Non-alcoholic fatty liver disease: pathogenesis and models.

Non-alcoholic fatty liver disease (NAFLD) is a complex disease characterized by a massive accumulation of lipids in the liver, with a continuous progression of simple steatosis, non-alcoholic steatohepatitis (NASH), cirrhosis, and hepatocellular carcinoma. Non-alcoholic fatty liver disease is associated with obesity, insulin resistance, and metabolic syndrome; it is a severe public health risk and is currently the most common liver disease of the world. In addition to the fatty infiltration of the liver in non-alcoholic fatty liver disease patients, the field of liver transplantation faces similar obstacles. NAFLD and NASH primarily involve lipotoxicity, inflammation, oxidative stress, and insulin resistance. However, the precise mechanisms and treatments remain unclear. Therapeutic approaches encompass exercise, weight control, as well as treatments targeting antioxidants and anti-inflammatory pathways. The role of animal models in research has become crucial as a key tool to explore the molecular mechanisms and potential treatments for non-alcoholic fatty liver disease and non-alcoholic steatohepatitis. Here, we summarized the current understanding of the pathogenesis of non-alcoholic fatty liver disease and non-alcoholic steatohepatitis and discussed animal models commonly used in recent years.

Tumor-infiltrating immune cells and survival in head and neck squamous cell carcinoma: a retrospective computational study.

The immune infiltration profiles of the tumor microenvironment have effects on the prognosis of head and neck squamous cell carcinoma (HNSCC). Whereas, HNSCC is a heterogeneous group of tumors, but past work has not taken this into consideration. Herein, we investigate the associations between survival and the function of immune cells in different tumorigenic sites of HNSCC. 1149 samples of HNSCC were collected from publicly accessible databases. Based on gene expression data, CIBERSORTx was applied to determine the proportion of 22 immune cell subpopulations. In the Cox regression model, the associations between overall survival, disease-free survival, and immune cells were examined, modeling gene expression and immune cell proportion as quartiles. Consensus cluster analysis was utilized to uncover immune infiltration profiles. Regardless of tumor sites, CD8+ T cells and activated CD4 memory T cells were associated with favorable survival, while eosinophils were the opposite. The survival of the hypopharynx, oral cavity, and larynx subsites was somewhat affected by immune cells, while the survival of the oropharynx subsite potentially was the most impacted. High expression of TIGIT, CIITA, and CXCR6 was linked to better survival, mainly in the oropharynx subsite. Immune cell clusters with four distinct survival profiles were discovered, of which the cluster with a high CD8+ T cell content had a better prognosis. The immune-infiltration pattern is related to the survival of HNSCC to varying degrees depending on the tumor sites; forthcoming studies into immune-mediated infiltration profiles will lay the groundwork for treating HNSCC with precision therapy.

A First-Principles Study of Mechanical and Electronic Properties of Cr0.5-xAl0.5TMxN Hard Coatings (TM = Ti, V, Y, Zr, Hf, and Ta).

The structural, mechanical, and electronic properties of cubic Cr0.5-xAl0.5TMxN, doped with TM (transition metal) elements (TM = Ti, V, Y, Zr, Hf, and Ta) at low concentrations (x = 0.03 and 0.06), was investigated by first-principles calculations. The results of the structural properties calculations reveal that the addition of Ti, Y, Hf, Zr, and Ta expand the volume, while V has the opposite effect. All doped compounds are thermodynamically stable, and Cr0.5-xAl0.5TMxN with TM = Ti is energetically more favorable than other doped compounds. At the same doping concentration, Cr0.5-xAl0.5VxN possesses the highest stiffness, hardness, and resistance to external forces due to its greatest mechanical properties, and Cr0.5-xAl0.5TaxN possesses the highest elastic anisotropy and the lowest Young's modulus. Substituting Cr atoms with TM atoms in a stepwise manner results in a decrease in the bulk modulus, shear modulus, Young's modulus, and theoretical hardness of Cr0.5-xAl0.5TMxN, while increasing its toughness. Based on the calculation results of the total and partial density of states of Cr0.5Al0.5N and Cr0.47Al0.5TM0.03N, all compounds exhibit metallic behavior as indicated by the finite density of states at the Fermi level. The contribution of Ti-3d, V-3d, and Ta-3d orbitals at Fermi level is significantly higher than that of other TM atoms, resulting in a more pronounced metallic character for Cr0.47Al0.5Ti0.03N, Cr0.47Al0.5V0.03N, and Cr0.47Al0.5Ta0.03N.

Radiomics based on T2-weighted and diffusion-weighted MR imaging for preoperative prediction of tumor deposits in rectal cancer.

AIM: Preoperative diagnosis of tumor deposits (TDs) in patients with rectal cancer remains a challenge. This study aims to develop and validate a radiomics nomogram based on the combination of T2-weighted (T2WI) and diffusion-weighted MR imaging (DWI) for the preoperative identification of TDs in rectal cancer. MATERIALS AND METHODS: A total of 199 patients with rectal cancer who underwent T2WI and DWI were retrospectively enrolled and divided into a training set (n â€‹= â€‹159) and a validation set (n â€‹= â€‹40). The total incidence of TDs was 37.2 â€‹% (74/199). Radiomics features were extracted from T2WI and apparent diffusion coefficient (ADC) images. A radiomics nomogram combining Rad-score (T2WI â€‹+ â€‹ADC) and clinical factors was subsequently constructed. The area under the receiver operating characteristic curve (AUC) was then calculated to evaluate the models. The nomogram is also compared to three machine learning model constructed based on no-Rad scores. RESULTS: The Rad-score (T2WI â€‹+ â€‹ADC) achieved an AUC of 0.831 in the training and 0.859 in the validation set. The radiomics nomogram (the combined model), incorporating the Rad-score (T2WI â€‹+ â€‹ADC), MRI-reported lymph node status (mLN-status), and CA19-9, showed good discrimination of TDs with an AUC of 0.854 for the training and 0.923 for the validation set, which was superior to Random Forests, Support Vector Machines, and Deep Learning models. The combined model for predicting TDs outperformed the other three machine learning models showed an accuracy of 82.5 â€‹% in the validation set, with sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of 66.7 â€‹%, 92.0 â€‹%, 83.3 â€‹%, and 82.1 â€‹%, respectively. CONCLUSION: The radiomics nomogram based on Rad-score (T2WI â€‹+ â€‹ADC) and clinical factors provides a promising and effective method for the preoperative prediction of TDs in patients with rectal cancer.

A Novel Nomogram to Predict Resectable Gastric Cancer Based on Preoperative Circulating Tumor Cell.

INTRODUCTION: Circulating tumor cells (CTCs) have been suggested to have an important prognostic role in gastrointestinal tumors. We developed a preoperative CTC-based nomogram to predict the prognosis of patients with resectable gastric cancer after surgery and established a risk stratification system based on the nomogram. METHODS: From January 2012 to June 2017, we screened 258 patients with gastric cancer treated with surgery from one center as the training cohort and 133 patients with gastric cancer treated with surgery from another as the validation cohort, screened prognostic factors for the training cohort using univariate and multivariate Cox risk proportional models, created predictive overall survival (OS) and a recurrence-free survival (RFS) nomogram, and plotted the receiver operating characteristic curve and calibration curve for this nomogram in the training and validation cohorts. Risk score stratification was performed according to the nomogram, and OS curves were plotted for the low, medium, and high-risk groups using the Kaplan-Meier method. RESULTS: The CTC positivity rate was 78.5% in all patients. CTC, TNM stage, and Ki-67 were the prognostic factors affecting OS and RFS after gastric cancer surgery. The nomogram consisted of these 3 variables. In the training group, the area under the curve of the nomogram for OS at 1, 3, and 5 years was 0.918, 0.829, and 0.813, respectively, and the area under the curve for RFS was 0.900, 0884, and 0.839, respectively. There was a statistically significant difference in OS among the low, medium, and high-risk groups according to the risk stratification system constructed from nomogram scores ( P < 0.001). DISCUSSION: Two nomograms based on preoperative CTC were established to predict OS and RFS after resectable gastric cancer. The 2 nomograms had good discrimination and calibration and significant stratification ability of the risk stratification system established according to them.

CENPN suppresses autophagy and increases paclitaxel resistance in nasopharyngeal carcinoma cells by inhibiting the CREB-VAMP8 signaling axis.

Chemotherapeutic resistance is one of the most common reasons for poor prognosis of patients with nasopharyngeal carcinoma (NPC). We found that CENPN can promote the growth, proliferation and apoptosis resistance of NPC cells, but its relationship with chemotherapeutic resistance in NPC is unclear. Here we verified that the CENPN expression level in NPC patients was positively correlated with the degree of paclitaxel (PTX) resistance and a poor prognosis through analysis of clinical cases. VAMP8 expression was significantly increased after knockdown of CENPN by transcriptome sequencing. We found in cell experiments that CENPN inhibited macroautophagy/autophagy and VAMP8 expression and significantly increased PTX resistance. Overexpression of CENPN reduced the inhibitory effects of PTX on survival, cell proliferation, cell cycle progression and apoptosis resistance in NPC cells by inhibiting autophagy. In turn, knockdown of CENPN can affect the phenotype of NPC cells by increasing autophagy to achieve PTX sensitization. Sequential knockdown of CENPN and VAMP8 reversed the PTX-sensitizing effect of CENPN knockdown alone. Experiments in nude mice confirmed that knockdown of CENPN can increase VAMP8 expression, enhance autophagy and increase the sensitivity of NPC cells to PTX. Mechanistic studies showed that CENPN inhibited the translocation of p-CREB into the nucleus of NPC cells, resulting in the decreased binding of p-CREB to the VAMP8 promoter, thereby inhibiting the transcription of VAMP8. These results demonstrate that CENPN may be a marker for predicting chemotherapeutic efficacy and a potential target for inducing chemosensitization to agents such as PTX.Abbreviations: 3-MA: 3-methyladenine; ATG5: autophagy related 5; CENPN: centromere protein N; CQ: chloroquine; CREB: cAMP responsive element binding protein; ChIP: chromatin immunoprecipitation assay; IC50: half-maximal inhibitory concentration; LAMP2A: lysosomal associated membrane protein 2A; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; NPC: nasopharyngeal carcinoma; NPG: nasopharyngitis; oeCENPN: overexpressed CENPN; PTX: paclitaxel; RAPA: rapamycin; RNA-seq: transcriptome sequencing; shCENPN: small hairpin RNA expression vector targeting the human CENPN gene; shCENPN-shVAMP8: sequential knockdown targeting the human CENPN gene and VAMP8 gene; shVAMP8: small hairpin RNA expression vector targeting the human VAMP8 gene; TEM: transmission electron microscopy; TIR: tumor inhibitory rate; VAMP8: vesicle associated membrane protein 8.

Enhancing nasopharyngeal carcinoma cell radiosensitivity by suppressing AKT/mTOR via CENP-N knockdown.

OBJECTIVE: Investigating the impact of centromere protein N (CENP-N) on radiosensitivity of nasopharyngeal carcinoma (NPC) cells. METHODS: Using immunohistochemistry and immunofluorescence to detect CENP-N expression in tissues from 35 patients with radiosensitive or radioresistant NPC. Assessing the effect of combined CENP-N knockdown and radiotherapy on various cellular processes by CCK-8, colony formation, flow cytometry, and Western blotting. Establishing a NPC xenograft model. When the tumor volume reached 100 mm3, a irradiation dose of 6 Gy was given, and the effects of the combined treatment were evaluated in vivo using immunofluorescence and Western blotting techniques. RESULTS: The level of CENP-N was significantly reduced in radiosensitive tissues of NPC (p < 0.05). Knockdown of CENP-N enhanced NPC radiosensitivity, resulting in sensitizing enhancement ratios (SER) of 1.44 (5-8 F) and 1.16 (CNE-2Z). The combined treatment showed significantly higher levels of proliferation suppression, apoptosis, and G2/M phase arrest (p < 0.01) compared to either CENP-N knockdown alone or radiotherapy alone. The combined treatment group showed the highest increase in Bax and γH2AX protein levels, whereas the protein Cyclin D1 exhibited the greatest decrease (p < 0.01). However, the above changes were reversed after treatment with AKT activator SC79. In vivo, the mean volume and weight of tumors in the radiotherapy group were 182 ± 54 mm3 and 0.16 ± 0.03 g. The mean tumor volume and weight in the combined treatment group were 84 ± 42 mm3 and 0.04 ± 0.01 g. CONCLUSION: Knockdown of CENP-N can enhance NPC radiosensitivity by inhibiting AKT/mTOR.

Gut microbial structural variation associates with immune checkpoint inhibitor response.

The gut microbiota may have an effect on the therapeutic resistance and toxicity of immune checkpoint inhibitors (ICIs). However, the associations between the highly variable genomes of gut bacteria and the effectiveness of ICIs remain unclear, despite the fact that merely a few gene mutations between similar bacterial strains may cause significant phenotypic variations. Here, using datasets from the gut microbiome of 996 patients from seven clinical trials, we systematically identify microbial genomic structural variants (SVs) using SGV-Finder. The associations between SVs and response, progression-free survival, overall survival, and immune-related adverse events are systematically explored by metagenome-wide association analysis and replicated in different cohorts. Associated SVs are located in multiple species, including Akkermansia muciniphila, Dorea formicigenerans, and Bacteroides caccae. We find genes that encode enzymes that participate in glucose metabolism be harbored in these associated regions. This work uncovers a nascent layer of gut microbiome heterogeneity that is correlated with hosts' prognosis following ICI treatment and represents an advance in our knowledge of the intricate relationships between microbiota and tumor immunotherapy.

Photochemical reductive deamination of alpha-amino aryl alkyl ketones.

Photochemical reductive deamination of alpha-amino aryl alkyl ketones under photosensitizer-free conditions is presented. This protocol features high efficiency and selectivity. A plausible reaction pathway is proposed based on ultraviolet-visible absorption investigation, control experiments and deuterium-labelling studies. Mechanistic study reveals that the alpha-hydrogen atom of the ketone product originated from water.

Machine Learning-Aided High-Throughput First-Principles Calculations to Predict the Formation Energy of µ Phase.

The µ phase is a type of hard and brittle constituent that exists in high-temperature alloys. The formation energy is a crucial thermochemical datum, and the accurate calculation of the formation energy of the µ phase contributes to the material design of high-temperature alloys. Traditional first-principles calculations demand significant computational time and resources. In this study, an innovative machine learning (ML)-based approach to accurately predict the formation energy of the µ phase is proposed. This approach involves the utilization of six algorithms and two model evaluation methods to construct the ML models. Leveraging a comprehensive data set containing 1036 binary configurations of the µ phase, the model trained using a 10-fold cross-validation technique, and the multilayer perceptron (MLP) algorithm achieves a mean absolute error (MAE) of 23.906 meV/atom. To validate its generalization performance, the trained model is further validated on 900 ternary configurations, resulting in an MAE of 32.754 meV/atom. Compared with solely using traditional first-principles calculations, our approach significantly reduces the computational time by at least 52%. Moreover, the ML model exhibits exceptional accuracy in predicting the lattice parameters of the µ phase. The MAE values for the a and c parameters are 0.024 and 0.214 Å, respectively, corresponding to low error rates of only 0.479 and 0.578%. Additionally, the ML model was utilized to accurately predict the formation energy of all of the possible ternary configurations. To enhance accessibility to the formation energy data of the µ phase, a user-friendly graphical user interface (GUI) was developed, ensuring convenient usability for researchers and practitioners.

Tumor-Associated Extracellular Microvesicles with Fluorine-Modified Carbohydrate Antigens Trigger a Stronger Antitumor Immune Response.

Abnormal glycosylation is a hallmark of tumor development, and tumor-associated carbohydrate antigens are potential immune targets for tumor therapy. Tumor-associated extracellular microvesicles are subcellular vesicles released from cell membranes that have immunogenicity similar to that of precursor cells. However, unmodified tumor-derived microvesicles have weaknesses, such as low immunogenicity, poor biostability, and short half-life in vivo. For the first time, we herein generated extracellular microvesicles containing modified tumor-associated carbohydrate antigens by constructing a cell line with highly expressed antigen-processing enzymes utilizing fluorine-modified monosaccharide substrates via a metabolic oligosaccharide engineering strategy. The microvesicles were applied to tumor immunity, achieving enhanced immunoprophylaxis and immunotherapy effects. Furthermore, the mechanisms of antitumor immunity were explored. Our findings may provide new insights into the adhibition of suitably modified extracellular microvesicles and the development of more effective carbohydrate-based anticancer vaccines.

A novel nomogram to predict low anterior resection syndrome (LARS) after ileostomy reversal for rectal cancer patients.

BACKGROUND AND AIM: Low anterior resection syndrome (LARS) in patients undergoing low or ultra-low anterior resection (LAR) is a common problem and significantly impacts the quality of life. Patients with an ileostomy after LAR are more likely to develop LARS. However, there hasn't been a model predicting LARS occurrence in these patients. This study aims to construct a nomogram to predict the probability of LARS occurrence in patients with temporary ileostomy and guide preventive strategies before reversal. METHODS: 168 patients undergoing LAR with ileostomy from one center were enrolled as the training cohort, and 134 patients of the same inclusion criteria from another center were enrolled as the validation cohort. The training cohort was screened for risk factors for major LARS using univariate and multivariate logistic regression. The nomogram was constructed using the filtered variables, the ROC curve was used to describe the model's discrimination, and the calibration was used to describe the accuracy. RESULTS: The optimal cut-off value for stoma closure time was 128 days. Three risk factors were identified using logistic regression analysis: preoperative radiotherapy (OR = 3.038, [95%CI 1.75-5.015], P = 0.005), stoma closure time (OR = 2.298, [95%CI 1.088-4.858], P = 0.029) and pN stage (OR = 1.739, [95%CI 1.235-3.980], P = 0.001). A nomogram was constructed based on these three variables and showed good performance predicting major LARS after stoma reversal. The area under the curve (AUC) was 0.827 in the training group and 0.821 in the validation group; The calibration curve suggested good precision in both groups. CONCLUSIONS: This novel nomogram can accurately predict the probability of major LARS occurrence after ileostomy reversal for rectal cancer patients. This model can help screen ileostomy patients with high risks and guide individualized preventive strategies before stoma reversal.

Specific knockout of Notch2 in Treg cells significantly inhibits the growth and proliferation of head and neck squamous cell carcinoma in mice.

OBJECTIVE: To investigate the effect of Notch2 gene knockout in Treg cells on head and neck squamous cell carcinoma (HNSCC) in mice. METHODS: A mouse model of HNSCC was constructed. Flow cytometry and immunofluorescence were used to examine the numbers of related immune cells and programmed cell death in tumor cells in the spleen and tumor microenvironment of mice. Western blotting was used to measure the expression of related proteins in tumor tissues. RESULTS: The tumor volume of regulatory T (Treg) cell-specific Notch2-knockout mice (experimental group) was significantly smaller than that of control mice (control group) (P < 0.05). Compared with those in the control group, the number of Treg cells and the expression of Ki67 in Treg cells in the spleen and tumor tissue were significantly decreased in the experimental group, while the numbers of CD45+ hematopoietic cells, CD4+ T cells, CD8+ T cells, T helper 1 (Th1) cells, CD11b+ cells (macrophages), and CD11b+CD11c+ cells (dendritic cells) and the expression of Ki67 in CD4+ T cells and CD8+ T cells were significantly increased (P < 0.05). There was no significant difference in the number of Th2 cells between the two groups (P > 0.05). Immunofluorescence analysis showed that the numbers of CD4+ T cells and CD8+ T cells in the tumor tissue in the experimental group were significantly higher than those in the control group (P < 0.05). Compared with that in the control group, programmed cell death in the experimental group was significantly increased (P < 0.05). Moreover, the expression levels of NLRP3, Caspase-1 and GSDMD in the tumor tissues of the experimental group were higher than those in the control group (P < 0.01), while the expression levels of BCL2, Bax, ATG5, LC3 and p62 were not significantly different (P > 0.05). CONCLUSIONS: Specific knockout of the Notch2 gene in Treg cells significantly decreases the function of Treg cells, inhibits the growth of HNSCC and improves the immune microenvironment in mice, thus effectively treating HNSCC.

DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing.

Long single-molecular sequencing technologies, such as PacBio circular consensus sequencing (CCS) and nanopore sequencing, are advantageous in detecting DNA 5-methylcytosine in CpGs (5mCpGs), especially in repetitive genomic regions. However, existing methods for detecting 5mCpGs using PacBio CCS are less accurate and robust. Here, we present ccsmeth, a deep-learning method to detect DNA 5mCpGs using CCS reads. We sequence polymerase-chain-reaction treated and M.SssI-methyltransferase treated DNA of one human sample using PacBio CCS for training ccsmeth. Using long (≥10 Kb) CCS reads, ccsmeth achieves 0.90 accuracy and 0.97 Area Under the Curve on 5mCpG detection at single-molecule resolution. At the genome-wide site level, ccsmeth achieves >0.90 correlations with bisulfite sequencing and nanopore sequencing using only 10× reads. Furthermore, we develop a Nextflow pipeline, ccsmethphase, to detect haplotype-aware methylation using CCS reads, and then sequence a Chinese family trio to validate it. ccsmeth and ccsmethphase can be robust and accurate tools for detecting DNA 5-methylcytosines.

[Corrigendum] Downregulation of Notch1 induces apoptosis and inhibits cell proliferation and metastasis in laryngeal squamous cell carcinoma.

Following the publication of this article, a concerned reader drew to the authors' attention that a pair of the 24 h scratch­wound assay data panels in Fig. 4A, and three of the migration and invasion assay data panels in Fig. 4B, exhibited overlapping sections, suggesting that data which were intended to have shown the results from differently performed experiments had originated from the same sources. In addition, the total number of cases for the LSCC sample data in Table II did not reflect the sum of the samples indicated in the 'negative', 'positive' and 'strong positive' categories. After having consulted their original data, the authors have realized that Table II and Fig. 4 contained some inadvertent errors: The authors divided their control group data into two subgroups, namely the non­transfection and negative­shRNA groups, although they overlooked details of the filing system they had devised for saving the data, and mistakenly included images from the non­transfection group in with the negative­shRNA group due to unclear file labeling. Moreover, in Table II, the data value for the 'positive' stained samples should have been written as '43', not '44'. The corrected versions of Table II and Fig. 4, which now shows the corrected data for the 'Negative­shRNA / 24 h' experiment in Fig. 4A and the 'Non­transfection / Invasion' and 'Negative­shRNA / Migration' experiments in Fig. 4B, are shown below and on the next page, respectively. The authors sincerely apologize for the errors that were introduced during the preparation of this table and this figure, thank the Editor of Oncology Reports for granting them the opportunity to publish this corrigendum, and regret any inconvenience that these mistakes may have caused to the readership. [Oncology Reports 34: 3111­3119, 2015; DOI: 10.3892/or.2015.4274].

Giant Cell Tumor and Giant Cell Reparative Granuloma of Bone of the Head: CT and MR Imaging Findings.

BACKGROUND: This study aimed to determine the features and differentiation of Giant Cell Reparative Granuloma (GCRG) and Giant Cell Tumor (GCT) of the head on CT and MRI. METHODS: This retrospective study included six patients with histopathology-confirmed head GCRG and 5 patients with histopathology-confirmed head GCT. All images were independently reviewed by two radiologists. The growth pattern, bone changes, MRI signal intensity, enhancement patterns and other image features were recorded. All patients received CT scans and MR images. RESULTS: All the lesions were located centrally in the bone. Osteolytic bone destruction and expansive growth patterns were observed on CT images. Four of six cases broke the cortical bone with residual cortical bone, and the last two showed a thin cortex in GCRG. Five cases broke the cortical bone with residual cortical bone in GCT. There were enhancing septations in GCT lesions on contrast- enhanced T1-Weighted Images (T1WI) while enhancing septations were not present in GCRG cases. The size of GCT lesions was larger than that of GRCG. GCRG and GCT showed iso-low signals on T1WI and iso-high signals on T2-Weighted Images (T2WI). There was a case with cystic or necrotic lesions in each of the two types of lesions. Osteolytic bone destruction and expansive growth patterns were observed in GCTs and GCRGs. CONCLUSION: The size of the GRCG lesion was smaller than that of the GCT. The presence of enhancing septations and the size of the lesion may distinguish GCTs from GCRG.

[Simultaneous determination of three components of sodium nitrophenolate in foodstuffs of animal origin by high performance liquid chromatography-tandem mass spectrometry using atmospheric pressure chemical ionization].

Sodium nitrophenolate (SNP) is a widely used universal growth regulator consisting of 5-nitroguaiacol sodium (5NG), 4-nitrophenol sodium (PNP), and 2-nitrophenol sodium (ONP). SNP has a positive influence on plants and animals as a feed additive that accelerates growth but is potentially hazardous to humans. SNP has been reported to be cytotoxic and mutagenic, which may increase the risk of cancer and pose a great threat to food safety. There are neither mature detection nor standard methods for the trace analysis of SNP in animal food. Therefore, the development of an accurate and precise analytical method is imperative. This innovative method has theoretical and practical significance for the control of SNP residues, offering advantages such as cost-effectiveness and time efficiency. It will be beneficial for the establishment of detection standards and management measures in foodstuffs of animal origin.In this study, a reliable method for the simultaneous determination of SNP residues in animal food (porcine muscle, chicken tissue, fish, and liver) was developed. For realizing the perfect limit of quantification, the application of back extraction coupled with high performance liquid chromatography-atmospheric pressure chemical ionization-tandem mass spectrometry (HPLC-APCI-MS/MS) was proposed to combine high sensitivity and high selectivity. The optimal method was as follows. First, 2.0 g samples were extracted with 10 mL 0.5 mol/L sodium hydroxide solution, followed by adjustment of the pH to acidity with 3 mol/L hydrochloric acid and the addition of sodium chloride (5.0 g) to saturate the inorganic phase. After back-extraction twice with 16 mL acetonitrile, the solution was merged and again saturated with 5 mL of sodium chloride solution. Second, the merged organic phase was cleaned up with 10 mL of n-hexane for defatting. The middle acetonitrile layer was then concentrated to nearly 1.5 mL at 40 ℃ in a N2 stream before dilution with the mobile phase to a volume of 3.0 mL and filtered. Finally, the analytes were separated on a C18 column (100 mm×4.6 mm, 3 µm) and subjected to gradient elution with a mixed solution of methanol and water. Mass spectrometric analysis, which was quantified using the external standard method, was carried out with an atmospheric pressure chemical ionization negative ion source and based on multiple reaction monitoring (MRM) mode. The key parameters, such as the extraction solvent, extraction steps, and purification method, were optimized.The calibration curves were linear in the ranges of 0.5-10 (5NG), 1.0-20 (PNP), and 2.5-50 µg/L (ONP) with correlation coefficients greater than 0.9999. The limit of quantification (LOQ) for 5NG was 1.0 µg/kg, double for PNP, and five times for ONP. The recoveries of the three different concentration levels in all the four matrices were in the range of 81.5%-98.4%, 81.5%-102%, and 81.4%-95.1%. The repeatability, expressed as the relative standard deviations (RSDs) of the three compounds, ranged from 1.51% to 5.98%, 1.10% to 8.85% and 0.91% to 8.61% (n=6). The developed method is characterized by an excellent purification effect, sensitivity, and accuracy. This method is suitable for the simultaneous and quantitative determination of SNP residues in foodstuffs of animal origin.

Patterns of immune infiltration and survival in endocrine therapy-treated ER-positive breast cancer: A computational study of 1900 patients.

Tumor-infiltrating immune cells (TIICs) play a critical role in breast cancer (BC) prognosis, but little is known regarding the efficacy of endocrine therapy in patients with ER-positive BC with diverse immunological phenotypes. To investigate whether TIICs affect survival after endocrine therapy in patients with different BC molecular subtypes, data were gathered from six studies totaling 1900 samples. CIBERSORTx was used to analyze the invasion of 22 immune cell subpopulations using a bulk gene expression profile. The relationships of immune-related metagenes and immune cell subsets with survival (distant metastasis-free survival, relapse-free survival, and overall survival) were studied using Cox regression models with cell proportions modeled in quartiles. The immune score and IGHG3 and LCK gene activity were linked to a better prognosis. Among the immune cells, monocytes, resting CD4+ memory T cells and plasma cells were correlated with prolonged survival, while neutrophils, Tregs, M0 macrophages, and M2 macrophages were associated with an unfavorable prognosis. Similar effects were reported for the luminal A subtype. In the luminal B subtype, γδ T cells and eosinophils were favorable prognostic factors. Covariate-adjusted multivariate Cox regression analysis revealed that high proportions of resting CD4+ memory T cells and resting dendritic cells were correlated with a good prognosis. Meanwhile, neutrophils were associated with an unfavorable prognosis. Understanding how monocytes and macrophages interact in the tumor microenvironment may be a promising study focus. Comprehensive research on the cellular immune response in tumors could help facilitate the development of new treatments.

msRepDB: a comprehensive repetitive sequence database of over 80 000 species.

Repeats are prevalent in the genomes of all bacteria, plants and animals, and they cover nearly half of the Human genome, which play indispensable roles in the evolution, inheritance, variation and genomic instability, and serve as substrates for chromosomal rearrangements that include disease-causing deletions, inversions, and translocations. Comprehensive identification, classification and annotation of repeats in genomes can provide accurate and targeted solutions towards understanding and diagnosis of complex diseases, optimization of plant properties and development of new drugs. RepBase and Dfam are two most frequently used repeat databases, but they are not sufficiently complete. Due to the lack of a comprehensive repeat database of multiple species, the current research in this field is far from being satisfactory. LongRepMarker is a new framework developed recently by our group for comprehensive identification of genomic repeats. We here propose msRepDB based on LongRepMarker, which is currently the most comprehensive multi-species repeat database, covering >80 000 species. Comprehensive evaluations show that msRepDB contains more species, and more complete repeats and families than RepBase and Dfam databases. (https://msrepdb.cbrc.kaust.edu.sa/pages/msRepDB/index.html).

The IRF2/CENP-N/AKT signaling axis promotes proliferation, cell cycling and apoptosis resistance in nasopharyngeal carcinoma cells by increasing aerobic glycolysis.

BACKGROUND: Centromere protein N (CENP-N) has been reported to be highly expressed in malignancies, but its role and mechanism in nasopharyngeal carcinoma (NPC) are unknown. METHODS: Abnormal CENP-N expression from NPC microarrays of GEO database was analyzed. CENP-N expression level was confirmed in NPC tissues and cell lines. Stable CENP-N knockdown and overexpression NPC cell lines were established, and transcriptome sequencing after CENP-N knockdown was performed. In vitro and in vivo experiments were performed to test the impact of CENP-N knockdown in NPC cells. ChIP and dual luciferase reporter assays were used to verify the combination of IRF2 and CENP-N. Western blot analysis, cellular immunofluorescence, immunoprecipitation and GST pulldown assays were used to verify the combination of CENP-N and AKT. RESULTS: CENP-N was confirmed to be aberrantly highly expressed in NPC tissues and cell lines and to be associated with high 18F-FDG uptake in cancer nests and poor patient prognosis. Transcriptome sequencing after CENP-N knockdown revealed that genes with altered expression were enriched in pathways related to glucose metabolism, cell cycle regulation. CENP-N knockdown inhibited glucose metabolism, cell proliferation, cell cycling and promoted apoptosis. IRF2 is a transcription factor for CENP-N and directly promotes CENP-N expression in NPC cells. CENP-N affects the glucose metabolism, proliferation, cell cycling and apoptosis of NPC cells in vitro and in vivo through the AKT pathway. CENP-N formed a complex with AKT in NPC cells. Both an AKT inhibitor (MK-2206) and a LDHA inhibitor (GSK2837808A) blocked the effect of CENP-N overexpression on NPC cells by promoting aerobic glycolysis, proliferation, cell cycling and apoptosis resistance. CONCLUSIONS: The IRF2/CENP-N/AKT axis promotes malignant biological behaviors in NPC cells by increasing aerobic glycolysis, and the IRF2/CENP-N/AKT signaling axis is expected to be a new target for NPC therapy.