Project description:Brain metastasis (BM) can affect up to 25% of non-small cell lung cancer (NSCLC) patients during their lifetime. Efforts to characterize patients that will develop BM have been fairly disappointing. Small non-coding microRNAs (miRNAs) regulate the expression of target mRNAs by repressing their translation or regulating their sequence-specific degradation. miRNAs play a role in regulating a variety of targets and, consequently, multiple pathways, which makes them a powerful tool to be exploited for early detection of disease, risk assessment, and prognosis. In this study, we investigated miRNAs that may serve as biomarkers to differentiate between NSCLC patients with and without BM. miRNA microarray profiling was performed on samples from clinically matched NSCLC from patients with BM (BM+) and without BM (BM-). miR-328 and miR-330-3p were able to correctly classify BM+ vs. BM- patients. Gene expression analysis comparing NSCLC parental and stably transfected miR-328 cells identified several significantly differentially-expressed genes, whose expression may be directly or indirectly regulated by miR-328.
Project description:Total RNA was extracted from BM-MDSCs treated with or without additional 34.7 mM KCl. Libraries were prepared according to standard Illumina protocols. RNA sequencing was performed by Shanghai Biotechnology Corporation (Shanghai, China). The raw reads were filtered by Seqtk before mapping to genome using Hisat2 (version:2.0.4). The fragments of genes were counted using stringtie (v1.3.3b) followed by TMM (trimmed mean of M values) normalization. Differential gene expression analysis was conducted using DESeq2 (version 1.20.0), with a significance threshold of a corrected p-value < 0.05 and an absolute fold change ≥ 2. The distribution of differentially expressed genes in KEGG pathways was analyzed using the clusterProfiler R package (version 3.8.1) to identify key biological mechanisms.
Project description:Purpose: Profiling the bulk transcriptomes of PBLs in sepsis-developed BM progression. Methods: The total RNA of PBLs from BM patients were extracted, and constructed into cDNA library. Raw data of mRNA profiles were sequenced by paired-end strategy. Gene-counts were generated through handling sequencing data with the combined workflow of UMI-tools, STAR, Subread package and Samtools. Results: Successfully acquirng multiple bulk-transcriptomic profiles of PBLs from BM patients in different sepsis conditions.
Project description:Purpose: Profiling the bulk transcriptomes of CSF cells in sepsis-developed BM progression. Methods: The total RNA of CSF cells from BM patients were extracted, and constructed into cDNA library. Raw data of mRNA profiles were sequenced by paired-end strategy. Gene-counts were generated through handling sequencing data with the combined workflow of UMI-tools, STAR, Subread package and Samtools. Results: Successfully acquirng multiple bulk-transcriptomic profiles of CSF cells from BM patients in different sepsis conditions.
Project description:Small nucleolar RNAs (snoRNA) function in guiding 2'-O-methylation and pseudouridylation of ribosomal RNAs. But we found that knock down of a C/D box snoRNA, Bm-15, can induce apoptosis of insect Spodoptera frugiperda Sf9 cells. For the genome sequence of Spodoptera frugiperda is incomplete, here with the de novo sequencing method, transcriptome of Spodoptera frugiperda cell line Sf9 were sequenced after being transfected with overexpression vector and repression probes of snoRNA Bm-15. Results showed that 21 apoptosis-related genes were up-regulated upon Bm-15 inhibition and down-regulated with Bm-15 overexpression.
