PI3K/Akt/FoxO Pathway Mediates Antagonistic Toxicity in HepG2 Cells Coexposed to Deoxynivalenol and Enniatins.

The emerging mycotoxins enniatins (ENNs) and the traditional mycotoxin deoxynivalenol (DON) often co-contaminate various grain raw materials and foods. While the liver is their common target organ, the mechanism of their combined effect remains unclear. In this study, the combined cytotoxic effects of four ENNs (ENA, ENA1, ENB, and ENB1) with DON and their mechanisms were investigated using the HepG2 cell line. Additionally, a population exposure risk assessment of these mycotoxins was performed by using in vitro experiments and computer simulations. The results showed that only ENA at 1/4 IC50 and ENB1 at 1/8 IC50 coexposed with DON showed an additive effect, while ENB showed the strongest antagonism at IC50 (CI = 3.890). Co-incubation of ENNs regulated the signaling molecule levels which were disrupted by DON. Transcriptome analysis showed that ENB (IC50) up-regulated the PI3K/Akt/FoxO signaling pathway and inhibited the expression of apoptotic genes (Bax, P53, Caspase 3, etc.) via phosphorylation of FoxO, thereby reducing the cytotoxic effects caused by DON. Both types of mycotoxins posed serious health risks, and the cumulative risk of coexposure was particularly important for emerging mycotoxins.

Characterization of the m6A/m1A/m5C/m7G-related regulators on the prognosis and immune microenvironment of glioma by integrated analysis of scRNA-seq and bulk RNA-seq data.

BACKGROUND: Proliferation, metabolism, tumor occurrence and development in gliomas are greatly influenced by RNA modifications. However, no research has integrated the four RNA methylation regulators of m6A, m1A, m5C and m7G in gliomas to analyze their relationship with glioma prognosis and intratumoral heterogeneity. METHODS: Based on three in-house single-cell RNA-sequencing (scRNA-seq) data, the glioma heterogeneity and characteristics of m6A/m1A/m5C/m7G-related regulators were elucidated. Based on publicly available bulk RNA-sequencing (RNA-seq) data, a risk-score system for predicting the overall survival (OS) for gliomas was established by three machine learning methods and multivariate Cox regression analysis, and validated in an independent cohort. RESULTS: Seven cell types were identified in gliomas by three scRNA-seq data, and 22 m6A/m1A/m5C/m7G-related regulators among the marker genes of different cell subtypes were discovered. Three m6A/m1A/m5C/m7G-related regulators were selected to construct prognostic risk-score model, including EIFA, NSUN6 and TET1. The high-risk patients showed higher immune checkpoint expression, higher tumor microenvironment scores, as well as higher tumor mutation burden and poorer prognosis compared with low-risk patients. Additionally, the area under the curve values of the risk score and nomogram were 0.833 and 0.922 for 3 year survival and 0.759 and 0.885 for 5 year survival for gliomas. EIF3A was significantly highly expressed in glioma tissues in our in-house RNA-sequencing data (p < 0.05). CONCLUSION: These findings may contribute to further understanding of the role of m6A/m1A/m5C/m7G-related regulators in gliomas, and provide novel and reliable biomarkers for gliomas prognosis and treatment.

Do atrophic gastritis and intestinal metaplasia reverse after Helicobacter pylori eradication?

BACKGROUND: It's still controversial whether Helicobacter pylori (H. pylori) eradication can reverse atrophic gastritis (AG) and intestinal metaplasia (IM). Therefore, we performed a meta-analysis to estimate the effect of H. pylori eradication on AG and IM. METHODS: We searched the PubMed, Web of Science and EMBASE datasets through April 2023 for epidemiological studies, which provided mean glandular atrophy (GA) or IM score before and after H. pylori eradication, or provided ORs, RRs or HRs and 95% CIs for the association of AG or IM with H. pylori eradication. Weighted mean difference (WMD) and pooled ORs and 95%CIs were used to estimate the effect of H. pylori eradication on AG and IM. RESULTS: Twenty articles with a total of 5242 participants were included in this meta-analysis. H. pylori eradication significantly decreased GA score in the antrum (WMD -0.36; 95% CI: -0.52, -0.19, p < 0.01), GA score in the corpus (WMD -0.35; 95% CI: -0.52, -0.19, p < 0.01), IM score in the antrum (WMD -0.16; 95% CI: -0.26, -0.07, p < 0.01) and IM score in the corpus (WMD -0.20; 95% CI: -0.37, -0.04, p = 0.01). H. pylori eradication significantly improved AG (pooled OR 2.96; 95% CI: 1.70, 5.14, p < 0.01) and IM (pooled OR 2.41; 95% CI: 1.24, 4.70, p < 0.01). The association remained significant in the subgroup analyses by study design, sites of lesions, regions and follow-up time. Although Publication bias was observed for AG, the association remained significant after trim-and-fill adjustment. CONCLUSIONS: H. pylori eradication could significantly improve AG and IM at early stage.

Predictive value of single-nucleotide polymorphism signature for nephrolithiasis recurrence: a 5-year prospective study.

Background: Genetic variations are linked to kidney stone formation. However, the association of single nucleotide polymorphism (SNPs) and stone recurrence has not been well studied. This study aims to identify genetic variants associated with kidney stone recurrences and to construct a predictive nomogram model using SNPs and clinical features to predict the recurrence risk of kidney stones. Methods: We genotyped 49 SNPs in 1001 patients who received surgical stone removal between Jan 1 and Dec 31 of 2012. All patients were confirmed stone-free by CT scan and then received follow-up at least 5 years. SNP associations with stone recurrence were analyzed by Cox proportion hazard model. A predictive nomogram model using SNPs and clinical features to predict the recurrence risk of kidney stones was developed by use of LASSO Cox regression. Results: The recurrence rate at 3, 5, 7 years were 46.8%, 71.2%, and 78.4%, respectively. 5 SNPs were identified that had association with kidney stone recurrence risk. We used computer-generated random numbers to assign 500 of these patients to the training cohort and 501 patients to the validation cohort. A nomogram that combined the 14-SNPs-based classifier with the clinical risk factors was constructed. The areas under the curve (AUCs) at 3, 5 and 7 years of this nomogram was 0.645, 0.723, and 0.75 in training cohort, and was 0.631, 0.708, and 0.727 in validation cohort, respectively. Results show that the nomogram presented a higher predictive accuracy than those of the SNP classifier or clinical factors alone. Conclusion: SNPs are significantly associated with kidney stone recurrence and should add prognostic value to the traditional clinical risk factors used to assess the kidney stone recurrence. A nomogram using clinical and genetic variables to predict kidney stone recurrence has revealed its potential in the future as an assessment tool during the follow-up of kidney stone patients.

Miniaturization in percutaneous nephrolithotomy: What is new?

Objective: To summarize recent advancements in mini-percutaneous nephrolithotomy (mini-PCNL) in surgical technique, stone removal strategy, lithotripsy, and surgical model from the current literature. Methods: We conducted a narrative review of relevant English-language articles up to October 2022 using the PubMed and Web of Science databases. The following keywords were used in the search: "percutaneous nephrolithotomy", "minimally invasive percutaneous nephrolithotomy", "mini-PCNL", "mini-perc", "mPCNL", and "miniaturization". Results: A series of new progress has been made in many aspects of mini-PCNL, such as further reduction of tract size-needle perc and further improvement of robotic-assisted PCNL-artificial intelligence-powered robotic devices. Conclusion: Many studies and trials have been conducted to reduce morbidity and increase the safety and effectiveness of mini-PCNL. It is crucial to realize that miniaturization of PCNL requires not only a smaller percutaneous tract size, but also an adjustment strategically in renal access, stone removal, lithotripsy, and surgical model in general. More large-scale prospective research needs to be carried out to further validate and optimize the safety and effectiveness of mini-PCNL.

Identification and validation of DNA methylation-driven gene PCDHB4 as a novel tumor suppressor for glioblastoma diagnosis and prognosis.

Aberrant DNA methylation is a critical regulator of gene expression in the development and progression of glioblastoma (GBM). However, the impact of methylation-driven gene PCDHB4 changes on GBM occurrence and progression remains unclear. Therefore, this study aimed to identify the PCDHB4 gene for early diagnosis and prognostic evaluation and clarify its functional role in GBM. Methylation-driven gene PCDHB4 was selected for GBM using the multi-omics integration method based on publicly available data sets. The diagnostic capabilities of PCDHB4 methylation and 5-hydroxymethylcytosines were validated in tissue and blood cell-free DNA (cfDNA) samples, respectively. Combined survival analysis of PCDHB4 methylation and immune infiltration cells evaluated the prognostic predictive performance of GBM patients. We identified that the PCDHB4 gene achieved high discriminative capabilities for GBM and normal tissues with an area under the curve value of 0.941. PCDHB4 hypermethylation was observed in cfDNA blood samples from GBM patients. Compared with GBM patients with PCDHB4 hypermethylation level, patients with PCDHB4 hypomethylation level had significantly poorer overall survival (p = 0.035). In addition, GBM patients with PCDHB4 hypermethylation and high infiltration of CD4+ T cell activation level had a favorable survival (p = 0.026). Moreover, we demonstrated that mRNA expression of PCDHB4 was downregulated in GBM tissues and upregulated in GBM cell lines with PCDHB4 demethylation, and PCDHB4 overexpression inhibited GBM cell proliferation and migration. In summary, we discovered a novel methylation-driven gene PCDHB4 for the diagnosis and prognosis of GBM and demonstrated that PCDHB4 is a tumor suppressor in vitro experiments.

Development and validation of cuproptosis molecular subtype-related signature for predicting immune prognostic characterization in gliomas.

PURPOSE: Cuproptosis, a novel programmed cell death, plays an important role in glioma growth, angiogenesis, and immune response. Nonetheless, the role of cuproptosis-related genes (CRGs) in the prognosis and tumor microenvironment (TME) of gliomas remains unknown. METHODS: By non-negative matrix factorization consensus clustering, 1286 glioma patients were classified based on the mRNA expression levels of 27 CRGs and investigated the association of immune infiltration and clinical characteristics with cuproptosis subtypes. A CRG-score system was constructed using LASSO and multivariate Cox regression methods and validated in independent cohorts to predict the prognosis of glioma patients. RESULTS: Glioma patients were divided into two cuproptosis subtypes. Cluster C2 was enriched in immune-related pathways, had higher macrophage M2, neutrophils, and CD8 + T cells, and poorer prognosis compared with cluster C1 which was enriched in metabolism-related pathways. We further constructed and validated the ten-gene CRG risk scores. Glioma patients in the high CRG-score group had higher tumor mutation burden, higher TME scores, and poorer prognoses compared with the low CRG-score group. Additionally, the AUC value of the CRG-score was 0.778 in predicting the prognosis of gliomas. WHO grading, IDH mutation, 1p/19q codeletion, and MGMT methylation were significant differences between high and low CRG-score groups. CONCLUSION: This study demonstrated that CRG-score was related to immune cell infiltration and could accurately predict gliomas' prognosis. Our findings may provide a novel understanding of the potential role of cuproptosis molecular pattern and TME in the immune response and prognosis of glioma patients.

Single-cell RNA-Seq and bulk RNA-Seq reveal reliable diagnostic and prognostic biomarkers for CRC.

PURPOSE: The potential role of epithelium-specific genes through the adenoma-carcinoma sequence in the development of colorectal cancer (CRC) remains unknown. Therefore, we integrated single-cell RNA sequencing and bulk RNA sequencing data to select diagnosis and prognosis biomarkers for CRC. METHODS: The CRC scRNA-seq dataset was used to describe the cellular landscape of normal intestinal mucosa, adenoma and CRC and to further select epithelium-specific clusters. Differentially expressed genes (DEGs) of epithelium-specific clusters were identified between intestinal lesion and normal mucosa in the scRNA-seq data throughout the adenoma-carcinoma sequence. Diagnostic biomarkers and prognostic biomarker (the risk score) for CRC were selected in the bulk RNA-seq dataset based on DEGs shared by the adenoma epithelium-specific cluster and the CRC epithelium-specific cluster (shared-DEGs). RESULTS: Among the 1063 shared-DEGs, we selected 38 gene expression biomarkers and 3 methylation biomarkers that had promising diagnostic power in plasma. Multivariate Cox regression identified  174 shared-DEGs as prognostic genes for CRC. We combined 1000 times LASSO-Cox regression and two-way stepwise regression to select 10 prognostic shared-DEGs to construct the risk score in the CRC meta-dataset. In the external validation dataset, the 1- and 5-year AUCs of the risk score were higher than those of stage, the pyroptosis-related genes (PRG) score and the cuproptosis-related genes (CRG) score. In addition, the risk score was closely associated with the immune infiltration of CRC. CONCLUSION: The combined analysis of the scRNA-seq dataset and the bulk RNA-seq dataset in this study provides reliable biomarkers for the diagnosis and prognosis of CRC.

Association between alcohol consumption and kidney stones in American adults: 2007-2016 NHANES.

Purpose: To investigate the association between alcohol consumption and kidney stones in American adults. Materials and methods: National Health and Nutrition Examination Survey (NHANES) datasets from 2007 to 2016 were utilized. Participants with a history of kidney stones and alcohol consumption aged 20 or older were included. Weighted proportions and regression analysis were used to assess the association between alcohol consumption and kidney stones by adjusting age, gender, race, marital status, education, recreational activities, smoking, and several comorbidities. Results: Eleven population samples (Q1-Q11) were included from the NHANES dataset based on 11 questions compiled from the Alcohol Use Questionnaire (ALQ). In the fully adjusted regression model, none of these 11 samples demonstrated a significant association with urolithiasis, that is, alcohol consumption was not significantly associated with the incidence of kidney stones, even among heavy drinkers. Conclusion: Alcohol consumption is not significantly associated with the prevalence of kidney stones. This finding requires a more adequate sample size and a more detailed review of the history of kidney stones to be further verified.

Acetate attenuates hyperoxaluria-induced kidney injury by inhibiting macrophage infiltration via the miR-493-3p/MIF axis.

Hyperoxaluria is well known to cause renal injury and end-stage kidney disease. Previous studies suggested that acetate treatment may improve the renal function in hyperoxaluria rat model. However, its underlying mechanisms remain largely unknown. Using an ethylene glycol (EG)-induced hyperoxaluria rat model, we find the oral administration of 5% acetate reduced the elevated serum creatinine, urea, and protected against hyperoxaluria-induced renal injury and fibrosis with less infiltrated macrophages in the kidney. Treatment of acetate in renal tubular epithelial cells in vitro decrease the macrophages recruitment which might have reduced the oxalate-induced renal tubular cells injury. Mechanism dissection suggests that acetate enhanced acetylation of Histone H3 in renal tubular cells and promoted expression of miR-493-3p by increasing H3K9 and H3K27 acetylation at its promoter region. The miR-493-3p can suppress the expression of macrophage migration inhibitory factor (MIF), thus inhibiting the macrophages recruitment and reduced oxalate-induced renal tubular cells injury. Importantly, results from the in vivo rat model also demonstrate that the effects of acetate against renal injury were weakened after blocking the miR-493-3p by antagomir treatment. Together, these results suggest that acetate treatment ameliorates the hyperoxaluria-induced renal injury via inhibiting macrophages infiltration with change of the miR-493-3p/MIF signals. Acetate could be a new therapeutic approach for the treatment of oxalate nephropathy.

Comparison of 24-hour urine composition prior to and after stone removal in nephrolithiasis: a prospective observational study.

BACKGROUND: To evaluate 24-hour urine composition prior to and after complete stone removal in nephrolithiasis patients to determine potential relationship between kidney stones and patient metabolic status. METHODS: A prospective observational study was performed with patient enrollment from March 2019 to August 2020. 24-hour urine samples were collected prior to stone removal and 4 weeks after double-J stent removal, and examined the following urinary parameters: volume, creatinine, sodium, calcium, uric acid, citrate, oxalate, potassium, phosphorous, magnesium, and pH value. For each parameter, pairwise t test was performed to compare samples prior to and after stone removal. The number of cases that changed from normal to abnormal or vice versa was also evaluated for each parameter. The study was registered at http://clinicaltrials.gov/ (NCT03846011). RESULTS: A total of 109 patients completed 24-hour urine collections prior to and after stone removal. The urinary calcium and phosphate levels increased significantly after stone removal, showing a mean difference of 0.55 mmol (P=0.015) and 2.35 mmol (P=0.001) respectively. None of the other urinary parameters demonstrated a statistically significant difference when means were compared. The percentage differences for all urinary parameters ranged from 5.4% to 14.1%. The percentages of patients that presented clinically significant changes in urinary parameter values from normal to abnormal or vice versa ranged from 4.6% to 20.1%. CONCLUSIONS: Ideally, evaluation of 24-hour urine compositions should be undertaken after total stone removal, especially for patients with calcium stones. For patients who cannot achieve total stone removal, 24-hour urine samples should be thoroughly interpreted as urinary calcium and phosphate levels might be depleted in the presence of urinary stones.

Propagation of Pearcey Gaussian beams in a strongly nonlocal nonlinear medium.

We introduce the propagation of Pearcey Gaussian (PG) beams in a strongly nonlocal nonlinear medium (SNNM) analytically. Our results show that PG beams propagating in the SNNM have two different focusing positions. The intensity peak appears at different focusing positions depending on the selection of the nonlinear parameters. In addition, the effects of the nonlinear parameters and the scaling factor on the trajectory, the position of the intensity focusing, the intensity evolution between focus locations, and the radiation force are studied.

Palladium/Norbornene-Catalyzed Decarbonylative Difunctionalization of Thioesters.

The transition-metal-catalyzed decarboxylation of aryl carboxylic acids has drawn significant attention as an efficient and practical tool for the synthesis of substituted arenes. However, the decarboxylative construction of polysubstituted arenes with different contiguous substituents has not been widely reported. Herein, we describe a novel decarbonylative Catellani reaction via palladium-catalyzed, norbornene (NBE)-mediated polyfunctionalization of aromatic thioesters, which serve as readily available carboxylic acid derivatives. A variety of alkenyl, alkyl, aryl, and sulfur moieties could be conveniently introduced into the ipso-positions of the aromatic thioesters. By combining carboxyl-directed C-H functionalization and the classical Catellani reaction, our protocol allows for the construction of 1,2,3-trisubstituted and 1,2,3,4-tetrasubstituted arenes from simple aromatic acids. Furthermore, the late-stage functionalization of a series of drug molecules highlights the potential utility of the reaction.

Identification of STXBP6-IRF1 positive feedback loop in regulation of PD-L1 in cancer.

The clinical success of immune checkpoint blockade against diverse human cancers highlights the critical importance of insightful understanding into mechanisms underlying PD-L1 regulation. IFN-γ released by intratumoral lymphocytes regulates PD-L1 expression in tumor cells through JAK-STAT-IRF1 pathway, while the molecular events prime IRF1 to translocate into nucleus are still obscure. Here we identified STXBP6, previously recognized involving in SNARE complex assembly, negatively regulates PD-L1 transcription via retention of IRF1 in cytoplasm. IFN-γ exposure stimulates accumulation of cytosolic IRF1, which eventually saturates STXBP6 and triggers nuclear translocation of IRF1. Nuclear IRF1 in turn inhibits STXBP6 expression and thereby liberates more IRF1 to migrate to nucleus. Therefore, we identified a novel positive feedback loop between STXBP6 and IRF1 in regulation of PD-L1 expression in cancer. Furthermore, we demonstrate STXBP6 overexpression significantly inhibits T cell activation both in vitro and in vivo. These findings offer new insight into the complexity of PD-L1 expression in cancer and suggest a valuable measure to predict the response to PD-1/PD-L1-based immunotherapy.

Poly C Binding Protein 1 Regulates p62/SQSTM1 mRNA Stability and Autophagic Degradation to Repress Tumor Progression.

Accumulating evidence show that Poly C Binding Protein 1 (PCBP1) is deleted in distinct types of tumors as a novel tumor suppressor, but its tumor suppression mechanism remains elusive. Here, we firstly describe that downregulation of PCBP1 is significantly associated with clinical ovarian tumor progression. Mechanistically, PCBP1 overexpression affects various autophagy-related genes expression at various expression levels to attenuate the intrinsic cell autophagy, including the autophagy-initiating ULK, ATG12, ATG7 as well as the bona fide marker of autophagosome, LC3B. Accordingly, knockdown of the endogenous PCBP1 in turn enhances autophagy and less cell death. Meanwhile, PCBP1 upregulates p62/SQSTM1 via inhibition p62/SQSTM1 autophagolysome and proteasome degradation as well as its mRNA stability, consequently accompanying with the caspase 3 or 8 activation for tumor cell apoptosis. Importantly, clinical ovary cancer sample analysis consistently validates the relevance of PCBP1 expression to both p62/SQSTM1 and caspase-8 to overall survival, and indicates PCBP1 may be a master player to repress tumor initiation. Taken together, our results uncover the tumorigenic mechanism of PCBP1 depletion and suggest that inhibition of tumor cell autophagy with autophagic inhibitors could be an effective therapeutical strategy for PCBP1-deficient tumor.

The complete chloroplast genome of Geodorum eulophioides (Orchidaceae).

Geodorum eulophioides Schltr., is a critically Endangered orchid (IUCN). In this study, we report the first complete chloroplast (cp) genome of G. eulophioides to provide the underlying information for genetic breeding and conservation studies of this species. The cp genome sequence of G. eulophioides is 149,466 bp in length, which contains one large single-copy region (LSC, 85,436 bp), one small single-copy region (SSC, 14,086 bp), and two inverted repeat regions (IRs, 24,972 bp). The cp genome encoded 177 genes, of which 106 were unique genes (78 protein-coding genes, 24 tRNAs, and 4 rRNAs). Phylogenetic analysis showed that G. eulophioides is closely related to the genera Eulophia.

[A DenseNet-based diagnosis algorithm for automated diagnosis using clinical ECG data].

OBJECTIVE: To train convolutional networks using multi-lead ECG data and classify new data accurately to provide reliable information for clinical diagnosis. METHODS: The data were pre-processed with a bandpass filter, and signal framing was adopted to adjust the data of different lengths to the same size to facilitate network training and prediction. The dataset was expanded by increasing the sample size to improve the detection rate of abnormal samples. A depth-wise separable convolution structure was used for more specific feature extraction for different channels of twelve-lead ECG data. We trained the two classifiers for each label using the improved DenseNet to classify different labels. RESULTS: The propose model showed an accuracy of 80.13% for distinguishing between normal and abnormal ECG with a sensitivity of 80.38%, a specificity of 79.91% and a F1 score of 79.35%. CONCLUSIONS: The model proposed herein can rapidly and effectively classify the ECG data. The running time of a single dataset on GPU is 33.59 ms, which allows real-time prediction to meet the clinical requirements.

The complete chloroplast genome of Cymbidium erythraeum (Orchidaceae).

Cymbidium erythraeum Lindl. is an endangered species of Orchidaceae and distributed in China and Bhutan, India, Myanmar, Nepal, and Vietnam. Here, we report the complete chloroplast (cp) genome sequence and the cp genome features of C. erythraeum. The complete chloroplast (cp) genome sequence of C. erythraeum is 156,327 bp in length and including one large single-copy region (LSC, 85,404 bp), one small single-copy region (SSC, 20,021 bp), and two inverted repeat regions (IRs, 25,426 bp). The cp genome encoded 136 genes, of which 107 were unique genes (80 protein-coding genes, 23 tRNAs, and four rRNAs). The phylogenetic relationships show that C. erythraeum is closely related to other species in the genus Cymbidium and is sister with C. tracyanum.

The complete chloroplast genome of Dendrobium harveyanum (Orchidaceae).

Dendrobium harveyanum is an endangered species of Orchidaceae. Here we report the complete chloroplast (cp) genome sequence and the cp genome features of D. harveyanum. The complete cp genome sequence of D. harveyanum is 157,292 bp in length and presented a typical quadripartite structure including one large single-copy region (LSC, 86,583 bp), one small single-copy region (SSC, 19,449 bp), and two inverted repeat regions (IRs, 25,630 bp each). The cp genome encoded 138 genes, of which 120 were unique genes. The phylogenetic relationships show that D. harveyanum is closely related to other species in Dendrobium.

The complete chloroplast genome of Cymbidium changningense (Orchidaceae).

Cymbidium changningense is an ornamental orchid and endemic specie in China. Here, we report the complete chloroplast (cp) genome sequence and the cp genome features of C. changningense. The cp genome was 155,388 bp in length with a typical quadripartite structure, which was comprised of one large single copy (LSC, 84,522 bp) region and one small single copy (SSC, 20,622 bp) region separated by two inverted repeat (IR, 25,122 bp) regions. The cp genome encoded 132 genes, of which 108 were unique genes (80 protein-coding genes, 24 tRNAs, and four rRNAs). The phylogenetic analysis showed that C. changningense was sister with C. erythraeum.