Identification and development of a five-gene signature to improve the prediction of mechanical ventilator-free days for patients with COVID-19.

OBJECTIVE: Coronavirus disease 2019 (COVID-19) is a highly contagious infectious disease caused by the newly discovered severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Severe COVID-19 infection causes complications in the respiratory tract, which results in pulmonary failure, thus requiring prolonged mechanical ventilation (MV). An increase in the number of patients with COVID-19 poses numerous challenges to the healthcare system, including the shortage of MV facilities. Despite continued efforts to improve COVID-19 diagnosis and treatment, no study has established a reliable predictive model for the risk assessment of deteriorating COVID-19 cases. MATERIALS AND METHODS: We extracted the expression profiles and clinical data of the GSE157103, GSE116560 and GSE21802 cohorts from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were identified as the intersection of the resulting differential genes as analysed via limma, edgeR and DESeq2 R packages. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed using the R package 'clusterProfiler'. Variables closely related to MV were examined using univariate Cox regression analysis, and significant variables were subjected to least absolute shrinkage and selection operator regression (LASSO) analysis for the construction of a risk model. Kaplan-Meier analysis and receiver operating characteristic (ROC) curves were generated to verify the predictive values of the risk model. RESULTS: We identified 198 unigenes that were differentially expressed in COVID-19 samples. Moreover, a five-gene signature (BTN3A1, GPR35, HAAO, SLC2A6 and TEX2) was constructed to predict the ventilator-free days of patients with COVID-19. In our study, we used the five-gene signature to calculate the risk score (MV score) for each patient. The results revealed a statistical correlation between the MV score and the scores of the Acute Physiology and Chronic Health Evaluation and Sequential Organ Failure Assessment of patients with COVID-19. Kaplan-Meier analysis revealed that the number of ventilator-free days was significantly reduced in the low-MVscore group compared to the high-MVscore group. The ROC curves revealed that our model had a good performance, and the areas under the ROC curve were 0.93 (3-week ROC) and 0.97 (4-week ROC). The 'Limma' package analysis revealed 71 upregulated genes and 59 downregulated genes in the high-MV score group compared to the low-MV score group. These DEGs were mainly enriched in cytokine signalling in immune system and cellular response to cytokine stimulus. CONCLUSIONS: This study identified a five-gene signature that can predict the length of ventilator-free days for patients with COVID-19.

[Analysis of treatment modalities and prognosis of patients with gallbladder cancer in China from 2010 to 2017].

Objective: To evaluate the clinical characteristics and prognosis of gallbladder cancer (GBC) patients in China. Methods: This retrospective multicenter cohort study enrolled 3 528 consecutive GBC patients diagnosed between January 2010 to December 2017 in 15 hospitals from 10 provinces. There were 1 345 (38.12%) males and 2 183 (61.88%) females.The age of diagnosis was (63.7±10.8) years old (range: 26 to 99 years old) .There were 213 patients (6.04%) in stage 0 to Ⅰ, whereas 1 059 (30.02%) in stage Ⅱ to Ⅲ, 1 874 (53.12%) in stage Ⅳ, and 382 (10.83%) unavailable. Surgery was performed on 2 255 patients (63.92%) . Three hundred and thirty-six patients received chemotherapy or radiotherapy (9.52%; of which 172 were palliative); 1 101 (31.21%) received only supportive treatment.The patient source, treatment and surgery, pathology, concomitant gallstone, and prognosis were analyzed. Results: Among the 3 528 GBC patients, 959 (27.18%) were from East China, 603 (17.09%) from East-North China, 1 533 (43.45%) from Central China, and 433(12.27%) from West China. Among the 1 578 resectable tumor, 665 (42.14%) underwent radical surgery, 913 (57.86%) underwent surgery that failed to follow the guidelines.Eight hundred and ninety-one (56.46%) patients were diagnosed before surgery, 254 (16.10%) during surgery, and 381 (24.14%) after surgery (time point of diagnosis couldn't be determined in 52 patients) .Among the 1 578 patients with resectable tumor, 759 (48.10%) had concomitant gallstone.Among the 665 patients underwent radical surgery, 69 (10.4%) showed positive resection margin, 510 (76.7%) showed negative resection margin, and 86 (12.9%) unreported margin status.The 5-year overall survival rate (5yOS) for the 3 528-patient cohort was 23.0%.The 5yOS for patients with resectable tumor was 39.6%, for patients with stage ⅣB tumor without surgery was 5.4%, and for patients with stage ⅣB tumor underwent palliative surgery was 4.7%. Conclusions: More than half GBC patients in China are diagnosed in stage Ⅳ.Curative intent surgery is valuable in improving prognosis of resectable GBC.The treatment of GBC needs further standardization.Effective comprehensive treatment for GBC is in urgent need.

LncRNA TATDN1 induces the progression of hepatocellular carcinoma via targeting miRNA-6089.

OBJECTIVE: To clarify the potential effect of long non-coding RNA (lncRNA) TATDN1 on accelerating the proliferative rate and cell cycle progression of hepatocellular carcinoma (HCC) via sponging miRNA-6089, thus participating in the progression of HCC. PATIENTS AND METHODS: TATDN1 expression in HCC tissues and normal tissues was first determined by quantitative Real Time-Polymerase Chain Reaction (qRT-PCR). The correlation between TATDN1 expression to metastasis and overall survival of HCC was analyzed. The cellular level of TATDN1 in HCC cell lines was examined as well. Regulatory effects of TATDN1 on cell cycle progression and viability of HepG2 and SMMC7721 cells were evaluated. Subsequently, a potential target of TATDN1 was screened out and verified by Dual-Luciferase reporter gene assay. The expression pattern and biological function of the target gene miRNA-6089 in HCC were also determined. In a similar way, LIX1L was verified to be the target of miRNA-6089 and tested for its biological function in HCC. RESULTS: TATDN1 was upregulated in HCC tissues and cell lines. The overexpression of TATDN1 accelerated the proliferative rate and cell cycle progression of HCC. MiRNA-6089, the target gene of TATDN1, was lowly expressed in HCC. The overexpression of miRNA-6089 partially reversed the promotive role of TATDN1 in regulating the proliferation and cell cycle of HCC cells. Subsequently, LIX1L was verified to be the target of miRNA-6089. The overexpression of LIX1L partially reversed the regulatory effect of miRNA-6089 on the proliferative rate and cell cycle progression of HCC. CONCLUSIONS: TATDN1 accelerates the proliferative rate and cell cycle progression of HCC by degrading miRNA-6089 to upregulate LIX1L.

The JAK2/STAT3 signaling pathway is required for inflammation and cell death induced by cerulein in AR42J cells.

OBJECTIVE: The study was designed to investigate the JAK2/STAT3 signaling pathway in pancreatitis and its association with inflammation and cell death to provide a potential treatment method for pancreatitis. MATERIALS AND METHODS: The rat pancreatic acinar AR42J cells were used for the study, and they were transfected with JAK2 and STAT3 siRNAs to mimic knockdown condition. Cerulein was used to treat AR42J cells. Western blot and ELISA were employed to detect the expression of related proteins. Flow cytometry was done to analysis the necrosis of AR42J cells. RESULTS: In this study, we found that cell death and the secretion of IL-6 and TGF-ß1 were significantly increased, and the JAK2/STAT3 signaling pathway was activated in cerulein-induced AP. To determine the role of JAK2 and STAT3, JAK2 siRNA and STAT3 siRNA were used to block JAK2 and STAT3, respectively. The levels of IL-6 and TGF-ß1 levels in the medium were lower in JAK2 siRNA and STAT3 siRNA-treated cells compared with controls. Flow cytometry analysis showed that the level of cell death, expression of cleaved caspase-3, and the release of LDH were decreased following JAK2 siRNA and STAT3 siRNA treatment. CONCLUSIONS: These findings point to a novel role for the JAK2/STAT3 signaling pathway in the progression of cerulein-induced AP.

Identification of long non-coding RNA involved in osteogenic differentiation from mesenchymal stem cells using RNA-Seq data.

The aim of this study was to identify long non-coding RNA (lncRNA) associated with osteogenic differentiation from mesenchymal stem cells (MSCs) using high-throughput RNA sequencing (RNA-Seq) data. RNA-Seq dataset was obtained from the European Bioinformatics Institute (accession No. PRJEB4496), including two replicates each for immortalized mesenchymal stem cells iMSC#3 cultured in growth medium (GM) and differentiation medium (DM) for 28 days. The clean reads were aligned to a hg19 reference genome by Tophat and assembled by Cufflinks to identify the known and novel transcripts. RPKM values were calculated to screen for differentially expressed RNA. Novel lncRNA were screened based on various filter criteria. Subsequently, the underlying function of novel lncRNAs were predicted by functional annotation by ERPIN, a co-expression network was constructed by WGCNA and the KEGG pathway enriched by KOBAS. A total of 3171 RNA differentially expressed between the DM and GM groups (2597 mRNA and 574 lncRNA) were identified. Among the 574 differentially expressed lncRNA, 357 were known and 217 were novel lncRNA. Furthermore, 32 novel lncRNA were found to be miRNA precursors (including miR-689, miR-640, miR-601, and miR-544). A total of 14,275 co-expression relationships and 217 co-expression networks were obtained between novel lncRNA and mRNA. The differentially expressed lncRNA and mRNA were enriched into 6 significant pathways, including those for cancer, ECM-receptor interaction, and focal adhesion. Therefore, novel lncRNAwere identified and their underlying function predicted, which may provide the basis for future analyses of the role of lncRNA in osteoblastic differentiation.

The role of intestinal mucosa oxidative stress in gut barrier dysfunction of severe acute pancreatitis.

BACKGROUND: Severe acute pancreatitis (SAP) is a serious systemic disease with a sustained high mortality rate. Extensive evidence has shown that gut barrier dysfunction plays a critical role in the pathophysiology of SAP. AIM: Investigating the role of intestinal mucosa oxidative stress in gut barrier dysfunction of SAP. MATERIALS AND METHODS: Twenty-four BALB/c mice were randomly divided into two groups with twelve mice each group. The SAP group mice received six intraperitoneal injections of cerulein (50 µg/kg) at 1-hour intervals, then given one intraperitoneal injection of 10 mg/kg lipopolysaccharide (LPS from E. coli) for inducing SAP. Normal saline was given to the mice of control group. The animals of each group were averaged to two batches. Four and eight hours after the final injection, respectively, mice were anesthetized and blood and tissue samples were harvested for examination. The pathological changes of pancreas and gut were observed and scored. The serum levels of diamine oxidase (DAO), amylase and tumor necrosis factor-alpha (TNF-α) were measured. The contents of malondialdehyde (MDA) and reduced glutathione (GSH) and activity of superoxide dismutase (SOD) and xanthine oxidase (XO) in gut mucosa were detected. In gut mucosa, the caspase-3 activity was measured and the cell apoptosis and apoptosis index (AI) were determined by terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling (TUNEL) assay. The data were analyzed by ANOVA and t-test. RESULTS: At four and eight hours after SAP induction, the SAP group mice had significantly higher pancreatic and gut pathological scores (p < 0.01) and increased serum levels of amylase (p < 0.05), DAO and TNF-α (p < 0.01) and increased MDA contents and XO activity of gut mucosa (p < 0.01) compared with those of control mice. There were significantly lower GSH contents (p < 0.05) and SOD activity (p < 0.01) of gut mucosa in the SAP mice. It was also observed that the gut mucosa cells of SAP mice had significantly higher caspase-3 activity and apoptosis index (p < 0.01). CONCLUSIONS: In SAP, waterfall-style release of inflammatory factors such as TNF-α led to ischemia-reperfusion injury of gut mucosa which resulted in serious oxidative stress and activation of caspase-3 pathway and severe apoptosis of gut mucosa. Therefore, intestinal mucosal oxidative stress may play an important role in the mechanism of gut barrier dysfunction.

Research on the molecular mechanism of Seretide treatment to asthma disease.

INTRODUCTION: Asthma is one of the most common chronic diseases in children. It is attributable to complicated coactions between various genetic factors and environmental allergens. AIM: We attempt to unfold the mechanism of asthmatic disorder and research the molecular mechanism of Seretide on asthmatic disease. MATERIALS AND METHODS: Using the GSE31773 microarray datasets downloaded from Gene Expression Omnibus database, we first screened the differentially expressed genes between healthy control and asthmatic samples cells based on classical t-test and false discovery rate < 0.05 as significant threshold. The underlying molecular mechanisms were investigated by Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis. In addition, the crosstalk network of pathways was also constructed. RESULTS: A total of 2011 differentially expressed genes were obtained by comparing asthmatic sample treated with Seretide and healthy controls. A total of 403 differentially expressed genes were collected between asthma samples untreated by Seretide and healthy sample controls. The enriched pathway of differentially expressed genes included signal transduction disorder (such as TGF-beta signaling pathway) and metabolism disorder (such as Phenylalanine metabolism). There were 27 pathway crosstalk pairs among 13 pathways. CONCLUSIONS: Our findings will help to clarify the molecular mechanism of Seretide and offer advices for asthma pathogenesis, Seretide therapy and follow-up treatment.