A P53-related microRNA model for predicting the prognosis of hepatocellular carcinoma patients

Studies have shown that microRNAs (miRNAs) play a vital role in tumor progression and patients’ prognosis. Therefore, we aimed to construct a miRNA model for forecasting the survival of hepatocellular carcinoma (HCC) patients. The gene expression data of 433 patients with HCC from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus public databases were remined by survival analysis and receptor manipulation characteristic curve (ROC). A prognostic model including six miRNAs (hsa-mir-26a-1-3p, hsa-mir-188-5p, hsa-mir-212-5p, hsa-mir-149-5p, hsa-mir-105-5p, and hsa-mir-132-5p) were constructed in the training dataset (TCGA, n = 333). HCC patients were stratified into a high-risk group and a low-risk group with significantly different survival (median: 2.75 vs. 8.93 years, log-rank test p < .001). Then we proved its performance of stratification in another independent dataset (GSE116182, median: 2.55 vs 6.96 years, log-rank test p = .008). Cox regression analysis showed that the prognostic model was an independent prognostic indicator for HCC patients. Then time-dependent ROC analyses were performed to test the prognostic ability of the model with that of TNM staging, we found the model had a better performance, especially at 5 years (AUC = 0.76). Functional prediction showed that the genes targeted by the six prognostic miRNAs in the prognostic model were highly expressed in the P53-related pathway. In conclusion, we constructed a prognostic miRNA model that could indicate the survival of HCC patients.     

Attending the breast screening programme after breast cancer treatment: A population-based study

IntroductionIn the Netherlands, breast cancer patients are treated and followed at least 5 years after diagnosis. Furthermore, all women aged 50–74 are invited biennially for mammography by the nationwide screening programme. The relation between the outpatient follow-up (follow-up visits in the outpatient clinic for 5 years after treatment) and the screening programme is not well established and attending the screening programme as well as outpatient follow-up is considered undesirable. This study evaluates potential factors influencing women to attend the screening programme during their outpatient follow-up (overlap) and the (re-)attendance to the screening programme after 5 years of outpatient follow-up.MethodsData of breast cancer patients aged 50–74 years, treated for primary breast cancer between 1996 and 2007 were selected from the Netherlands Cancer Registry and linked to the National Breast Cancer Screening Programme in the Northern region. Cox regression analyses were used to study women (re-)attending the screening programme over time, possible overlap with the outpatient follow-up and factors influencing this.ResultsIn total 11 227 breast cancer patients were included, of whom 19% attended the screening programme after breast cancer treatment, 4.4% within 5 years and 15.4% after more than 5 years. Factors that independently influenced attendance within 5 years as well as more than 5 years after treatment were: interval tumours (HR 0.77; 95%CI 0.61–0.97 and HR 0.69; 95%CI 0.53–0.88, ref: screen-detected tumours), receiving adjuvant radiotherapy (HR 0.65; 95%CI 0.47–0.90 and HR 0.66; 95%CI 0.47–0.93; ref: none) and diagnosis of in situ tumours (HR 1.67; 95%CI 1.25–2.23 and HR 1.39; 95%CI 1.05–1.85; ref: stage I tumours). Non-screen related tumours (HR 0.41; 95%CI 0.29–0.58) and recent diagnosis (HR 0.89 per year; 95%CI 0.86–0.92) were only associated with attendance within 5 years after treatment.ConclusionThe interrelation between outpatient follow-up and screening should be improved to avoid overlap and low attendance to the screening programme after outpatient follow-up. Breast cancer patients should be informed that attending the screening programme during the outpatient follow-up is not necessary.     

Fine needle aspiration biopsy of neuroendocrine breast carcinoma metastatic to the thyroid. A case report

BACKGROUND: Tumors showing neuroendocrine differentiation arise in a wide range of organs, and metastatic neuroendocrine tumors may be difficult to differentiate from primary tumors. This report describes an unusual case of metastatic breast carcinoma with neuroendocrine differentiation that presented as a solitary thyroid nodule. The diagnosis was made by fine needle aspiration biopsy (FNAB). CASE: A 52-year-old woman presented with a thyroid nodule and bilateral enlarged supraclavicular fossa lymph nodes. FNAB revealed a neuroendocrine carcinoma. Further questioning revealed that the patient had had a breast carcinoma resected eight years previously. The diagnosis of metastatic neuroendocrine breast carcinoma was established by immunocytochemistry. The patient received antiestrogen therapy but subsequently developed skeletal metastases. CONCLUSION: Neuroendocrine carcinomas from various sites show similar cytologic features. In this case, a diagnosis of breast carcinoma metastatic to the thyroid was suggested by the clinical history and confirmed by FNAB with immunocytochemistry.     

Melatonin is an appropriate candidate for breast cancer treatment: Based on known molecular mechanisms

Breast cancer is the most prevalent cancer and one of the most important causes of death in women throughout the world. Breast cancer risk factors include smoking, alcohol consumption, personal and family history, hypertension, and hormone therapy, long-term use of nonsteroidal anti-inflammatory drugs and tobacco usage. Surgery, chemotherapy, radiotherapy, immunotherapy, and neoadjuvant therapy are the current means for breast cancer treatment. Despite hormonal agents and chemotherapy, which have beneficial effects on lowering breast cancer death rate, the reaction of different people to these treatments is still a challenging point. Melatonin (N-acetyl-5-methoxy tryptamine) is a methoxy indole compound that is mainly secreted by the pineal gland at night; it is as an antioxidant, anti-inflammatory, and oncostatic agent. On the basis of recent studies, melatonin has antitumor properties on different cancer types and it may suppress cancer development in vitro and as well as in animal models. It is suggested that melatonin inhibits the development of breast cancer by various mechanisms. This paper summarizes the roles of melatonin in breast cancer treatment from the aspect of its molecular actions.     

Identification of m6A methyltransferase-related lncRNA signature for predicting immunotherapy and prognosis in patients with hepatocellular carcinoma

N6-methyladenosine (m6A) methyltransferase has been shown to be an oncogene in a variety of cancers. Nevertheless, the relationship between the long non-coding RNAs (lncRNAs) and hepatocellular carcinoma (HCC) remains elusive. We integrated the gene expression data of 371 HCC and 50 normal tissues from The Cancer Genome Atlas (TCGA) database. Differentially expressed protein-coding genes (DE-PCGs)/lncRNAs (DE-lncRs) analysis and univariate regression and Kaplan–Meier (K–M) analysis were performed to identify m6A methyltransferase-related lncRNAs. Three prognostic lncRNAs were selected by univariate and LASSO Cox regression analyses to construct the m6A methyltransferase-related lncRNA signature. Multivariate Cox regression analyses illustrated that this signature was an independent prognostic factor for overall survival (OS) prediction. The Gene Set Enrichment Analysis (GSEA) suggested that the m6A methyltransferase-related lncRNAs were involved in the immune-related biological processes (BPs) and pathways. Besides, we discovered that the lncRNAs signature was correlated with the tumor microenvironment (TME) and the expression of critical immune checkpoints. Tumor Immune Dysfunction and Exclusion (TIDE) analysis revealed that the lncRNAs could predict the clinical response to immunotherapy. Our study had originated a prognostic signature for HCC based on the potential prognostic m6A methyltransferase-related lncRNAs. The present study had deepened the understanding of the TME status of HCC patients and laid a theoretical foundation for the choice of immunotherapy.     

Analysis of methylation-driven genes for predicting the prognosis of patients with head and neck squamous cell carcinoma

To help provide evidence for prognosis prediction and personalized targeted therapy for patients with head and neck squamous cell carcinoma (HNSCC), we investigated prognosis-specific methylation-driven genes in HNSCC. Survival time data, RNA sequencing data, and methylation data for HNSCC patients were downloaded from The Cancer Genome Atlas. The MethylMix R package based on the β mixture model was utilized to screen genes with different methylation statuses in tumor tissues and adjacent normal tissues, and a total of 182 HNSCC-related methylation-driven genes were then identified. A survival prediction scoring model based on multivariate Cox analysis was developed to screen the genes related to the prognosis of HNSCC, and a linear risk model of the methylation status of six genes (INA, LINC01354, TSPYL4, MAGEB2, EPHX3, and ZNF134) was constructed. The prognostic values of the six genes were further independently explored by survival analysis combined with methylation and gene expression analyses. The 5-year survival rate in the high-risk group of patients in the test set was 30.4% (95% CI: 22.7%-40.8%) and that in the low-risk group of patients was 65.5% (95% CI: 56.1%-76.5%). The area under the receiver operating characteristic curve for the model was 0.723, which further verified the specificity and sensitivity of the model. In addition, subsequent combined survival analysis revealed that all six genes could be used as independent prognostic markers and thus might be potential drug targets. The innovative method provides new insight into the molecular mechanism and prognosis of HNSCC.     

Factors predicting the stratified academic achievement trajectories of foreign-born Canadian adolescents: A population-based study

The study looked at the stratified math and language arts trajectories of foreign-born adolescents (aged 14–19) in British Columbia (BC), Canada, and identified social position factors that predicted this variation. Leveraging data from the Ministry of Health, Ministry of Education and Citizenship and Immigration Canada, the study looked longitudinally at a population-based cohort of foreign-born adolescents in BC (N?=?9,113), in comparison to a Canadian-born random sample (N?=?22,845). Utilizing Group-based Trajectory Modeling, the study found that foreign-born adolescents were stratified into a range of math and language arts trajectory groups over high school (grade 10 to 12), and group membership was predicted by key social position factors. The results supported moving away from a one-size-fits-all understanding of the impact of migration on adolescent development and identified key factors that predicted math and language arts outcomes for foreign-born Canadian adolescents.     

Solid papillary carcinoma of the breast with neuroendocrine features in a pregnant woman: a case report

Solid papillary carcinoma, a special form of breast carcinoma with neuroendocrine differentiation, usually presents in women aged 60 years or more. (Koern 2010). According to our best knowledge, we present the second case of such a tumor in pregnant women.     

A simple model for predicting the performance of affinity chromatography columns

Summary This paper presents a simple model for affinity chromatography, the approach used is based on the equilibrium stage model introduced by Martin and Synge (1941). The current development eliminates the need for an equilibrium assumption by using a simplified rate equation to describe the adsorption process. Although it is not mathematically rigorous this method has proved useful for the design of column experiments in our laboratory.     

A sequence-coupled vector-projection model for predicting the specificity of GalNAc-transferase.

The specificity of GalNAc-transferase is consistent with the existence of an extended site composed of nine subsites, denoted by R4, R3, R2, R1, R0, R1', R2', R3', and R4', where the acceptor at R0 is either Ser or Thr to which the reducing monosaccharide is being anchored. To predict whether a peptide will react with the enzyme to form a Ser- or Thr-conjugated glycopeptide, a new method has been proposed based on the vector-projection approach as well as the sequence-coupled principle. By incorporating the sequence-coupled effect among the subsites, the interaction mechanism among subsites during glycosylation can be reflected and, by using the vector projection approach, arbitrary assignment for insufficient experimental data can be avoided. The very high ratio of correct predictions versus total predictions for the data in both the training and the testing sets indicates that the method is self-consistent and efficient. It provides a rapid means for predicting O-glycosylation and designing effective inhibitors of GalNAc-transferase, which might be useful for targeting drugs to specific sites in the body and for enzyme replacement therapy for the treatment of genetic disorders.     

A cost-benefit analysis of methods for the determination of biomass concentration in wastewater treatment

The measurement of biomass concentration is important in biological wastewater treatment. This paper compares the accuracy and costs of the traditional volatile suspended solids (VSS) and the proposed suspended organic carbon (SOC) methods. VSS and SOC values of a dilution system were very well correlated (R(2)=0.9995). VSS and SOC of 16 samples were determined, the mean SOC/VSS ratio (0.52, n=16, sigma=0.01) was close to the theoretical value (0.53). For costing analysis, two hypothetical cases were analysed. In case A, it is assumed that 108 samples are analysed annually from two continuous reactors. Case B represents a batch experiment to be carried out in 24 incubated serum bottles. The savings, when using the SOC method, were 11,987 pounds for case A and 90 pounds for case B. This study suggests the use of SOC method as a time saving and lower cost biomass concentration measurement.     

Stability of membrane proteins: relevance for the selection of appropriate methods for high-resolution structure determinations

High stability is a prominent characteristic of integral membrane proteins of known atomic structure. But rather than being an intrinsic property, it may be due to a selection exerted by biochemical procedures prior to structure determination, since solubilization results in the transient exposure of membrane proteins to solution conditions. This may cause structural perturbations that interfere with 3D crystallization and hence with X-ray analysis. This problem also affects the preparation of samples for electron crystallography and NMR studies and may account for the fact that high-resolution structures of representatives of whole groups, such as transport proteins and signal transducers, have not been elucidated so far by any method. A knowledge of the proportion of labile proteins among membrane proteins, and of the kinetics of their denaturation, is therefore necessary. Establishing stability profiles, developing methods to maintain lateral pressure, or preventing contact with water (or both) should prove significant in establishing the structures of conformationally flexible proteins.