Detection of multiple types of cancer driver mutations using targeted RNA sequencing in non-small cell lung cancer.

BACKGROUND: DNA-based next-generation sequencing has been widely used in the selection of target therapies for patients with nonsmall cell lung cancer (NSCLC). RNA-based next-generation sequencing has been proven to be valuable in detecting fusion and exon-skipping mutations and is recommended by National Comprehensive Cancer Network guidelines for these mutation types. METHODS: The authors developed an RNA-based hybridization panel targeting actionable driver oncogenes in solid tumors. Experimental and bioinformatics pipelines were optimized for the detection of fusions, single-nucleotide variants (SNVs), and insertion/deletion (indels). In total, 1253 formalin-fixed, paraffin-embedded samples from patients with NSCLC were analyzed by DNA and RNA panel sequencing in parallel to assess the performance of the RNA panel in detecting multiple types of mutations. RESULTS: In analytical validation, the RNA panel achieved a limit of detection of 1.45-3.15 copies per nanogram for SNVs and 0.21-6.48 copies per nanogram for fusions. In 1253 formalin-fixed, paraffin-embedded NSCLC samples, the RNA panel identified a total of 124 fusion events and 26 MET exon 14-skipping events, in which 14 fusions and six MET exon 14-skipping mutations were missed by DNA panel sequencing. By using the DNA panel as the reference, the positive percent agreement and the positive predictive value of the RNA panel were 98.08% and 98.62%, respectively, for detecting targetable SNVs and 98.15% and 99.38%, respectively, for detecting targetable indels. CONCLUSIONS: Parallel DNA and RNA sequencing analyses demonstrated the accuracy and robustness of the RNA sequencing panel in detecting multiple types of clinically actionable mutations. The simplified experimental workflow and low sample consumption will make RNA panel sequencing a potentially effective method in clinical testing.

Spatio-temporal association mining of intercity PM2.5 pollution: Hubei Province in China as an example.

The complex interaction between emissions, meteorology, and atmospheric chemistry makes accurate predictions of particulate pollution difficult. Advanced data mining techniques can reveal potential laws, providing new possibilities for understanding the evolution and causes of air pollution. Based on the Granger method and block modeling analysis, this paper explored the intercity spillover effects of hourly PM2.5 in Hubei Province, China, to determine the specific role (i.e., overflow, limited overflow, bilateral, inflow, and limited inflow) of each city on regional pollution formation. Furthermore, a dynamic Apriori algorithm considering time-lag effects was used to mine the spatio-temporal associations of extreme PM2.5 pollution events among different cities. Results suggest that the northern and central cities with high-level PM2.5 concentration in Hubei have a significant spillover effect, whereas the eastern and southern cities generally play a role as the sink of pollutants. Based on the association rules of extreme PM2.5 pollution, four main pollutant transport channels were excavated and well matched with the trajectories extracted by the atmospheric model. This paper provides new insights for exploring the interaction of intercity particulate pollution, which is a supplement and cross-validation of the model results.

Changes in the Microbial Community Diversity of Oil Exploitation.

To systematically evaluate the ecological changes of an active offshore petroleum production system, the variation of microbial communities at several sites (virgin field, wellhead, storage tank) of an oil production facility in east China was investigated by sequencing the V3 to V4 regions of 16S ribosomal ribonucleic acid (rRNA) of microorganisms. In general, a decrease of microbial community richness and diversity in petroleum mining was observed, as measured by operational taxonomic unit (OTU) numbers, α (Chao1 and Shannon indices), and ß (principal coordinate analysis) diversity. Microbial community structure was strongly affected by environmental factors at the phylum and genus levels. At the phylum level, virgin field and wellhead were dominated by Proteobacteria, while the storage tank had higher presence of Firmicutes (29.3-66.9%). Specifically, the wellhead displayed a lower presentence of Proteobacteria (48.6-53.4.0%) and a higher presence of Firmicutes (24.4-29.6%) than the virgin field. At the genus level, the predominant genera were Ochrobactrum and Acinetobacter in the virgin field, Lactococcus and Pseudomonas in the wellhead, and Prauseria and Bacillus in the storage tank. Our study revealed that the microbial community structure was strongly affected by the surrounding environmental factors, such as temperature, oxygen content, salinity, and pH, which could be altered because of the oil production. It was observed that the various microbiomes produced surfactants, transforming the biohazard and degrading hydro-carbon. Altering the microbiome growth condition by appropriate human intervention and taking advantage of natural microbial resources can further enhance oil recovery technology.

Melatonin prevents adverse myocardial infarction remodeling via Notch1/Mfn2 pathway.

Mitochondrial dysfunction is linked with myocardial infarction (MI), a disorder in which Notch1 has attracted increasing attention. However, the involvement of Notch1 in mitochondrial impairment after an MI is poorly understood, as is the role of mitochondrial fusion-associated protein 2 (Mfn2). Moreover, whether melatonin potentiates the Notch1/Mfn2 pathway in post-MI cardiac damage remains unclear. In our study, small interfering RNAs against Notch1 or Mfn2 and Jagged1 peptide were delivered via intramyocardial injection. At 3 days after these treatments, MI was induced by ligation of the anterior descending branch. We found that this ablation of Notch1 or Mfn2 aggravated post-MI injury, including worsened mitochondrial damage and increased generation of reactive oxygen species (ROS). In contrast, Jagged1 improved mitochondrial structure and function, decreased ROS production and attenuated post-MI injury. Interestingly, though Mfn2 expression was mildly regulated by Notch1 signaling in myocardium, Mfn2 deficiency nearly eliminated the cardioprotection by Jagged1, as evidenced by suppressed cardiac function, aggravated myocardial fibrosis, increased cell apoptosis, worsened mitochondrial impairment and enhanced oxidative stress. These observations revealed that Mfn2 plays an indispensable role in protection against MI-induced injury by Notch1. The mechanism might involve disrupting a damaging cycle of mitochondrial damage and ROS generation. Furthermore, melatonin activated Notch1 signaling and increased Mfn2 expression were reversed by luzindole, a nonselective antagonist of the melatonin receptor. Notably, melatonin attenuated post-MI injury in normal mice, but not in mice deficient in Notch1 or Mfn2. These results demonstrate that melatonin attenuates post-MI injury via the Notch1/Mfn2 pathway in a receptor-dependent manner.