A novel lncRNA-mRNA-miRNA signature predicts recurrence and disease-free survival in cervical cancer

Cervical cancer (CC) patients have a poor prognosis due to the high recurrence rate. However, there are still no effective molecular signatures to predict the recurrence and survival rates for CC patients. Here, we aimed to identify a novel signature based on three types of RNAs [messenger RNA (mRNAs), microRNA (miRNAs), and long non-coding RNAs (lncRNAs)]. A total of 763 differentially expressed mRNAs (DEMs), 46 lncRNAs (DELs), and 22 miRNAs (DEMis) were identified between recurrent and non-recurrent CC patients using the datasets collected from the Gene Expression Omnibus (GSE44001; training) and The Cancer Genome Atlas (RNA- and miRNA-sequencing; testing) databases. A competing endogenous RNA network was constructed based on 23 DELs, 15 DEMis, and 426 DEMs, in which 15 DELs, 13 DEMis, and 390 DEMs were significantly associated with disease-free survival (DFS). A prognostic signature, containing two DELs (CD27-AS1, LINC00683), three DEMis (hsa-miR-146b, hsa-miR-1238, hsa-miR-4648), and seven DEMs (ARMC7, ATRX, FBLN5, GHR, MYLIP, OXCT1, RAB39A), was developed after LASSO analysis. The built risk score could effectively separate the recurrence rate and DFS of patients in the high- and low-risk groups. The accuracy of this risk score model for DFS prediction was better than that of the FIGO (International Federation of Gynecology and Obstetrics) staging (the area under receiver operating characteristic curve: training, 0.954 vs 0.501; testing, 0.882 vs 0.656; and C-index: training, 0.855 vs 0.539; testing, 0.711 vs 0.508). In conclusion, the high predictive accuracy of our signature for DFS indicated its potential clinical application value for CC patients.

Exploring of a prognostic long non-coding RNA signature of hepatocellular carcinoma by using public database / 中华流行病学杂志

Objective@#To explore an effective long non-coding RNA (lncRNA) signature in predicting the prognosis of hepatocellular carcinoma through the analysis on RNA sequencing data of hepatocellular carcinoma patients and peritumoral tissues in the Cancer Genome Atlas (TCGA) database.@*Methods@#The clinical characteristics and RNA sequencing data of 377 hepatocellular carcinoma patients were obtained from TCGA database by the end of February 2018. Then, differentially expressed lncRNAs between 50 pairs of tumor and peritumoral tissues were explored using student’s t-test. Next, a lncRNA signature was established through LASSO Cox regression analysis. All the patients were divided into four groups (<P25, P25-, P50-, ≥P75) based on the cut-off quartiles signature. Finally, compared with the control group (<P25), the hazard ratios (HRs) of three groups (P25-, P50-, ≥P75) were calculated by using Cox regression. The survival outcomes of patients in the four groups were compared to evaluate the capacity of the lncRNA signature model.@*Results@#A total of 951 differentially expressed lncRNAs were identified between tumor and peritumoral tissues. A three-lncRNA signature, including LNCSRLR, MKLN1-AS and ZFPM2-AS1, was established to predict the prognosis of hepatocellular carcinoma patients. The outcome suggested that the death risk of the ≥P75 group was 1.57 times larger than that of the <P25 group (95%CI: 1.06-2.31, P<0.05).@*Conclusion@#The three-lncRNA signature, which established by LNCSRLR, MKLN1-AS and ZFPM2-AS1, was significantly associated with the prognosis of hepatocellular carcinoma patients based on TCGA database data.

Expression of potassium channel genes predicts clinical outcome in lung cancer

Lung cancer is the most common cause of cancer deaths worldwide and several molecular signatures have been developed to predict survival in lung cancer. Increasing evidence suggests that proliferation and migration to promote tumor growth are associated with dysregulated ion channel expression. In this study, by analyzing high-throughput gene expression data, we identify the differentially expressed K⁺ channel genes in lung cancer. In total, we prioritize ten dysregulated K⁺ channel genes (5 up-regulated and 5 down-regulated genes, which were designated as K-10) in lung tumor tissue compared with normal tissue. A risk scoring system combined with the K-10 signature accurately predicts clinical outcome in lung cancer, which is independent of standard clinical and pathological prognostic factors including patient age, lymph node involvement, tumor size, and tumor grade. We further indicate that the K-10 potentially predicts clinical outcome in breast and colon cancers. Molecular signature discovered through K⁺ gene expression profiling may serve as a novel biomarker to assess the risk in lung cancer.

Expression profile of mitochondrial voltage-dependent anion channel-1 (VDAC1) influenced genes is associated with pulmonary hypertension

Several human diseases have been associated with mitochondrial voltage-dependent anion channel-1 (VDAC1) due to its role in calcium ion transportation and apoptosis. Recent studies suggest that VDAC1 may interact with endothelium-dependent nitric oxide synthase (eNOS). Decreased VDAC1 expression may limit the physical interaction between VDAC1 and eNOS and thus impair nitric oxide production, leading to cardiovascular diseases, including pulmonary arterial hypertension (PAH). In this report, we conducted meta-analysis of genome-wide expression data to identify VDAC1 influenced genes implicated in PAH pathobiology. First, we identified the genes differentially expressed between wild-type and Vdac1 knockout mouse embryonic fibroblasts in hypoxic conditions. These genes were deemed to be influenced by VDAC1 deficiency. Gene ontology analysis indicates that the VDAC1 influenced genes are significantly associated with PAH pathobiology. Second, a molecular signature derived from the VDAC1 influenced genes was developed. We suggest that, VDAC1 has a protective role in PAH and the gene expression signature of VDAC1 influenced genes can be used to i) predict severity of pulmonary hypertension secondary to pulmonary diseases, ii) differentiate idiopathic pulmonary artery hypertension (IPAH) patients from controls, and iii) differentiate IPAH from connective tissue disease associated PAH.

A fast identification method of notoginseng radix etrhizoma based on molecular signature / 中国药学杂志

OBJECTIVE: To establish a fast identification method of Panax notoginseng, molecular signature which can be used as fast authentication of P. notoginseng were screened according to comparison results of 248 Panax ITS2 sequences from GenBank and 46P. notoginseng ITS2 sequences from this study. METHODS: ITS2 Sequences obtained in this study were assembled using Codoncode Aligner, and then were imported to MEGA 6.0 together with Panax ITS2 sequences from GenBank. The comparison was conducted using MUSCLE method and then unique molecular signature of P. notoginseng was found in this comparison results. RESULTS: The length of ITS2 sequences of P. notoginseng was 230 bp, and the aligned ITS2 sequences of Panax was 258 bp. Based on one SNP site of P. notoginseng, one unique molecular signature was developed, 5'-AACCCATCAT TCCCTCGCGG GAGTCCATGC GGAGG-3'. If unknown samples contained the signature sequence after amplification, it would be identified to be Panax notoginseng and vice versa. CONCLUSION: The molecular signature obtained from this study can be used for fast authentication of varying kinds of P. notogin: sengcrude drugs and powders and authentication of mixed samples.

Microbial forensics: An upcoming investigative discipline.

Microorganisms make good weapons and bioterorism has been known to exist since centuries. This has most recently been highlighted by the terrorist attack using anthrax in the fall of 2001 in U.S. Although such attacks of bioterrorism are few, forensic evidence to criminally prosecute the perpetrator is necessary. To strengthen defence against bio crimes, a comprehensive technological network involving various fields needs to be developed. Microbial forensics is one such new discipline combining microbiology and forensic science. It uses advanced molecular techniques like microarray analysis and DNA fingerprinting etc. to associate the source of the causative agent with a specific individual or group by measuring variations between related strains. High quality assurance and quality control standards for microbial forensics will ensure highly reliable results that will stand up in the court of law. The more precise and refined a microbial system becomes, the more proper guidelines for investigations will be defined. An integrated approach towards developing this field of microbial forensics needs to be followed, to meet the challenges of bioterrorism more effectively.