MACC: a visual interactive knowledgebase of metabolite-associated cell communications.

Metabolite-associated cell communications play critical roles in maintaining the normal biological function of human through coordinating cells, organs and physiological systems. Though substantial information of MACCs has been continuously reported, no relevant database has become available so far. To address this gap, we here developed the first knowledgebase (MACC), to comprehensively describe human metabolite-associated cell communications through curation of experimental literatures. MACC currently contains: (a) 4206 carefully curated metabolite-associated cell communications pairs involving 244 human endogenous metabolites and reported biological effects in vivo and in vitro; (b) 226 comprehensive cell subtypes and 296 disease states, such as cancers, autoimmune diseases, and pathogenic infections; (c) 4508 metabolite-related enzymes and transporters, involving 542 pathways; (d) an interactive tool with user-friendly interface to visualize networks of multiple metabolite-cell interactions. (e) overall expression landscape of metabolite-associated gene sets derived from over 1500 single-cell expression profiles to infer metabolites variations across different cells in the sample. Also, MACC enables cross-links to well-known databases, such as HMDB, DrugBank, TTD and PubMed etc. In complement to ligand-receptor databases, MACC may give new perspectives of alternative communication between cells via metabolite secretion and adsorption, together with the resulting biological functions. MACC is publicly accessible at: http://macc.badd-cao.net/.

Comparison of two swept-source optical coherence tomography devices, a Scheimpflug camera system and a ray-tracing aberrometer in the measurement of corneal power in patients with cataract.

PURPOSE: To assess the differences and similarities in the corneal curvature obtained by two swept-source optical coherence tomography (SS-OCT) devices, Scheimpflug imaging system and one ray tracing aberrometer in patients with cataracts. Moreover, this study aimed to compare the differences in posterior corneal (PK), total corneal (TK) and true net power (TNP) measurements among the IOLMaster 700, CASIA2, and Pentacam. METHODS: A total of 200 eyes of 200 patients (116 female, 58%) were enrolled in this study, with a mean age of 65.9 ± 9.5 years. The flattest (Kf), steepest (Ks), and mean cornal powers (Km), J0, and J45 were obtained using two SS-OCT-based biometric devices, one rotating camera system and one ray-tracing aberrometer. The PK, TK and TNP values were also measured using these devices. To evaluate the differences and similarities between the devicves, the Friedman test, Pearson correlation coefficient (r), intraclass coefficient correlation (ICC) and Bland‒Altman plots with 95% limits of agreement (LoA) were used, and boxplots and stacked histograms were generated to describe the distributions of the data. RESULTS: There were no significant differences between the IOLMaster 700 and Pentacam for any of the keratometry values. Additionally, there were no significant differences between the IOLMaster 700 and iTrace in evaluating J0 and J45. Bland‒Altman plots revealed relatively wide LoA widths, almost larger than 1 diopter for the keratometry values and almost larger than 0.5 diopter for J0 and J45 values among the four devices. In terms of PK and TK values, significant differences and low ICCs were found among the three devices. CONCLUSIONS: Although strong correlations and good agreement were found among the IOLMaster700, CASIA2, Pentacam and iTrace for Kf, Ks, Km and J0, J45, it seems that the measurements should not be used interchangeably because of the wide LoA widths and the presence of significant differences among the devices. Similarly, due to significant differences and low ICCs, the PK, TK and TNP values obtained by IOLMaster 700, CASIA2, and Pentacam should not be used interchangeably.

Cobalt oxide nanoparticles: An effective growth promoter of Arabidopsis plants and nano-pesticide against bacterial leaf blight pathogen in rice.

Recently, the application of cobalt oxide nanoparticles (Co3O4NPs) has gained popularity owing to its magnetic, catalytic, optical, antimicrobial, and biomedical properties. However, studies on its use as a crop protection agent and its effect on photosynthetic apparatus are yet to be reported. Here, Co3O4NPs were first green synthesized using Hibiscus rosa-sinensis flower extract and were characterized using UV-Vis spectroscopy, Fourier transform infrared spectroscopy, X-ray diffraction (XRD), transmission/scanning electron microscopy methods. Formation of the Co3O4NPs was attested based on surface plasmon resonance at 210 nm. XRD assay showed that the samples were crystalline having a mean size of 34.9 nm. The Co3O4NPs at 200 µg/ml inhibited the growth (OD600 = 1.28) and biofilm formation (OD570 = 1.37) of Xanthomonas oryzae pv. oryzae (Xoo) respectively, by 72.87% and 79.65%. Rice plants inoculated with Xoo had disease leaf area percentage (DLA %) of 57.25% which was significantly reduced to 11.09% on infected plants treated with 200 µg/ml Co3O4NPs. Also, plants treated with 200 µg/ml Co3O4NPs only had significant increment in shoot length, root length, fresh weight, and dry weight in comparison to plants treated with double distilled water. The application of 200 µg/ml Co3O4NPs on the Arabidopsis plant significantly increased the photochemical efficacy of PSII (ΦPSII) and photochemical quenching (qP) respectively, by 149.10% and 125.00% compared to the control while the non-photochemical energy dissipation (ΦNPQ) was significantly lowered in comparison to control. In summary, it can be inferred that Co3O4NPs can be a useful agent in the management of bacterial phytopathogen diseases.

Establishment and application of ERA-LFD method for rapid detection of feline calicivirus.

Feline calicivirus (FCV) has a single-stranded, positive-sense RNA genome, and it is responsible for many infectious respiratory diseases in cats. In addition, more worryingly, highly virulent strains of FCV can cause high mortality in felines. Therefore, a rapid and reliable diagnosis tool plays an important role in controlling the outbreak of FCV. In this study, enzymatic recombinase amplification (ERA) assay combined with lateral flow dipstick (LFD) was developed for the detection of FCV, targeting a relatively conversed position of FCV-ORF1. The results showed that the optimal reaction condition was at 40 °C for 30 min. ERA-LFD method was highly sensitive with the detection limit as low as 3.2 TCID50 of FCV RNA per reaction. The specificity analysis demonstrated no cross-reactivity with feline parvovirus (FPV), feline herpesvirus (FHV) and feline infectious peritonitis virus (FIPV). ERA-LFD was highly repeatable and reproducible, with the intra-assay and inter-assay coefficients of variation for this method both less than 7%. The general test showed that all the recombinant plasmids with known mutant sites and FCV strains with different mutant sites stored in our laboratory were all detected by this method. Of the 23 samples, 14 samples were tested positive for FCV by ERA-LFD and RT-qPCR, respectively. In summary, ERA-LFD assay was a fast, accurate and convenient diagnosis tool for the detection of FCV. KEY POINTS: • The detection principle of ERA-LFD was introduced. • Almost all the currently known FCV strains can be detected. • ERA-LFD is easy to operate and can be used for field detection.

Elevated carbon dioxide reduces a common soybean leaf endophyte.

Free-air CO2 enrichment (FACE) experiments have elucidated how climate change affects plant physiology and production. However, we lack a predictive understanding of how climate change alters interactions between plants and endophytes, critical microbial mediators of plant physiology and ecology. We leveraged the SoyFACE facility to examine how elevated [CO2 ] affected soybean (Glycine max) leaf endophyte communities in the field. Endophyte community composition changed under elevated [CO2 ], including a decrease in the abundance of a common endophyte, Methylobacterium sp. Moreover, Methylobacterium abundance was negatively correlated with co-occurring fungal endophytes. We then assessed how Methylobacterium affected the growth of co-occurring endophytic fungi in vitro. Methylobacterium antagonized most co-occurring fungal endophytes in vitro, particularly when it was more established in culture before fungal introduction. Variation in fungal response to Methylobacterium within a single fungal operational taxonomic unit (OTU) was comparable to inter-OTU variation. Finally, fungi isolated from elevated vs. ambient [CO2 ] plots differed in colony growth and response to Methylobacterium, suggesting that increasing [CO2 ] may affect fungal traits and interactions within the microbiome. By combining in situ and in vitro studies, we show that elevated [CO2 ] decreases the abundance of a common bacterial endophyte that interacts strongly with co-occurring fungal endophytes. We suggest that endophyte responses to global climate change will have important but largely unexplored implications for both agricultural and natural systems.

Circular RNA circZNF292 regulates H2 O2 -induced injury in human lens epithelial HLE-B3 cells depending on the regulation of the miR-222-3p/E2F3 axis.

Circular RNAs (circRNAs) play important roles in the pathogenesis of age-related cataract (ARC). CircRNA zinc finger protein 292 (circZNF292, hsa_circ_0004058) is downregulated in ARC lens capsules. Here, we focused on its precise roles in oxidative stress underlying the pathogenesis of ARC. CircZNF292, microRNA (miR)-222-3p, and E2F transcription factor 3 (E2F3) were quantified by quantitative real-time polymerase chain reaction or western blot. Cell viability was assessed by the cell counting kit-8 assay. Cell cycle distribution and apoptosis were detected by flow cytometry. The activities of superoxide dismutase, catalase, and malondialdehyde were measured using the corresponding assay kit. Targeted correlations among circZNF292, miR-222-3p, and E2F3 were verified by the dual-luciferase reporter, RNA immunoprecipitation and RNA pull-down assays. Our data showed that circZNF292 was downregulated in ARC tissues and H2 O2 -treated human lens epithelial B3 (HLE-B3) cells. Increased expression of circZNF292 alleviated H2 O2 -induced cell viability suppression, apoptosis promotion, and oxidative stress enhancement. Mechanistically, circZNF292 directly targeted miR-222-3p, and circZNF292 regulated E2F3 expression through miR-222-3p. MiR-222-3p was a functional mediator of circZNF292 in modulating H2 O2 -induced injury in HLE-B3 cells. Furthermore, reduced level of miR-222-3p ameliorated H2 O2 -induced HLE-B3 cell damage by upregulating E2F3. Our present study demonstrated that increased expression of circZNF292 ameliorated H2 O2 -induced injury in HLE-B3 cells at least in part through the miR-222-3p/E2F3 axis, highlighting a novel insight into the involvement of circRNAs in the pathogenesis of ARC.

The Eighth Edition of the American Joint Committee on Cancer Distant Metastases Stage Classification for Metastatic Pancreatic Neuroendocrine Tumors Might Be Feasible for Metastatic Pancreatic Ductal Adenocarcinomas.

BACKGROUND: Significant modifications have been made to the 8th edition of the American Joint Committee on Cancer (AJCC) distant metastases (M) stage classification for metastatic pancreatic neuroendocrine tumors (PanNETs). We aimed to validate this revised classification among metastatic PanNET patients using the Surveillance, Epidemiology, and End Results database. We further sought to evaluate the feasibility of applying this classification to metastatic pancreatic neuroendocrine carcinoma (PanNEC) and pancreatic ductal adenocarcinoma (PDAC) patients. METHODS: Stage IV pancreatic neuroendocrine neoplasm (PanNEN, including G1/G2 PanNET and G3 PanNEC classified according to the World Health Organization [WHO] 2010 grading scheme) and PDAC patients with metastatic disease diagnosed between 2010 and 2015 were identified and restaged according to the revised M stage classification for PanNET. Overall survival (OS) was compared using Kaplan-Meier analysis and log-rank test. Uni- and multivariate Cox regression models were utilized to identify prognostic factors. RESULTS: A total of 1,371 stage IV PanNEN and 634 PDAC patients were included. Among PanNEN patients, liver (75.0%) was the most common metastatic site, followed by distant lymph nodes (8.5%), lung (8.4%), bone (7.3%), and brain (1.0%). The 5-year OS for PanNET patients with M1a, M1b, and M1c stage was 44.15, 53.32, and 19.70%, respectively. However, survival comparison showed no significant difference between M1a and M1b stages among PanNET patients. Similar findings were noted after applying this classification to PanNEC patients. Multivariate analysis showed that the age at diagnosis and the number of distant metastatic sites were independent prognostic factors for metastatic PanNEN patients. Interestingly, excellent survival discrimination by M stage among stage IV PDAC patients was noted (M1a vs. M1b vs. M1c, 5-year OS: 5.42, 2.46, and 0%, respectively). CONCLUSION: Our study is the first large sample-based validation of the AJCC 8th M stage classification for PanNET. The revised classification did not effectively stratify metastatic PanNEN patients. However, further study is warranted to validate this classification for PanNET patients according to the WHO 2017 classification. Interestingly, the revised M stage classification might be feasible for PDAC patients with metastatic disease.

Interleukin 10 promotes immune response by increasing the survival of activated CD8+ T cells in human papillomavirus 16-infected cervical cancer.

Human papillomavirus (HPV)-specific CD8+ T cells are present in HPV-infected cervical cancer patients and have demonstrated potent antitumor properties. However, these cells cannot control tumor progression in most patients. To investigate the underlying mechanisms involved in suppressing or promoting CD8+ T cell functions, we focused on interleukin 10 (IL-10), a pleiotropic cytokine with controversial roles in antitumor immunity. We found that compared to healthy controls, circulating CD8+ T cells in HPV 16-infected cervical cancer patients expressed significantly higher levels of IL-10. Interestingly, these CD8+ T cells from cervical cancer patients, but not those from healthy controls, responded to HPV 16 E6/E7 peptide stimulation by increasing IL-10 expression, demonstrating an antigen-specific IL-10 release. Addition of exogenous IL-10 improved the survival, but did not increase the proliferation, of peptide-stimulated CD8+ T cells. CD8+ T cells cultured in the presence of IL-10 also resulted in significantly higher interferon gamma (IFN-gamma) and granzyme B concentration, primarily due to improved cell survival. In resected cervical tumors, the frequency of tumor-infiltrating IL-10+ CD8+ T cells was positively correlated with the frequency of tumor-infiltrating IFN-gamma+ and granzyme B+ CD8+ T cells. Tumor-associated macrophages were more potent than peripheral blood monocyte-derived macrophages at inducing IL-10 expression in CD8+ T cells, possibly explaining the elevated IL-10+ CD8+ T cell frequency in cervical cancer patients. Together, these results are consistent with an immunostimulatory role of IL-10, which promoted CD8+ T cell response by increasing the survival of activated CD8+ T cells.

Alternative splicing and trans-splicing events revealed by analysis of the Bombyx mori transcriptome.

Alternative splicing and trans-splicing events have not been systematically studied in the silkworm Bombyx mori. Here, the silkworm transcriptome was analyzed by RNA-seq. We identified 320 novel genes, modified 1140 gene models, and found thousands of alternative splicing and 58 trans-splicing events. Studies of three SR proteins show that both their alternative splicing patterns and mRNA products are conserved from insect to human, and one isoform of Srsf6 with a retained intron is expressed sex-specifically in silkworm gonads. Trans-splicing of mod(mdg4) in silkworm was experimentally confirmed. We identified integrations from a common 5'-gene with 46 newly identified alternative 3'-exons that are located on both DNA strands over a 500-kb region. Other trans-splicing events in B. mori were predicted by bioinformatic analysis, in which 12 events were confirmed by RT-PCR, six events were further validated by chimeric SNPs, and two events were confirmed by allele-specific RT-PCR in F(1) hybrids from distinct silkworm lines of JS and L10, indicating that trans-splicing is more widespread in insects than previously thought. Analysis of the B. mori transcriptome by RNA-seq provides valuable information of regulatory alternative splicing events. The conservation of splicing events across species and newly identified trans-splicing events suggest that B. mori is a good model for future studies.

Effect of UV exposure and natural aging on the in vitro PAHs bioaccessibility associated with tire wear particles in soil.

Tire wear particles (TWP), as an emerging type of microplastics, are a significant source of contaminants in roadside soils due to their high concentration of pollutants, including polycyclic aromatic hydrocarbons (PAHs). This study explored the impact of ultraviolet (UV) exposure and natural aging on the in vitro bioaccessibility of PAHs associated with TWP in soil on a China-wide scale. Our findings suggested that UV exposure amplified the negative charge of TWP by 75 % and increased the hydrophobic groups on the particle surface. The bioaccessibility of 3- and 4-ring PAHs in TWP was significantly (p < 0.05) heightened by UV exposure. After 20 types of soils containing 2 % UV-exposed TWP underwent natural aging, the bioaccessibility of PAHs saw a significant decrease (p < 0.05) to 16-48 %, compared to 28-96 % in the unaged group. Soil pH and electrical conductivity (EC) were the two primary soil properties positively influencing the reduction of in vitro PAHs concentration and PAHs bioaccessibility. According to the prediction results, soils in southern China presented the highest potential region for the release of bioaccessible PAHs from TWP, highlighting the regional specificity of environmental impact. Our study provides valuable insights into the biological impact of PAHs associated with TWP on a regional scale, and offers scientific evidence for targeted soil risk management strategies.

Hierarchical organic microspheres from diverse molecular building blocks.

Microspherical structures find broad application in chemistry and materials science, including in separations and purifications, energy storage and conversion, organic and biocatalysis, and as artificial and bioactive scaffolds. Despite this utility, the systematic diversification of their morphology and function remains hindered by the limited range of their molecular building blocks. Drawing upon the design principles of reticular synthesis, where diverse organic molecules generate varied porous frameworks, we show herein how analogous microspherical structures can be generated under mild conditions. The assembly of simple organic molecules into microspherical structures with advanced morphologies represents a grand challenge. Beginning with a partially condensed Schiff base which self-assembles into a hierarchical organic microsphere, we systematically synthesized sixteen microspheres from diverse molecular building blocks. We subsequently explicate the mechanism of hierarchical assembly through which these hierarchical organic microspheres are produced, isolating the initial monomer, intermediate substructures, and eventual microspheres. Furthermore, the open cavities present on the surfaces of these constructs provided distinctive adsorptive properties, which we harnessed for the immobilization of enzymes and bacteriophages. Holistically, these hierarchical organic microspheres provide an approach for designing multi-functional superstructures with advanced morphologies derived from simple organic molecules, revealing an extended length scale for reticular synthesis.

Predicting the risk category of thymoma with machine learning-based computed tomography radiomics signatures and their between-imaging phase differences.

The aim of this study was to develop a medical imaging and comprehensive stacked learning-based method for predicting high- and low-risk thymoma. A total of 126 patients with thymomas and 5 patients with thymic carcinoma treated at our institution, including 65 low-risk patients and 66 high-risk patients, were retrospectively recruited. Among them, 78 patients composed the training cohort, while the remaining 53 patients formed the validation cohort. We extracted 1702 features each from the patients' arterial-, venous-, and plain-phase images. Pairwise subtraction of these features yielded 1702 arterial-venous, arterial-plain, and venous-plain difference features each. The Mann‒Whitney U test and least absolute shrinkage and selection operator (LASSO) and SelectKBest methods were employed to select the best features from the training set. Six models were built with a stacked learning algorithm. By applying stacked ensemble learning, three machine learning algorithms (XGBoost, multilayer perceptron (MLP), and random forest) were combined by XGBoost to produce the the six basic imaging models. Then, the XGBoost algorithm was applied to the six basic imaging models to construct a combined radiomic model. Finally, the radiomic model was combined with clinical information to create a nomogram that could easily be used in clinical practice to predict the thymoma risk category. The areas under the curve (AUCs) of the combined radiomic model in the training and validation cohorts were 0.999 (95% CI 0.988-1.000) and 0.967 (95% CI 0.916-1.000), respectively, while those of the nomogram were 0.999 (95% CI 0.996-1.000) and 0.983 (95% CI 0.990-1.000). This study describes the application of CT-based radiomics in thymoma patients and proposes a nomogram for predicting the risk category for this disease, which could be advantageous for clinical decision-making for affected patients.

Unveiling a Potent Small Molecule Disruptor for RNA G-Quadruplexes Tougher Than DNA G-Quadruplex Disruption.

This research presents a unique small molecule characterized by its ability to effectively disrupt RNA G-quadruplexes (G4s), which are notably more stable than their DNA counterparts. We conducted a comprehensive series of in vitro experiments to thoroughly assess the disruptive capabilities of this molecule on RNA G4s. These experiments included comparisons with established G4 stabilizers and DNA G4 disruptors, providing a multifaceted evaluation of the molecule's efficacy. Our extensive in vitro analyses demonstrated that this molecule effectively alters G4 structures and interactions with the BG4 protein, a well-recognized G4-specific antibody. These findings underscore the molecule's potential to modulate G4-protein interactions, indicating promising applications for manipulating cellular functions associated with G4 dynamics in future research.

Efficacy of a real-time intelligent quality-control system for the detection of early upper gastrointestinal neoplasms: a multicentre, single-blinded, randomised controlled trial.

Background: Oesophagogastroduodenoscopy (OGD) quality and identification of the early upper gastrointestinal (UGI) neoplasm play an important role in detecting the UGI neoplasm. However, the optimal method for quality control in daily OGD procedures is currently lacking. We aimed to evaluate the efficacy of a real-time intelligent quality-control system (IQCS), which combines OGD quality control with lesion detection of early UGI neoplasms. Methods: We performed a multicentre, single-blinded, randomised controlled trial at 6 hospitals in China. Patients aged 40-80 years old who underwent painless OGD were screened for enrolment in this study. Patients with a history of advanced UGI cancer, stenosis, or obstruction in UGI tract were excluded. Eligible subjects were randomly assigned (1:1) to either the routine or IQCS group to undergo standard OGD examination and OGD examination aided by IQCS, respectively. Patients were masked to the randomisation status. The primary outcome was the detection of early UGI neoplasms. All analyses were done on a per-protocol basis. This trial is registered with ClinicalTrials.gov, NCT04720924. Findings: Between January 16, 2021 and December 23, 2022, 1840 patients were randomised (IQCS group: 919, routine group: 921). The full analysis set consisted of 914 in the IQCS group and 915 in the routine group. The early UGI neoplasms detection rate in the IQCS group (6.1%, 56/914) was significantly higher than in the routine group (2.3%, 21/915; P = 0.0001). The IQCS group had fewer blind spots (2.3 vs. 6.2, P < 0.0001). The IQCS group had higher stomach cleanliness on cardia or fundus (99.5% vs. 87.9%, P < 0.0001), body (98.9% vs. 88.0%, P < 0.0001), angulus (99.8% vs. 88.4%, P < 0.0001) and antrum or pylorus (100.0% vs. 87.4%, P < 0.0001). The inspection time (576.2 vs. 574.5s, P = 0.91) and biopsy rate (57.2% vs. 56.6%, P = 0.83) were not different between the groups. The early UGI neoplasms detection rate in the IQCS group increased in both non-academic centres (RR = 3.319, 95% CI 1.277-9.176; P = 0.0094) and academic centres (RR = 2.416, 95% CI 1.301-4.568; P = 0.0034). The same improvements were observed for both less-experienced endoscopists (RR = 2.650, 95% CI 1.330-5.410; P = 0.0034) and experienced endoscopists (RR = 2.710, 95% CI 1.226-6.205; P = 0.010). No adverse events or serious adverse events were reported in the two groups. Interpretation: The IQCS improved the OGD quality and increased early UGI neoplasm detection in different hospital types and endoscopist experiences. IQCS could play an important role in primary basic hospitals and non-expert endoscopists to improve the diagnostic accuracy of early UGI neoplasms. The effectiveness of IQCS in real-world clinical settings needs a larger population validation. Funding: Key R&D Program of Shandong Province, China (Major Scientific and Technological Innovation Project), National Natural Science Foundation of China, the Taishan Scholars Program of Shandong Province, the National Key Research and Development Program of China, and the Shandong Provincial Natural Science Foundation.

A multi-omics study to investigate the progression of the Correa pathway in gastric mucosa in the context of cirrhosis.

BACKGROUND: Patients with liver cirrhosis (LC) are prone to gastric mucosa damage. We investigated the alterations of gastric mucosa in LC patients and their possible mechanisms through multi-omics. RESULTS: We observed significant gastric mucosa microbial dysbiosis in LC subjects. Gastric mucosal microbiomes of LC patients contained a higher relative abundance of Streptococcus, Neisseria, Prevotella, Veillonella, and Porphyromonas, as well as a decreased abundance in Helicobacter and Achromobacter, than control subjects. The LC patients had higher levels of bile acids (BAs) and long-chain acylcarnitines (long-chain ACs) in serum. The gastric mucosal microbiomes were associated with serum levels of BAs and long-chain ACs. Transcriptome analyses of gastric mucosa revealed an upregulation of endothelial cell specific molecule 1, serpin family E member 1, mucin 2, caudal type homeobox 2, retinol binding protein 2, and defensin alpha 5 in LC group. Besides, the bile secretion signaling pathway was significantly upregulated in the LC group. CONCLUSIONS: The alterations in the gastric mucosal microbiome and transcriptome of LC patients were identified. The impaired energy metabolism in gastric mucosal cells and bile acids might aggravate the inflammation of gastric mucosa and even exacerbate the Correa's cascade process. The gastric mucosal cells might reduce bile acid toxicity by bile acid efflux and detoxification. TRIAL REGISTRATION: ChiCTR2100051070.

Preoperative US Integrated Random Forest Model for Predicting Delphian Lymph Node Metastasis in Patients with Papillary Thyroid Cancer.

BACKGROUND: Delphian lymph node (DLN) has been considered to be a gate that predicts widespread lymph node involvement, higher recurrence and mortality rates of head and neck cancer. OBJECTIVE: This study aimed to establish a preoperative ultrasonography integrated machine learning prediction model to predict Delphian lymph node metastasis (DLNM) in patients with diagnosed papillary thyroid carcinoma (PTC). METHODS: Ultrasonographic and clinicopathologic variables of PTC patients from 2014 to 2021 were retrospectively analyzed. The risk factors associated with DLNM were identified and validated through a developed random forest (RF) algorithm model based on machine learning and a logistic regression (LR) model. RESULTS: A total of 316 patients with 402 thyroid lesions were enrolled for the training dataset and 280 patients with 341 lesions for the validation dataset, with 170 (28.52%) patients developed DLNM. The elastography score of ultrasonography, central lymph node metastasis, lateral lymph node metastasis, and serum calcitonin were predictive factors for DLNM in both models. The RF model has better predictive performance in the training dataset and validation dataset (AUC: 0.957 vs. 0.890) than that in the LR model (AUC: 0.908 vs. 0.833). CONCLUSION: The preoperative ultrasonography integrated RF model constructed in this study could accurately predict DLNM in PTC patients, which may provide clinicians with more personalized clinical decision-making recommendations preoperatively. Machine learning technology has the potential to improve the development of DLNM prediction models in PTC patients.

Metabarcoding reveals response of rice rhizosphere bacterial community to rice bacterial leaf blight.

Rice bacterial leaf blight (BLB) is a major disease affecting cultivated rice and caused by the bacterium Xanthomonas oryzae pv. oryzae (Xoo). It is well established that rhizosphere microorganisms could help improve the adaptability of plants to biotic stresses. However, it is still unclear about the response mechanism of rice rhizosphere microbial community to BLB infection. Here, we used 16S rRNA gene amplicon sequencing to explore the effect of BLB on the rice rhizosphere microbial community. The results show that the alpha diversity index of the rice rhizosphere microbial community decreased significantly at the onset of BLB and then gradually recovered to normal levels. Beta diversity analysis indicated that BLB significantly affected community composition. In addition, there were significant differences in the taxonomic composition between healthy and diseased groups. For example, ceretain genera were more abundant in diseased rhizospheres, namely Streptomyces, Sphingomonas, and Flavobacterium, among others. In addition, the size and complexity of the rhizosphere co-occurrence network increased after disease onset compared to healthy groups. Also, hub microbe Rhizobiaceae and Gemmatimonadaceae were identified in the diseased rhizosphere co-occurrence network, and these hub microbes played an important role in maintaining network stability. In conclusion, our results provide important insights into the rhizosphere microbial community response to BLB and also provide important data and ideas in using rhizosphere microbes to control BLB.

Prediction of immune infiltration and prognosis for patients with urothelial bladder cancer based on the DNA damage repair-related genes signature.

Objectives: To analyze the correlations between the expression and effect of DNA damage repair genes and the immune status and clinical outcomes of urothelial bladder cancer (BLCA) patients. In addition, we evaluate the efficacy and value of utilizing the DNA damage repair genes signature as a prognosis model for BLCA. Methods: Two subtype groups (C1 and C2) were produced based on the varied expression of DNA damage repair genes. Significantly differentiated genes and predicted enriched gene pathways were obtained between the two subtypes. Seven key genes were obtained from the DNA damage repair-related genes and a 7-gene signature prognosis model was established based on the key genes. The efficacy and accuracy of this model in prognosis prediction was evaluated and verified in two independent databases. Also, the difference in biological functions, drug sensitivity, immune infiltration and affinity between the high-risk group and low-risk group was analyzed. Results: The DNA damage repair gene signature could significantly differentiate the BLCA into two molecular subgroups with varied genetic expression and enriched gene pathways. Seven key genes were screened out from the 232 candidate genes for prognosis prediction and a 7-gene signature prognosis model was established based on them. Two independent patient cohorts (TCGA cohort and GEO cohort) were utilized to validate the efficacy of the prognosis model, which demonstrated an effective capability to differentiate and predict the overall survival of BLCA patients. Also, the high-risk group and low-risk group derived from the 7-gene model exhibited significantly differences in drug sensitivity, immune infiltration status and biological pathways enrichment. Conclusions: Our established 7-gene signature model based on the DNA damage repair genes could serve as a novel prognosis predictive tool for BLCA. The differentiation of BLCA patients based on the 7-gene signature model may be of great value for the appropriate selection of specific chemotherapy agents and immune-checkpoint blockade therapy administration.

ALOX5 deficiency contributes to bladder cancer progression by mediating ferroptosis escape.

Ferroptosis is an iron-dependent form of regulated cell death driven by the lethal lipid peroxides. Previous studies have demonstrated that inducing ferroptosis holds great potential in cancer therapy, especially for patients with traditional therapy failure. However, cancer cells can acquire ferroptosis evasion during progression. To date, the therapeutic potential of inducing ferroptosis in bladder cancer (BCa) remains unclear, and whether a ferroptosis escape mechanism exists in BCa needs further investigation. This study verified that low pathological stage BCa cells were highly sensitive to RSL3-induced ferroptosis, whereas high pathological stage BCa cells exhibited obviously ferroptosis resistance. RNA-seq, RNAi-mediated loss-of-function, and CRISPR/Cas9 experiments demonstrated that ALOX5 deficiency was the crucial factor of BCa resistance to ferroptosis in vitro and in vivo. Mechanistically, we found that ALOX5 deficiency was regulated by EGR1 at the transcriptional level. Clinically, ALOX5 expression was decreased in BCa tissues, and its low expression was associated with poor survival. Collectively, this study uncovers a novel mechanism for BCa ferroptosis escape and proposes that ALOX5 may be a valuable therapeutic target and prognostic biomarker in BCa treatment.

BarH-like homeobox 2 represses the transcription of keratin 16 and affects Ras signaling pathway to suppress nasopharyngeal carcinoma progression.

Nasopharyngeal carcinoma (NPC) refers to a malignancy initiating from the superior mucosal epithelium of the nasopharynx. Optimal therapies for NPC are still needed. In this investigation, we attempted to explore whether BarH-like homeobox 2 (BARX2), a well-known tumor suppressor, had anti-cancer properties on NPC, and the possible mechanisms. After searching for NPC-related databases, we determined BARX2 as one of the core genes in NPC. The results of RT-qPCR and immunohistochemistry or Western blot demonstrated that BARX2 was reduced in NPC patients and cells. Ectopic expression of BARX2 reverted the malignant phenotype of NPC cells. Mechanistically, BARX2 bound to the keratin 16 (KRT16) promoter to downregulate its expression. In addition, BARX2 was found to reduce the phosphorylation levels of MEK and ERK. Further KRT16 upregulation in cells overexpressing BARX2 promoted malignant aggressiveness of C666-1 and HNE3 cells and activated the Ras signaling pathway. BARX2 inhibited the growth and metastasis of tumors and suppressed the Ras signaling pathway in vivo. In conclusion, our findings indicate that BARX2 reverts malignant phenotypes of NPC cells by downregulating KRT16 in a Ras-dependent fashion. BARX2 might act as a possible therapeutic regulator for NPC.