Comprehensive characterization of a time-course transcriptional response induced by autotoxins in Panax ginseng using RNA-Seq

The lists for all the differentially expressed genes. (XLS 1362 kb

Radiotherapy Upregulates Programmed Death Ligand-1 through the Pathways Downstream of Epidermal Growth Factor Receptor in Glioma

Background: In the present study, we aimed to investigate the role of epidermal growth factor receptor (EGFR) pathway in the up-regulation of programmed death ligand-1 (PD-L1) caused by radiotherapy (RT). Materials and Methods: Tissue microarrays (TMA) consisting of glioma cancer specimens from 64 patients were used to examine the correlation between PD-L1 and EGFR levels. Furthermore, we performed in vitro experiments to assess the role of EGFR pathway in RT-upregulated PD-L1 expression using human glioma cell lines U87 and U251. Results: Our data demonstrated that the PD-L1 expression was significantly correlated with EGFR expression in glioma specimens (χ2 = 5.00, P = 0.025). The expressions of PD-L1 at the protein and mRNA levels were both significantly up-regulated by RT (P  0.05). The combination of RT with EGFR inhibitor exhibited the same effect on antitumor immune response compared with the combination of RT with PD-L1 neutralizing antibody (Ab). Conclusions: RT could up-regulate the PD-L1 expression through the pathways downstream of EGFR in glioma

Boletín de Segovia: Número 11 - 1918 enero 25

Copia digital. Madrid : Ministerio de Cultura. Subdirección General de Coordinación Bibliotecaria, 200

Time-Course Transcriptome Analysis Reveals Resistance Genes of <i>Panax ginseng</i> Induced by <i>Cylindrocarpon destructans</i> Infection Using RNA-Seq

<div><p><i>Panax ginseng</i> C. A. Meyer is a highly valued medicinal plant. <i>Cylindrocarpon destructans</i> is a destructive pathogen that causes root rot and significantly reduces the quality and yield of <i>P</i>. <i>ginseng</i>. However, an efficient method to control root rot remains unavailable because of insufficient understanding of the molecular mechanism underlying <i>C</i>. <i>destructans</i>-<i>P</i>. <i>ginseng</i> interaction. In this study, <i>C</i>. <i>destructans</i>-induced transcriptomes at different time points were investigated using RNA sequencing (RNA-Seq). <i>De novo</i> assembly produced 73,335 unigenes for the <i>P</i>. <i>ginseng</i> transcriptome after <i>C</i>. <i>destructans</i> infection, in which 3,839 unigenes were up-regulated. Notably, the abundance of the up-regulated unigenes sharply increased at 0.5 d postinoculation to provide effector-triggered immunity. In total, 24 of 26 randomly selected unigenes can be validated using quantitative reverse transcription (qRT)-PCR. Gene ontology enrichment analysis of these unigenes showed that “defense response to fungus”, “defense response” and “response to stress” were enriched. In addition, differentially expressed transcription factors involved in the hormone signaling pathways after <i>C</i>. <i>destructans</i> infection were identified. Finally, differentially expressed unigenes involved in reactive oxygen species and ginsenoside biosynthetic pathway during <i>C</i>. <i>destructans</i> infection were indentified. To our knowledge, this study is the first to report on the dynamic transcriptome triggered by <i>C</i>. <i>destructans</i>. These results improve our understanding of disease resistance in <i>P</i>. <i>ginseng</i> and provide a useful resource for quick detection of induced markers in <i>P</i>. <i>ginseng</i> before the comprehensive outbreak of this disease caused by <i>C</i>. <i>destructans</i>.</p></div

Boletín de Segovia: Número 79 - 1892 junio 29

Copia digital. Madrid : Ministerio de Cultura. Subdirección General de Coordinación Bibliotecaria, 200

Additional file 9: of Comprehensive characterization of a time-course transcriptional response induced by autotoxins in Panax ginseng using RNA-Seq

The RNA-Seq profiles and qRT-PCR validations for P5CS, P5CR and APX. (TIFF 747 kb

Additional file 8: of Comprehensive characterization of a time-course transcriptional response induced by autotoxins in Panax ginseng using RNA-Seq

The RNA-Seq profiles and qRT-PCR validations for the ROS-related genes. (TIFF 1356 kb

Significant enrichment functional groups of DEGs.

<p>The most significant GO terms (<i>P</i> < 0.05) of differentially expressed unigenes are graphically presented by comparing with total transcripts. The x-axis represents log10 of the enrichment <i>P</i> value. The y-axis indicates the number of unigenes in log2 value. The size of each point is proportional to the percentage (DEG associated with GO terms/All unigenes associated with GO terms).</p

Heatmap showing the FPKM values of up-regulated RGs.

<p>The FPKM for the RGs in the control and six infected stages was used for hierarchical analysis. The heatmap shows the expression abundance of the RGs. The colors correspond to the value of FPKM, ranging from green (low expression) to red (high expression).</p

Heatmap showing the FPKM values of uniquely expressed unigenes upon infection.

<p>The FPKM for the uniquely expressed unigenes upon infection in the control and six infected stages was used for hierarchical analysis. The colors correspond to the value of FPKM, ranging from green (low expression) to red (high expression).</p