Construction and validation of a prognostic signature for mucinous colonic adenocarcinoma based on N7-methylguanosine-related long non-coding RNAs.

Background: Mucinous colonic adenocarcinoma remains a challenging disease due to its high propensity for metastasis and recurrence. N7-methylguanosine (m7G) and long non-coding RNA (lncRNA) are closely associated with the occurrence and progression of tumors. However, research on m7G-related lncRNA in mucinous colonic adenocarcinoma is lacking. Therefore, we sought to explore the prognostic impact of m7G-related lncRNAs in mucinous adenocarcinoma (MC) patients. Methods: In this study, Pearson analysis was used to identify m7G-related lncRNAs from transcriptome data in The Cancer Genome Atlas (TCGA). Univariate Cox regression analysis and least absolute shrinkage and selection operator (LASSO) regression were used to further screen m7G-related lncRNAs and incorporate them into a prognostic signature. Based on the risk model, patients were divided into low- and high-risk groups and randomly assigned to the training set and test sets in a 6:4 ratio. Kaplan-Meier, receiver operating characteristic (ROC) curve, multivariate regression, and nomogram analyses were used to confirm the accuracy of the signature. The CIBERSORT algorithm was used to calculate the degree of immune cell infiltration (ICI). Finally, the correlation of the prognostic signature with tumor mutational burden (TMB) and immunophenotype score (IPS) was evaluated. Results: A total of 432 m7G-related lncRNAs were identified by Pearson analysis. Univariate Cox regression, LASSO regression and survival analysis were performed to further select six m7G-related lncRNAs (P<0.05): AC254629.1, LINC01133, LINC01134, MHENCR, SMIM2-AS1, and XACT. Based on the risk model, heat maps, Kaplan-Meier curves, and ROC curves were constructed, and the results showed that there were significant differences in expression levels and survival status between the two risk groups. The area under the ROC curve (AUC) values for 3-, 5-, and 10-year survival in the training set were 0.944, 0.957, and 1.000, respectively. And in the test set were 0.964, 1.000, and 1.000, respectively. Subsequently, univariate and multivariate regression analyses of clinical characteristics and risk score were performed. The results of risk score were [hazard ratio (HR): 6.458, 95% confidence interval (CI): 2.708-15.403, P<0.001; HR: 7.280, 95% CI: 2.500-21.203, P<0.001], respectively. Using the risk score as an independent prognostic factor, the AUC of it over 3, 5, and 10 years was 0.911, 0.955, and 0.961, respectively. Calibration plots for the nomogram show that the model calibration line is very close to the ideal calibration line, indicating good calibration. The level of ICI was significantly different in the different risk groups. Survival analysis showed that, regardless of TMB risk, patients with MC and a high-risk score consistently had a poor overall survival (OS). Conclusions: The m7G-related lncRNA prognostic signature has potential value for the prognosis of mucinous colonic adenocarcinoma.

Modification and Expression of mRNA m6A in the Lateral Habenular of Rats after Long-Term Exposure to Blue Light during the Sleep Period.

Artificial lighting, especially blue light, is becoming a public-health risk. Excessive exposure to blue light at night has been reported to be associated with brain diseases. However, the mechanisms underlying neuropathy induced by blue light remain unclear. An early anatomical tracing study described the projection of the retina to the lateral habenula (LHb), whereas more mechanistic reports are available on multiple brain functions and neuropsychiatric disorders in the LHb, which are rarely seen in epigenetic studies, particularly N6-methyladenosine (m6A). The purpose of our study was to first expose Sprague-Dawley rats to blue light (6.11 ± 0.05 mW/cm2, the same irradiance as 200 lx of white light in the control group) for 4 h, and simultaneously provide white light to the control group for the same time to enter a sleep period. The experiment was conducted over 12 weeks. RNA m6A modifications and different mRNA transcriptome profiles were observed in the LHb. We refer to this experimental group as BLS. High-throughput MeRIP-seq and mRNA-seq were performed, and we used bioinformatics to analyze the data. There were 188 genes in the LHb that overlapped between differentially m6A-modified mRNA and differentially expressed mRNA. The Kyoto Encyclopedia of Genes and Genomes and gene ontology analysis were used to enrich neuroactive ligand-receptor interaction, long-term depression, the cyclic guanosine monophosphate-dependent protein kinase G (cGMP-PKG) signaling pathway, and circadian entrainment. The m6A methylation level of the target genes in the BLS group was disordered. In conclusion, this study suggests that the mRNA expression and their m6A of the LHb were abnormal after blue light exposure during the sleep period, and the methylation levels of target genes related to synaptic plasticity were disturbed. This study offers a theoretical basis for the scientific use of light.

DPred_3S: identifying dihydrouridine (D) modification on three species epitranscriptome based on multiple sequence-derived features.

Introduction: Dihydrouridine (D) is a conserved modification of tRNA among all three life domains. D modification enhances the flexibility of a single nucleotide base in the spatial structure and is disease- and evolution-associated. Recent studies have also suggested the presence of dihydrouridine on mRNA. Methods: To identify D in epitranscriptome, we provided a prediction framework named "DPred_3S" based on the machine learning approach for three species D epitranscriptome, which used epitranscriptome sequencing data as training data for the first time. Results: The optimal features were evaluated by the F-score and integration of different features; our model achieved area under the receiver operating characteristic curve (AUROC) scores 0.955, 0.946, and 0.905 for Saccharomyces cerevisiae, Escherichia coli, and Schizosaccharomyces pombe, respectively. The performances of different machine learning algorithms were also compared in this study. Discussion: The high performances of our model suggest the D sites can be distinguished based on their surrounding sequence, but the lower performance of cross-species prediction may be limited by technique preferences.

The prognostic value of the Naples prognostic score for patients with non-small-cell lung cancer.

The Naples prognostic score (NPS) is an effective inflammatory and nutritional scoring system widely applied as a prognostic factor in various cancers. We aimed to analyze the prognostic value of the NPS in patients diagnosed with non-small-cell lung cancer (NSCLC). We prospectively collected 395 patients diagnosed with NSCLC between January 2016 and December 2018 in two university-affiliated hospitals. Patients were divided into three groups according to their pretreatment NPS (Group 0: NPS = 0; Group 1: NPS = 1-2; Group 2: NPS = 3-4). Kaplan-Meier survival curves indicated that patients with higher NPS had a poorer overall survival (OS) and progress-free survival (PFS) (both P < 0.05). NPS was further confirmed as an independent prognostic factors of OS and PFS by multivariable survival analysis (both P < 0.05). Furthermore, stratifying by TNM stage, NPS also has significant predictive performance for OS and PFS in both early (I-IIIA) and advanced (IIIB-IV) stage NSCLC (all P < 0.05). The time-dependent receiver operating characteristic curve analysis demonstrated that NPS was more superior to other prognostic factors in predicting OS and PFS. In conclusion, NPS may serve as an effective indicator to predict OS and PFS in NSCLC patients regardless of TNM stage.

The association between meat consumption and the metabolic syndrome: a cross-sectional study and meta-analysis.

The findings regarding the associations between red meat, fish and poultry consumption, and the metabolic syndrome (Mets) have been inconclusive, and evidence from Chinese populations is scarce. A cross-sectional study was performed to investigate the associations between red meat, fish and poultry consumption, and the prevalence of the Mets and its components among the residents of Suzhou Industrial Park, Suzhou, China. A total of 4424 participants were eligible for the analysis. A logistic regression model was used to estimate the OR and 95 % CI for the prevalence of the Mets and its components according to red meat, fish and poultry consumption. In addition, the data of our cross-sectional study were meta-analysed under a random effects model along with those of published observational studies to generate the summary relative risks (RR) of the associations between the highest v. lowest categories of red meat, fish and poultry consumption and the Mets and its components. In the cross-sectional study, the multivariable-adjusted OR for the highest v. lowest quartiles of consumption was 1·23 (95 % CI 1·02, 1·48) for red meat, 0·83 (95 % CI 0·72, 0·97) for fish and 0·93 (95 % CI 0·74, 1·18) for poultry. In the meta-analysis, the pooled RR for the highest v. lowest categories of consumption was 1·20 (95 % CI 1·06, 1·35) for red meat, 0·88 (95 % CI 0·81, 0·96) for fish and 0·97 (95 % CI 0·85, 1·10) for poultry. The findings of both cross-sectional studies and meta-analyses indicated that the association between fish consumption and the Mets may be partly driven by the inverse association of fish consumption with elevated TAG and reduced HDL-cholesterol and, to a lesser extent, fasting plasma glucose. No clear pattern of associations was observed between red meat or poultry consumption and the components of the Mets. The current findings add weight to the evidence that the Mets may be positively associated with red meat consumption, inversely associated with fish consumption and neutrally associated with poultry consumption.

Integrated Profiles of Transcriptome and mRNA m6A Modification Reveal the Intestinal Cytotoxicity of Aflatoxin B1 on HCT116 Cells.

Aflatoxin B1 (AFB1) is widely prevalent in foods and animal feeds and is one of the most toxic and carcinogenic aflatoxin subtypes. Existing studies have proved that the intestine is targeted by AFB1, and adverse organic effects have been observed. This study aimed to investigate the relationship between AFB1-induced intestinal toxicity and N6-methyladenosine (m6A) RNA methylation, which involves the post-transcriptional regulation of mRNA expression. The transcriptome-wide m6A methylome and transcriptome profiles in human intestinal cells treated with AFB1 are presented. Methylated RNA immunoprecipitation sequencing and mRNA sequencing were carried out to determine the distinctions in m6A methylation and different genes expressed in AFB1-induced intestinal toxicity. The results showed that there were 2289 overlapping genes of the differentially expressed mRNAs and differentially m6A-methylation-modified mRNAs. After enrichment of the signaling pathways and biological processes, these genes participated in the terms of the cell cycle, endoplasmic reticulum, tight junction, and mitophagy. In conclusion, the study demonstrated that AFB1-induced HCT116 injury was related to the disruptions to the levels of m6A methylation modifications of target genes and the abnormal expression of m6A regulators.

Growth differentiation factor-15 and lactoferrin immuno-expression in breast cancer: relationship with body iron-status and survival outcome.

We aimed to evaluate the expression of growth differentiation factor-15 (GDF-15) and lactoferrin (Lf) in tumor and their relationship with the body iron-status and overall survival (OS) outcome of patients with breast cancer. A retrospective cohort study of female patients with primary breast cancer was performed. Clinical tumor samples from the Second Affiliated Hospital of Soochow University between December 2008 and June 2014 were collected. The immuno-expression of GDF-15 and Lf was stratified into positive or negative expression. Kaplan-Meier method and Cox proportional hazards regression model were used for data analysis. 74 breast cancer patients with a mean age of 52 years were included into our study. 14 (18.9%) patients were died by the end of August 1, 2019. The serum iron level of patients with GDF-15 (+)/Lf(-) expression was higher than that of patients with other expression patterns (18.2 ± 5.4 vs. 15.5 ± 5.0 µmol/L, P = 0.038), but was not associated with OS. In univariate Cox analyses, GDF-15(+) and GDF-15(+)/Lf(-) were significantly correlated with high mortality risk (HR = 3.75, 95%CI 1.05-13.48, P = 0.025; HR = 5.00, 95%CI 1.56-16.04, P = 0.004, respectively). After adjusted for age, menopause status and primary tumor grade, the association between GDF-15 and OS disappeared. However, the association between GDF-15/Lf and OS still existed in GDF-15(+)/Lf(-) (HR = 4.50, 95%CI 1.31-15.51, P = 0.017). The combined immuno-expression pattern of GDF-15 and Lf was significant associated with high serum iron level. GDF-15/Lf could be a powerful biomarker to predict survival outcome of patients with breast cancer but still needed to be confirmed by future studies.

The Geriatric Nutritional Risk Index as a Prognostic Factor in Patients with Advanced Non-Small-Cell Lung Cancer.

The Geriatric Nutritional Risk Index (GNRI) is widely applied as a prognostic factor in different cancers. We aimed to analyze the prognostic value of the GNRI in 257 patients diagnosed with advanced non-small-cell lung cancer (NSCLC). Patients with GNRI >98, 92-98, and <92 were grouped into normal, low risk and moderate/high risk groups, respectively. There were 45.1% patients at risk for malnutrition. Kaplan-Meier survival curves indicated that patients with lower GNRI scores had a poorer overall survival (OS). Two-year OS for normal, low risk and moderate/high risk groups were 57.4%, 42.3% and 15.8%, respectively. In multivariate survival analysis, GNRI (<92), body mass index (BMI, ≥24 kg/m2), combined therapy, hemoglobin and neutrophil-to-lymphocyte ratio (NLR) were independent prognostic factors of OS. Stratifying by age groups, GNRI (<92), hemoglobin and NLR were independent prognostic factors of OS in patients aged <65 years. GNRI (<92), smoking, BMI (≥24 kg/m2) and platelet-to-lymphocyte ratio were independent prognostic factors of OS in patients aged ≥65 years. In conclusion, GNRI was a significant prognostic factor in advanced NSCLC patients regardless of age. A decreased GNRI may be considered as a clinical trigger for nutritional support in advanced NSCLC patients, though additional studies are still required to confirm the best cut-point.

ZBED1/DREF: A transcription factor that regulates cell proliferation.

Maintenance of genomic diversity is critically dependent on gene regulation at the transcriptional level. This occurs via the interaction of regulatory DNA sequence motifs with DNA-binding transcription factors. The zinc finger, BED-type (ZBED) gene family contains major DNA-binding motifs present in human transcriptional factors. It encodes proteins that present markedly diverse regulatory functions. ZBED1 has similar structural and functional properties to its Drosophila homolog DNA replication-related element-binding factor (DREF) and plays a critical role in the regulation of transcription. ZBED1 regulates the expression of several genes associated with cell proliferation, including cell cycle regulation, chromatin remodeling and protein metabolism, and some genes associated with apoptosis and differentiation. In the present review, the origin, structure and functional role of ZBED1 were comprehensively assessed. In addition, the similarities and differences between ZBED1 and its Drosophila homolog DREF were highlighted, and future research directions, particularly in the area of clinical cancer, were discussed.

Mild Acid-Responsive "Nanoenzyme Capsule" Remodeling of the Tumor Microenvironment to Increase Tumor Penetration.

Dense extracellular matrix (ECM) severely impedes the spread of drugs in solid tumors and induces hypoxia, reducing chemotherapy efficiency. Different proteolytic enzymes, such as collagenase (Col) or bromelain, can directly attach to the surface of nanoparticles and improve their diffusion, but the method of ligation may also impair the enzymatic activity due to conformational changes or blockage of the active site. Herein, a "nanoenzyme capsule" was constructed by combining collagenase nanocapsules (Col-nc) with heavy-chain ferritin (HFn) nanocages encapsulating the chemotherapy drug doxorubicin (DOX) to enhance tumor penetration of the nanoparticles by hydrolyzing collagen from the ECM. Col-nc could protect the activity of the enzyme before reaching the site of action while being degraded under mildly acidic conditions in tumors, and the released proteolytic enzyme could digest collagen. In addition, HFn as a carrier could effectively load DOX and had a self-targeting ability, enabling the nanoparticles to internalize into cancer cells more effectively. From in vivo and in vitro studies, we found that collagen was effectively degraded by Col-nc/HFn(DOX) to increase the accumulation and penetration of nanoparticles in the solid tumor site and could alleviate hypoxia inside the tumor to enhance the antitumor effects of DOX. Therefore, the strategy of increasing nanoparticle penetration in this system is expected to provide a potential approach for the clinical treatment of solid tumors.

A traceable nanoplatform for enhanced chemo-photodynamic therapy by reducing oxygen consumption.

Tumor hypoxia impedes the efficiencies of oxygen-dependent photodynamic therapy (PDT) and chemotherapy. Herein, we design a traceable nanoplatform (DOX/Met/BSA-HA-CDs) by reducing oxygen (O2) consumption to overcome the hypoxia-caused cancer therapy. Carbon dots (CDs) are used not only as a PDT agent but also applied for in vivo traceable imaging. Metformin (Met), a potent antihyperglycemic agent, to improve tumor oxygenation and enhance the efficiencies of hypoxia-caused cancer therapy. In the hypoxic tumor microenvironment, Met was released more rapidly than DOX, which is advantageous for improving hypoxic cancer to exert a better therapeutic efficiency. Ex vivo immunofluorescence staining revealed that the DOX/Met/BSA-HA-CDs nanoparticles greatly reduce O2 consumption in tumor site. Followed by in vivo synergistic treatment achieved considerably enhanced cancer therapeutic efficiency. This system holds great clinical promise as a traceable imaging approach to guide the improvement of PDT and chemotherapy efficiencies through utilizing a simple, safe method improved hypoxic tumor microenvironment.

Salinomycin may inhibit the cancer stem-like populations with increased chemoradioresistance that nasopharyngeal cancer tumorspheres contain.

Tumor recurrence and metastasis of nasopharyngeal cancer (NPC) often result in the failure of treatment due to chemoradioresistance. Cancer stem cells (CSCs) have been observed to drive tumor initiation and tumor chemoradioresistance. Therefore, the poor prognosis of advanced NPC is likely to result from the failure to kill CSCs. Sphere formation may be used as an experimental method to enrich potential CSC subpopulations. At present, there are few reports on NPC tumorspheres. The present study focused on examining the cancer stem-like properties of NPC tumorspheres from NPC cell lines. Western blot analysis revealed that NPC tumorspheres had a higher expression of stem cell markers Nanog homeobox and SRY-box 2, compared with parental cells. It was additionally verified that NPC tumorspheres contained a high aldehyde dehydrogenase (ALDH) enzymatic activity compared with parental cells. ALDH+ cells were amplified by 9- to 10-fold in tumorspheres, compared with parental cells (1.8 vs. 16.9%). The tumorsphere cells exhibited an increased half maximal inhibitory concentration value of >10-fold with cisplatin compared with the control parental cells. Compared with the parental cells, the percentage of side population cells in the tumorsphere cell population increased significantly (10.3 vs. 2.3%; P<0.05). NPC tumorsphere cells demonstrated enhanced resistance to radiation. Further investigation verified that salinomycin inhibited NPC CSCs by selectively targeting its stem cells. Altogether, the data revealed that NPC tumorspheres contain cancer stem-like populations with increased chemoradioresistance. It was suggested that the serum-free culture of NPC cells may provide an appropriate model for researching the sensitivity of CSCs to therapeutic agents. It was additionally revealed that salinomycin is an efficient inhibitor of NPC CSCs, supporting the hypothesis that salinomycin may eliminate CSCs and imply a need for further clinical evaluation.

Radiation-resistant cancer stem-like cell properties are regulated by PTEN through the activity of nuclear ß-catenin in nasopharyngeal carcinoma.

Radiotherapy is the primary and most important treatment for nasopharyngeal carcinoma (NPC). Cancer stem-like cells (CSCs) have been shown to be resistant to radiation. The phosphatase and tensin homolog deleted on chromosome 10 (PTEN) tumor suppressor gene has been suggested to play a role in stem cell self-renewal. In the present study, we sorted PTEN-/+ cells using a flow cytometer. The clone formation assay showed that PTEN- cells were more radioresistant than PTEN+ NPC cells. We found that PTEN- cells demonstrated a significant increase in tumorsphere formation and CSCs markers compared with PTEN+ cells. Silencing the expression of PTEN with siRNA resulted in increased expression of p-AKT, active ß-catenin and Nanog. siPTEN cells irradiated showed more radioresistant and DNA damage than parental cells. We also confirmed that down-regulation of ß-catenin expression with shRNA resulted in a reduced percentage of side population cells and expression of Nanog. shß-catenin cells significantly decreased survivin expression at 4 Gy irradiation in PTEN- cells compared with PTEN+ cells. In siPTEN cells, ß-catenin staining shifted from the cytoplasmic membrane to the nucleus. Furthermore, immunofluorescence showed that following irradiation of PTEN- cells, at 4 Gy, active ß-catenin was mainly found in the nucleus. Immunohistochemistry analysis also demonstrated that the PTEN-/p-AKT+/ß-catenin+/Nanog+ axis may indicate poor prognosis and radioresistance in clinical NPC specimens. Thus, our findings strongly suggest that PTEN- cells have CSCs properties that are resistant to radiation in NPC. PTEN exerts these effects through the downstream effector PI3K/AKT/ß-catenin/Nanog axis which depends on nuclear ß-catenin accumulation.

Salinomycin overcomes radioresistance in nasopharyngeal carcinoma cells by inhibiting Nrf2 level and promoting ROS generation.

Radiotherapy is the most important treatment for nasopharyngeal carcinoma (NPC). Radioresistant cancer cells have been shown to potentially result in residual disease that can lead to recurrence and metastasis. Salinomycin (SAL) has been identified as a promising anticancer drug during chemical screening, but it is unclear whether SAL plays a role in radioresistance. The nuclear factor erythroid-2-related factor 2 (Nrf2) is a crucial regulator of the cellular antioxidant system. There are currently numerous data indicating that Nrf2 has an important role in cancer radioresistance. In the present study, we found that SAL can reverse radioresistance in radioresistant SUNE1 (SUNE1IR) cells using a clone formation assay. In addition, SAL promoted radiation-induced apoptosis in radioresistant NPC cells. Our data show that radioresistant SUNE1IR cells exhibited a significant increase in the protein level of Nrf2 compared to parental cells, and SAL inhibited increased Nrf2 in SUNE1IR cells. Moreover, we knocked down Nrf2 with shRNA in CNE2 cells and Western blot analysis demonstrated that irradiation (IR)-induced increase in Nrf2 protein expression was significantly downregulated by SAL. The clone formation assay showed that Nrf2-deficient CNE2 cells were more sensitive to IR than parental cells. Importantly, we confirmed that combination treatment of Nrf2-deficient CNE2 cells with SAL and IR markedly increased the level of reactive oxygen species (ROS) and DNA damage. Taken together, our findings demonstrate, for the first time, that SAL sensitized radioresistant cells to IR by inhibition of Nrf2 and the promotion of ROS generation in NPC. These results may contribute to the development of SAL-based therapy for NPC patients.