Construction of a novel mRNA-signature prediction model for prognosis of bladder cancer based on a statistical analysis.

BACKGROUND: Bladder cancer (BC) is a common malignancy neoplasm diagnosed in advanced stages in most cases. It is crucial to screen ideal biomarkers and construct a more accurate prognostic model than conventional clinical parameters. The aim of this research was to develop and validate an mRNA-based signature for predicting the prognosis of patients with bladder cancer. METHODS: The RNA-seq data was downloaded from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). Differentially expressed genes (DEGs) were screened in three datasets, and prognostic genes were identified from the training set of TCGA dataset. The common genes between DEGs and prognostic genes were narrowed down to six genes via Least Absolute Shrinkage and Selection Operator (LASSO) regression, and stepwise multivariate Cox regression. Then the gene-based risk score was calculated via Cox coefficient. Time-dependent receiver operating characteristic (ROC) and Kaplan-Meier (KM) survival analysis were used to assess the prognostic power of risk score. Multivariate Cox regression analysis was applied to construct a nomogram. Decision curve analysis (DCA), calibration curves, and time-dependent ROC were performed to assess the nomogram. Finally, functional enrichment of candidate genes was conducted to explore the potential biological pathways of candidate genes. RESULTS: SORBS2, GPC2, SETBP1, FGF11, APOL1, and H1-2 were screened to be correlated with the prognosis of BC patients. A nomogram was constructed based on the risk score, pathological stage, and age. Then, the calibration plots for the 1-, 3-, 5-year OS were predicted well in entire TCGA-BLCA patients. Decision curve analysis (DCA) indicated that the clinical value of the nomogram was higher than the stage model and TNM model in predicting overall survival analysis. The time-dependent ROC curves indicated that the nomogram had higher predictive accuracy than the stage model and risk score model. The AUC of nomogram time-dependent ROC was 0.763, 0.805, and 0.806 for 1-year, 3-year, and 5-year, respectively. Functional enrichment analysis of candidate genes suggested several pathways and mechanisms related to cancer. CONCLUSIONS: In this research, we developed an mRNA-based signature that incorporated clinical prognostic parameters to predict BC patient prognosis well, which may provide a novel prognosis assessment tool for clinical practice and explore several potential novel biomarkers related to the prognosis of patients with BC.

Severity of acute gastrointestinal injury grade is a predictor of all-cause mortality in critically ill patients: a multicenter, prospective, observational study.

BACKGROUND: In 2012, the European Society of Intensive Care Medicine proposed a definition for acute gastrointestinal injury (AGI) based on current medical evidence and expert opinion. The aim of the present study was to evaluate the feasibility of using the current AGI grading system and to investigate the association between AGI severity grades with clinical outcome in critically ill patients. METHODS: Adult patients at 14 general intensive care units (ICUs) with an expected ICU stay ≥24 h were prospectively studied. The AGI grade was assessed daily on the basis of gastrointestinal (GI) symptoms, intra-abdominal pressures, and feeding intolerance (FI) in the first week of admission to the ICU. RESULTS: Among the 550 patients enrolled, 456 patients (82.9%) received mechanical ventilation, and 470 patients were identified for AGI. The distribution of the global AGI grade was 24.5% with grade I, 49.4% with grade II, 20.6% with grade III, and 5.5% with grade IV. AGI grading was positively correlated with 28- and 60-day mortality (P < 0.0001). Univariate Cox regression analysis showed that age, sepsis, diabetes mellitus, coronary artery disease, the use of vasoactive drugs, serum creatinine and lactate levels, mechanical ventilation, Acute Physiology and Chronic Health Evaluation II (APACHE II) score, and the global AGI grade were significantly (P ≤ 0.02) associated with 60-day mortality. In a multivariate analysis including these variables, diabetes mellitus (HR 1.43, 95% CI 1.03-1.87; P = 0.05), the use of vasoactive drugs (HR 1.56, 95% CI 1.12-2.11; P = 0.01), serum lactate (HR 1.15, 95% CI 1.06-1.24; P = 0.03), global AGI grade (HR 1.65, 95% CI 1.28-2.12; P = 0.008), and APACHE II score (HR 1.04, 95% CI 1.02-1.06; P < 0.001) were independently associated with 60-day mortality. In a subgroup analysis of 402 patients with 7-day survival, in addition to clinical predictors and the AGI grade on the first day of ICU stay, FI within the first week of ICU stay had an independent and incremental prognostic value for 60-day mortality (χ2 = 41.9 vs. 52.2, P = 0.007). CONCLUSIONS: The AGI grading scheme is useful for identifying the severity of GI dysfunction and could be used as a predictor of impaired outcomes. In addition, these results support the hypothesis that persistent FI within the first week of ICU stay is an independent determinant for mortality. TRIAL REGISTRATION: Chinese Clinical Trial Registry identifier: ChiCTR-OCS-13003824 . Registered on 29 September 2013.

Findings of ventilator-measured P0.1 in assessing respiratory drive in patients with severe ARDS.

BACKGROUND: Providers should adjust the depth of sedation to promote lung-protective ventilation in patients with severe ARDS. This recommendation was based on the assumption that the depth of sedation could be used to assess respiratory drive. OBJECTIVE: To assess the association between respiratory drive and sedation in patients with severe ARDS by using ventilator-measured P0.1 and RASS score. METHODS: Loss of spontaneous breathing was observed within 48 h of mechanical ventilation in patients with severe ARDS, and spontaneous breathing returned after 48 hours. P0.1 was measured by ventilator every 12 ± 2 hours, and the RASS score was measured synchronously. RESULTS: The RASS score was moderately correlated with P0.1 (R𝑆𝑝𝑒𝑎𝑟𝑚𝑎𝑛, 0.570; 95% CI, 0.475 to 0.637; p= 0.00). However, only patients with a RASS score of -5 were considered to have no excessive respiratory drive, but there was a risk for loss of spontaneous breathing. A P0.1 exceeding 3.5 cm H2O in patients with other RASS scores indicated an increase in respiratory drive. CONCLUSION: RASS score has little clinical significance in evaluating respiratory drive in severe ARDS. P0.1 should be evaluated by ventilator when adjusting the depth of sedation to promote lung-protective ventilation.

SCNN1B regulates the proliferation, migration, and collagen deposition of human lung fibroblasts.

The aim of this study was to investigate the role of amiloride-sensitive sodium channel protein 1B (SCNN1B) on the proliferation and migration of human lung fibroblasts and the possible mechanism that promote the development of acute respiratory distress syndrome (ARDS). Cultivate human embryonic lung fibroblasts (MRC-5) in vitro and screen out the most effective small interfering RNA to silence the expression of SCNN1B. Then, quantitative real-time PCR (qRT-PCR), CCK-8, Transwell, and Western blot detections were performed separately. The results of qRT-PCR showed that all three SCNN1B siRNAs were able to significantly decrease the mRNA expression level of SCNN1B compared with the si-NC group (P < 0.01), with the most significant decrease in the SCNN1B siRNA-83 group. Additionally, compared with the si-NC group, the proliferation ability of MRC-5 cells in the si-SCNN1B group was significantly enhanced, and the migration rate was significantly decreased (P < 0.01). Western blot results showed that low expression of SCNN1B significantly inhibited the protein expression levels of collagen deposition related proteins Collagen I and Heat shock proteins 47 (P < 0.01). In summary, SCNN1B can inhibit cell proliferation and promote cell migration and extracellular matrix deposition of human lung fibroblasts, and may be involved in the occurrence and development of ARDS.

A Bioinformatic Analysis of Immune-Related Prognostic Genes in Clear Cell Renal Cell Carcinoma Based on TCGA and GEO Databases.

BACKGROUND: Clear cell renal cell carcinoma (ccRCC) is a commonly occurring tumor. Through a deeper understanding of the immune regulatory mechanisms in the tumor microenvironment, immunotherapy may serve as a potential treatment for cancer patients. This study aimed at identifying the survival-related immune cells and hub genes, which could be potential targets for immunotherapy in ccRCC. METHODS: The gene expression profiles and clinical data of ccRCC patients were extracted from UCSC Xena and Gene Expression Omnibus (GEO) databases. Kaplan-Meier (KM) survival and Least Absolute Shrinkage and Selection Operator (LASSO) regression analyses were utilized to select the survival-related tumor-infiltrating immune cells. Multivariate Cox regression was utilized to develop a signature based on the tumor-infiltrating immune cells (TIICs). Based on the signature, the risk score was calculated, following which the samples were divided into high-risk and low-risk groups. Differentially expressed genes (DEGs) between the two risk groups were identified. Functional enrichment analysis was performed and cytoHubba plug-in of Cytoscape was used to identify the hub genes. Multiple datasets were utilized to validate these hub genes, including the Gene Expression Profiling Interactive Analysis (GEPIA), UALCAN, and the Human Protein Atlas (HPA), and the GEO datasets. Finally, a correlation analysis was performed to evaluate the relationship between the hub genes and TIICs. RESULTS: Four immune survival-related cells, including T cell CD4 memory-activated, T cell regulatory (Tregs), eosinophils, and mast cell resting were identified. Nine immune-specific hub genes were identified, which included APOE, CASR, CTLA4, CXCL8, EGF, F2, KNG1, MMP9, and IL6. Furthermore, these hub genes were significantly correlated with clinical traits and closely associated with some TIICs. CONCLUSION: A total of four survival-related immune cell types and nine hub genes were found to be closely associated with ccRCC. These findings may have implications for the development of novel potential immunotherapeutic targets for ccRCC.

Transcriptomics analysis for the identification of potential age-related genes and cells associated with three major urogenital cancers.

Age is one of the most important risk factors of the occurrence for tumor patients. The majority of patients with urogenital cancers are the elderly, whose clinical characteristics are greatly affected by age and ageing. Our study aimed to explore age-related genes, cells, and biological changes in three common urogenital cancers via integrative bioinformatics analysis. First, mRNA (count format) and clinical data for bladder cancer, prostate cancer and renal cell carcinoma were downloaded from the Cancer Genome Atlas (TCGA). Through the comparison of clinicopathological characteristics, genes expression and cells infiltration between the old group and the young group, it was found that the clinical characteristics, genes and cells in the tumor microenvironment of different ages were quite different. And 4 key cells, 14 hub genes and some potential pathways were identified and considered as important factors. More importantly, we analyzed the differential landscape of the genes and cells from different perspectives, and confirmed its importance. In conclusion, we identified genes and cell types associated with age-related changes in the tumour microenvironment in urogenital cancer patients. These genes and cell types may play a critical role in the age-associated differences in clinicopathological characteristics among urogenital cancers, thus providing a link between ageing and cancer occurrence. The findings of this study may pave the way for the development of age-tailored approaches to treat cancer and other age-related diseases.

Integrative analysis of immune molecular subtypes and microenvironment characteristics of bladder cancer.

The emergence of immunotherapy has provided an option of treatment methods for bladder cancer (BC). However, the beneficiaries of immunotherapy are still limited to small-scale patients, and immunotherapy-related adverse events often occur. It is a major challenge for clinical work to study the immune subtypes of BC and the molecular mechanism of immune escape, and identify the immune responders accurately. Here, we explore the immune molecular subtypes of bladder cancer and potential escape mechanisms. First, we screened the expression profiles of 303 differentially expressed immune-related genes in BC patients from the Cancer Genome Atlas (TCGA) database, and successfully identified 4 molecular subtypes of BC. By comparing the clinical characteristics, immune cells infiltration, the expression of checkpoint genes, human leukocyte antigen (HLA) genes, and gene mutation status of different subtypes, we identified different clinical and immunological characteristics of 4 subtypes. Among 4 subtypes, Cluster 2 met the general characteristics of immunotherapy responders and responded well to immunotherapy, while Cluster 4 had the highest expression of immune characteristics, and is similar to the immune environment of normal bladder tissue. Then, the weighted gene co-expression network analysis (WGCNA) of immune-related genes revealed that brown module was positively correlated with subtypes. Pathway enrichment analysis explored the major pathways associated with subtypes, which are also associated with immune escape mechanisms. Moreover, the decision tree model, which was constructed by the principle of random forest screening factors, was also validated in internal validation set and external validation set from the Gene Expression Omnibus (GEO) cohort (GSE133624), and could achieve accurate subtypes prediction for BC patients with high-throughput sequencing. Taken together, we explored the immune molecular subtypes and their mechanisms of BC, and these results may provide guidance for the development of new BC immunotherapy strategies.

Identification of prognostic biomarkers associated with stromal cell infiltration in muscle-invasive bladder cancer by bioinformatics analyses.

Muscle-invasive bladder cancer (MIBC) is one of the common malignant tumors. Patients with MIBC still have high tumor recurrence and progression rates after surgery. Bioinformatics analysis of stromal infiltration-related genes in the tumor microenvironment (TME) of MIBC patients was performed in this study to determine the major stromal cells types and biomarkers for their progression and poor prognosis. The ESTIMATE algorithm was applied to evaluate the stromal score and immune score of samples from MIBC patients in The Cancer Genome Atlas (TCGA) and found that stromal score was closely related to the clinical characteristics of the patients. The Gene Set Enrichment Analysis (GSEA) further revealed that stromal cells were involved in biological processes such as activation of leukocytes and positive regulation of cell migration during MIBC progression, as well as PI3K-Akt, MAPK, and Rap1 signaling pathways. Five hub genes related to prognosis, including ACTA2, COL5A1, DCN, LUM, and PRRX1 were identified by the Weighted Gene Co-Expression Network Analysis (WGCNA), Protein-Protein Interaction (PPI), survival analysis, and Oncomine, Gene Expression Omnibus (GEO) database validation. Besides, we identified five stromal cell types associated with overall survival time, among which chondrocytes and fibroblasts were identified as the major stromal cell types through correlation analysis. Finally, the Receiver Operating Characteristic (ROC) curve and immunohistochemistry were used to verify the diagnostic value and expression of hub genes in different invasive tumors. In summary, we investigated the biological behavior of stromal cells in the TME of MIBC to promote tumor progression obtained hub genes associated with progression and poor prognosis and identified the main stromal cells types in the TME.

Prognostic Value of Prolonged Feeding Intolerance in Predicting All-Cause Mortality in Critically Ill Patients: A Multicenter, Prospective, Observational Study.

BACKGROUND: The 2012 European Society of Intensive Care Medicine (ESICM) guidelines provided a clear definition of feeding intolerance (FI). The study aimed to investigate the association between FI based on the current ESICM definition and clinical outcome and to further explore the effect of the duration of FI on mortality. METHODS: Adult patients from 14 general intensive care units (ICUs) with an expected ICU stay ≥24 hours were prospectively studied. Based on FI duration in the first week of admission to the ICU, FI was categorized as 7-day persistent feeding tolerance (FT), delayed FT, delayed FI, and 7-day persistent FI. The primary outcomes were 28-day and 60-day all-cause mortality. RESULTS: Of 499 patients, the prevalence of 3-day and 7-day persistent FI was 39.2% (n = 196) and 25.4% (n = 106), respectively. The patients with 3-day FT had lower risk of 28-day and 60-day mortality rates and higher prevalence in ventilator weaning and vasoactive medication on the seventh day of ICU admission than those with 3-day FI. Three-day FI remained an independent predictor for 60-day mortality. In a subgroup analysis including 418 patients with 7-day survival, compared with those with 7-day persistent FT, the odds ratios of 60-day mortality were 1.67, 1.97, and 2.62 in the patients with delayed FT, delayed FI, and 7-day persistent FI, respectively. CONCLUSION: FI was associated with increased mortality and longer duration of mechanical ventilation and vasoactive support. Prolonged or relapsing FI represented an incremental risk of adverse outcomes in critically ill patients.

Effectiveness of enteral feeding protocol on clinical outcomes in critically ill patients: A before and after study.

BACKGROUND AND OBJECTIVE: Enteral nutrition (EN) feeding protocol was proposed to have positive impact on critically ill patients. However, current studies showed conflicting results. The present study aimed to investigate whether enteral feeding protocol was able to improve clinical outcomes in critically ill patients. METHODS: A before (stage 1) and after (stage 2) interventional study was performed in 10 tertiary care hospitals. All patients expected to stay in the intensive care unit (ICU) for over three days were potentially eligible. Clinical outcomes such as 28-day mortality, ICU length of stay, duration of mechanical ventilation (MV), and nosocomial infection were compared between the two stages. MAIN RESULTS: A total of 410 patients were enrolled during the study period, including 236 in stage 1 and 174 in stage 2. EN feeding protocol was able to increase the proportion of EN in day 2 (41.8±22.3 vs. 50.0±28.3%; p = 0.006) and day 6 (70.3±25.2 vs. 77.6±25.8%; p = 0.006). EN percentages tended to be higher in stage 1 than that in stage 2 on other days, but statistical significance was not reached. There was no difference in 28-day mortality between stage 1 and 2 (0.14 vs. 0.14; p = 0.984). Implementation of EN feeding protocol marginally reduced ICU length of stay (19.44±18.48 vs. 16.29±16.19 days; p = 0.077). There was no difference in the duration of MV between stage a and stage 2 (14.24±14.49 vs. 14.51±17.55 days; p = 0.877). CONCLUSIONS: The study found that the EN feeding protocol was able to increase the proportion of EN feeding, but failed to reduce 28-day mortality, incidence of nosocomial infection or duration of MV.

Effectiveness of enteral feeding protocol on clinical outcomes in critically ill patients: a study protocol for before-and-after design.

INTRODUCTION: Enteral feed is an important component of nutritional therapy in critically ill patients and underfeeding has been associated with adverse outcomes. The article developed an enteral feeding protocol and planed a before-and-after comparative trial to explore whether implementation of enteral feeding protocol was able to improve clinical outcomes. METHODS AND ANALYSIS: The study will be conducted in intensive care units (ICUs) of ten tertiary care academic centers. Critically ill patients expected to stay in ICU for over 3 days and require enteral nutrition (EN) were potentially eligible. This is a before-and-after study comprising three phases: The first phase is the period without enteral feeding protocol; the second phase involves four-week training program, and the last phase is to perform the protocol in participating centers. We plan to enroll a total of 350 patients to provide an 80% power and 0.05 error rate to detect a 15% reduction of mortality. The primary outcome is 28-day mortality. ETHICS AND DISSEMINATION: Ethical approval to conduct the research has been obtained from all participating centers. Additionally, the results will be published in peer-reviewed journal. TRIAL REGISTRATION: The study was registered at International Standard Registered Clinical/soCial sTudy Number (ISRCTN) registry (ISRCTN10583582).