IntroductionLong noncoding RNAs (lncRNAs) are emerging as key players in the development and progression of cancer. However, the biological role and clinical significance of most lncRNAs in lung carcinogenesis remain unclear. In this study, we identified and explored the role of a novel lncRNA, lung cancer associated transcript 1 (LCAT1), in lung cancer.MethodsWe predicted and validated LCAT1 from RNA-sequencing (RNA-seq) data of lung cancer tissues. The LCAT1–miR-4715-5p–RAC1 axis was assessed by dual-luciferase reporter and RNA immunoprecipitation (RIP) assays. Signaling pathways altered by LCAT1 knockdown were identified using RNA-seq. Furthermore, the mechanism of LCAT1 was investigated using loss-of-function and gain-of-function assays in vivo and in vitro.ResultsLCAT1 is an oncogene that is significantly upregulated in lung cancer tissues and associated with poor prognosis. LCAT1 knockdown caused growth arrest and cell invasion in lung cancer cells in vitro, and inhibited tumorigenesis and metastasis in the mouse xenografts. Mechanistically, LCAT1 functions as a competing endogenous RNA for miR-4715-5p, thereby leading to the upregulation of the activity of its endogenous target, Rac family small GTPase 1 (RAC1). Moreover, EHop-016, a small molecule inhibitor of RAC1, as an adjuvant could improve the Taxol monotherapy against lung cancer cells in vitro.ConclusionsLCAT1–miR-4715-5p–RAC1/PAK1 axis plays an important role in the progression of lung cancer. Our findings may provide valuable drug targets for treating lung cancer. The novel combination therapy of Taxol and EHop-016 for lung cancer warrants further investigation, especially in lung cancer patients with high LCAT1 expression.
Root rot is an important disease hampering the sustainable cultivation of Panax notoginseng. Culture-dependent and independent techniques were used to elucidate the dominant fungal pathogen of rusty root rot of P. notoginseng. Based on Illumina sequencing profiles for fungi using ITS primers, five phyla—namely Ascomycota, Basidiomycota, Glomeromycota, Zygomycota, and Chytridiomycota—were identified, and the analyses showed that the Ascomycota was the dominant phylum (∼50 to 97%), especially in the symptomatic samples. Out of 226 total genera identified, seven genera had over 1% average abundance, including Ilyonectria, Fusarium, Tetracladium, Cladosporium, Rhizophagus, Alternaria, and Perisporiopsis. However, only Ilyonectria was the predominant genera in the symptomatic samples (∼76 to 80%), while the others, including Fusarium, had higher abundances in asymptomatic samples. Based on in vitro and in vivo pathogenicity, the isolate G3B was demonstrated to be the pathogen causing rusty root rot of P. notoginseng, and it was identified as Ilyonectria mors-panacis. Based on primers F2-R2 targeting the His3 gene of Ilyonectria, real-time quantitative PCR (qPCR) was performed as an additional proof confirming that I. mors-panacis was the dominant pathogen in the symptomatic samples during the years of the study (2014-2015).
Culture-dependent and culture-independent methods were compared and evaluated in the study of the endophytic diversity of Dendrobium officinale. Culture-independent methods consisted of polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and metagenome methods. According to the results, differences were found between the three methods. Three phyla, namely Firmicutes, Proteobacteria, and Actinobacteria, were detected using the culturedependent method, and two phyla, Firmicutes and Proteobacteria, were detected by the DGGE method. Using the metagenome method, four major phyla were determined, including Proteobacteria (76.54%), Actinobacteria (18.56%), Firmicutes (2.27%), and Bacteroidetes (1.56%). A distinct trend was obtained at the genus level in terms of the method and the corresponding number of genera determined. There were 449 genera and 16 genera obtained from the metagenome and DGGE methods, respectively, and only 7 genera were obtained through the culture-dependent method. By comparison, all the genera from the culture-dependent and DGGE methods were contained in the members determined using the metagenome method. Overall, culture-dependent methods are limited to 'finding' endophytic bacteria in plants. DGGE is an alternative to investigating primary diversity patterns; however, the metagenome method is still the best choice for determining the endophytic profile in plants. It is essential to use multiphasic approaches to study cultured and uncultured microbes.
Ilyonectria mors-panacis is the cause of a serious disease hampering the production of Panax notoginseng, an important Chinese medicinal herb, widely used for its anti-inflammatory, antifatigue, hepato-protective, and coronary heart disease prevention effects. Here, we report the first Illumina-Pacbio hybrid sequenced draft genome assembly of I. mors-panacis strain G3B and its annotation. The availability of this genome sequence not only represents an important tool toward understanding the genetics behind the infection mechanism of I. mors-panacis strain G3B but also will help illuminate the complexities of the taxonomy of this species.
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