain largely unknown. In this study, we identified 1,399 oxidative stress genes from GeneCards with a relevance score ≥7. Data for analysis were accessed from The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) database, and were utilized as training set and validation set respectively. Univariate Cox analysis, least absolute shrinkage and selection operator (LASSO) Cox regression and multivariate Cox were employed to construct a prognostic signature in ccRCC. Finally, a prognostic signature including four different oxidative stress genes was constructed from 1,399 genes, and its predictive performance was verified through Kaplan-Meier survival analysis and the receiver operating characteristic (ROC) curve. Interestingly, we found that there was significant correlation between the expression of oxidative stress genes and the immune infiltration and the sensitivity of tumor cells to chemotherapeutics. Moreover, the highest hazard ratio gene urocortin (UCN) was chosen for further study; some necessary vitro experiments proved that the UCN could promote the ability of ccRCC proliferation and migration and contribute to the degree of oxidative stress. In conclusion, it was promising to predict the prognosis of ccRCC through the four oxidative stress genes signature. UCN played oncogenic roles in ccRCC by influencing proliferation and oxidative stress pathway, which was expected to be the novel therapeutic target for ccRCC.

A predictive signature based on enhancer RNA associates with immune infiltration and aids treatment decision in clear cell renal cell carcinoma.

Clear cell renal cell carcinoma (ccRCC) is a prevalent urinary malignancy. Despite the recent development of better diagnostic tools and therapy, the five-year survival rate for individuals with advanced and metastatic ccRCC remains dismal. Unfortunately, ccRCC is less susceptible to radiation and chemotherapy. Consequently, targeted therapy and immunotherapy play a crucial role in the treatment of ccRCC. Enhancer RNAs (eRNAs) are noncoding RNAs transcribed by enhancers. Extensive research has shown that eRNAs are implicated in a variety of cancer signaling pathways. However, the biological functions of eRNAs have not been systematically investigated in ccRCC. In this study, we conducted a comprehensive investigation of the role of eRNAs in the onset and management of ccRCC. Patient prognosis-influencing eRNAs and target genes were chosen to construct a predictive signature. On the basis of the median riskscore, ccRCC patients were split into high- and low-risk subgroups. The prediction efficiency was assessed in several cohorts, and multi-omics analysis was carried out to investigate the differences and underlying mechanisms between the high- and low-risk groups. In addition, we investigated its potential to facilitate clinical treatment choices. The riskscore might be used to forecast a patient's response to immunotherapy and targeted therapy, giving a revolutionary method for selecting treatment regimens with pinpoint accuracy.

A novel flavone-based ESIPT ratiometric fluorescent probe for selective sensing and imaging of hydrogen polysulfides.

Hydrogen polysulfides (H2Sn) as an important member of reactive sulfur species is closely relevant to many physiological functions in redox homeostasis and metabolism. Dual-channel monitor the changes of H2Sn level in vivo is highly desired. Herein we design a simple ratiometric fluorescent probe based on flavone skeleton for highly selective detection of H2Sn. The probe HF-NA-MC bearing 2-fluoro-5-nitrobenzoic acid group inhibited the intramolecular ESIPT process, which show the blue fluorescence of adjacent naphthalene unit. In the presence of H2Sn, the enol form of probe is converted to conjugated keto form, resulted in a 90 nm red-shift of fluorescence emission from 450 nm to 540 nm. The ratiometric intensity (I540/I450) of the probe exhibits a good linear relationship toward H2Sn in the range of 0-120 µM, and the detection limit is estimated to be 0.63 µM. The ratiometric fluorescent probe shows high specificity and anti-interference ability for H2Sn over other related reactive sulfur species. The probe HF-NA-MC shows promising outlook and could be applied to the confocal imaging of H2Sn by dual emission channels in Hela cells.

P2Y12 receptor as a new target for electroacupuncture relieving comorbidity of visceral pain and depression of inflammatory bowel disease.

BACKGROUND: The P2Y12 receptor is a kind of purinoceptor that is engaged in platelet aggregation, and P2Y12 inhibitors have been used in clinical antithrombotic therapy. The P2Y12 receptor in microglia induces interleukin-1ß (IL-1ß) expression, which is a key mediator of depression in the brain. Although peripheral P2Y12 is involved in neuropathic pain, whether P2Y12 expression in the medial prefrontal cortex (mPFC) is associated with comorbidities of visceral pain and depression remains unclear. Accumulating evidence suggests that electroacupuncture (EA) is effective in treating inflammatory bowel disease (IBD), but its mechanism is unknown. This study aimed to determine whether P2Y12 expression in the mPFC is associated with comorbidities of visceral pain and depression in IBD and whether EA treats IBD by targeting the P2Y12 receptor. METHODS: We used 2,4,6-trinitrobenzene sulfonic acid (TNBS)-induced IBD mice. P2Y12 short hairpin RNA (shRNA) was stereotaxically injected into the bilateral mPFC. EA was performed on bilateral "Dachangshu" (BL25) acupoints once a day for 7 days. Von Frey filaments and colorectal distension were used to detect the mechanical pain threshold and visceral pain sensitivity. The sucrose preference test, tail suspension test and forced swimming test were used to evaluate depression in mice. Western blotting was used to test the expression of P2Y12 and IL-1ß. Immunofluorescence staining was used to assess microglial activity. RESULTS: We found that IBD mice presented visceral pain and depression associated with increased P2Y12 expression in the mPFC. P2Y12 shRNA significantly attenuated visceral pain and depression in IBD mice. P2Y12 shRNA significantly downregulated IL-1ß expression and inhibited the activation of microglia in the mPFC of IBD mice. Meanwhile, EA played a similar role of P2Y12 shRNA. EA significantly downregulated P2Y12 expression, weakened the activation of microglia, and then inhibited IL-1ß expression in the mPFC, thus relieving visceral pain and depression in IBD mice. CONCLUSION: The present study provided new ideas that the P2Y12 receptor in the mPFC could be a new target for the treatment of comorbid visceral pain and depression by EA. This may not only deepen our understanding of the analgesic and antidepressant mechanisms of EA but also promote the application of EA to treat IBD.

[Correlation between expression level of functional genes and tanshinones' accumulation in Salvia miltiorrhiza from different areas].

OBJECTIVE: To study the relationship between functional gene expression in Salvia miltiorrhiza from different producing areas and active principles, which might provide scientific basis for the gene regulation of tanshinones. METHOD: The quantitative determination of cryptotanshinone and tanshinone II A was carried out by using HPLC method, expression level of 3 functional genes of SmAACT, SmCMK and SmIPPI were investigated by real-time PCR method. RESULT: The content of active principles together with expression level of SmAACT and SmCMK were higher in S. miltiorrhiza from genuine producing areas including Henan and Shanxi, but lower in samples from Beijing which was non-genuine producing area. CONCLUSION: Expression level of SmAACT and SmCMK had close relationships involving tanshinones' accumulation, but the SmIPPI gene had not.

[Correlation analysis between single nucleotide polymorphism of beta-amyrin synthase and content of glycyrrhizic acid in Glycyrrhiza uralensis].

OBJECTIVE: To analyze the correlation between content of glycyrrhizic acid and the single nucleotide polymorphism of beta-amyrin synthase (bAS) in Glycyrrhiza uralensis. METHOD: glycyrrhizic acid content in 80 samples of the cultivated G. uralensis were determined by HPLC; According to the very significant level (P < 0.000 1), 80 samples in accordance with glycyrrhizic acid will be grouped by SAS 9.0; Using RT-PCR strategy to amplification the Open Reading Frame of beta-amyrin synthase with the template of total RNA extracted from roots of G. uralensis and then using DNAman to analyze the relationship between glycyrrhizic acid content and the single nucleotide polymorphism of beta-amyrin synthase (bAS). RESULT: There exited two mutation sites 94 bp and 254 bp, G/A conversion occurred at 94 bp site, which belonged to a missense mutation. G/A conversion led to the corresponding amino acid conversion (Gly --> Asp); C/T conversion occurred at 254 bp site, which belonged to a synonymous mutation. According to sequence variation, the samples were divided into four genotypes: G-T genotype, A-T genotype, G/A-C genotype and G-T genotype. CONCLUSION: A-T genotype, G/A-C genotype and G-T genotype are correlated with the high content of glycyrrhizic acid.