scholarly journals Abnormal gene expression and gene fusion in lung adenocarcinoma with high-throughput RNA sequencing

2014 ◽  
Vol 21 (2) ◽  
pp. 74-82 ◽  
Author(s):  
Z-H Yang ◽  
R Zheng ◽  
Y Gao ◽  
Q Zhang ◽  
H Zhang
Keyword(s):  
Gene Expression ◽  
Lung Adenocarcinoma ◽  
Rna Sequencing ◽  
High Throughput ◽  
Gene Fusion

Abstract 46: High-Density Lipoproteins Control Monocyte Differentiation Through microRNA Intercellular Communication

2013 ◽  
Vol 33 (suppl_1) ◽  
Author(s):  
Kasey C Vickers ◽  
Michael G Levin ◽  
Michael P Anderson ◽  
Qing Xu ◽  
Joshua Anzinger ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Sequencing ◽  
High Throughput ◽  
Small Rna ◽  
Cellular Response ◽  
Culture Media ◽  
Recipient Cell ◽  
Inflammatory Cells ◽  
High Density Lipoproteins ◽  
Small Rna Sequencing

Many HDL-microRNAs (miRNA) are well-characterized post-transcriptional regulators of inflammation, and are significantly increased on HDL with hypercholesterolemia and atherosclerosis in humans and mice. Therefore, we hypothesize that inflammatory cells uniquely control their own gene expression through cellular miRNA export to HDL and then regulate recipient cell gene expression through HDL-mediated miRNA delivery. To test this hypothesis, we used high-throughput proteomics, Open Arrays, small RNA sequencing, and gene expression microarrays. Human monocytes (plasma elutriation) were differentiated into dendritic cells and multiple macrophage phenotypes. Each cell-type was incubated with pure reconstituted HDL (rHDL), which was then purified from culture media by apolipoprotein A-I immunoprecipitation after 24 h, and both cellular and HDL-miRNAs were profiled using TaqMan Open Arrays. Macrophages were found to export high levels of miRNAs to HDL that inhibit monocyte/macrophage differentiation (miR-146a, miR-223); however, monocytes were also found to export many miRNAs associated with differentiation, including miR-92a, miR-222, miR-17, miR-20a, miR106a, and miR-21. Furthermore, many miRNAs were found to be transcribed in inflammatory cells, but completely exported to HDL and not retained in the cell. Most interestingly, HDL treatment was found to induce miR-223 transcription in monocytes, as determined by primary miR-223 transcript levels; however, intracellular levels of the mature form (miR-223) did not change. These results suggest that HDL induces the export of miRNAs it transports. PAR-CLIP with high-throughput small RNA sequencing was used to demonstrate that miRNAs are transferred from macrophages to endothelial cells and loaded onto cellular Argonaute 2-continaining RNA-induced silencing complexes. To demonstrate this in mice, human HDL, containing endogenous levels of miR-223, were injected into miR-223-null mice and inflammation-associated miRNA delivery was mapped in vivo. In summary, we found profound differences in the cellular response to HDL treatment and HDL-miRNA communication amongst inflammatory cell phenotypes that are physiologically relevant to cardiovascular disease.

scholarly journals Gene expression profiling by targeted RNA sequencing in pathological stage I lung adenocarcinoma with a solid component

Lung Cancer ◽  
2020 ◽  
Vol 147 ◽  
pp. 56-63
Author(s):  
Yoshiteru Kidokoro ◽  
Tomohiko Sakabe ◽  
Tomohiro Haruki ◽  
Taichi Kadonaga ◽  
Kanae Nosaka ◽  
...  
Keyword(s):  
Gene Expression ◽  
Lung Adenocarcinoma ◽  
Gene Expression Profiling ◽  
Rna Sequencing ◽  
Expression Profiling ◽  
Stage I ◽  
Solid Component ◽  
Pathological Stage

scholarly journals Microbial single-cell RNA sequencing by split-pool barcoding

Science ◽  
2020 ◽  
Vol 371 (6531) ◽  
pp. eaba5257 ◽  
Author(s):  
Anna Kuchina ◽  
Leandra M. Brettner ◽  
Luana Paleologu ◽  
Charles M. Roco ◽  
Alexander B. Rosenberg ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Rna Sequencing ◽  
High Throughput ◽  
Single Cell Analysis ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Growth Stages ◽  
High Throughput Analysis ◽  
Single Cell Rna Sequencing

Single-cell RNA sequencing (scRNA-seq) has become an essential tool for characterizing gene expression in eukaryotes, but current methods are incompatible with bacteria. Here, we introduce microSPLiT (microbial split-pool ligation transcriptomics), a high-throughput scRNA-seq method for Gram-negative and Gram-positive bacteria that can resolve heterogeneous transcriptional states. We applied microSPLiT to >25,000 Bacillus subtilis cells sampled at different growth stages, creating an atlas of changes in metabolism and lifestyle. We retrieved detailed gene expression profiles associated with known, but rare, states such as competence and prophage induction and also identified unexpected gene expression states, including the heterogeneous activation of a niche metabolic pathway in a subpopulation of cells. MicroSPLiT paves the way to high-throughput analysis of gene expression in bacterial communities that are otherwise not amenable to single-cell analysis, such as natural microbiota.

Embryonic gene expression of Coregonus palaea (whitefish) under pathogen stress as analyzed by high-throughput RNA-sequencing

2015 ◽  
Vol 47 (1) ◽  
pp. 130-140 ◽  
Author(s):  
Laetitia G.E. Wilkins ◽  
Emily S. Clark ◽  
Laurent Farinelli ◽  
Claus Wedekind ◽  
Luca Fumagalli
Keyword(s):  
Gene Expression ◽  
Rna Sequencing ◽  
High Throughput

scholarly journals Gene expression and splicing alterations analyzed by high throughput RNA sequencing of chronic lymphocytic leukemia specimens

BMC Cancer ◽  
2015 ◽  
Vol 15 (1) ◽  
Author(s):  
Wei Liao ◽  
Gwen Jordaan ◽  
Phillipp Nham ◽  
Ryan T. Phan ◽  
Matteo Pelegrini ◽  
...  
Keyword(s):  
Gene Expression ◽  
Chronic Lymphocytic Leukemia ◽  
Rna Sequencing ◽  
High Throughput ◽  
Lymphocytic Leukemia

scholarly journals Gene Expression Profile in Primary Tumor Is Associated with Brain-Tropism of Metastasis from Lung Adenocarcinoma

2021 ◽  
Vol 22 (24) ◽  
pp. 13374
Author(s):  
Yen-Yu Lin ◽  
Yu-Chao Wang ◽  
Da-Wei Yeh ◽  
Chen-Yu Hung ◽  
Yi-Chen Yeh ◽  
...  
Keyword(s):  
Gene Expression ◽  
Brain Metastasis ◽  
Brain Metastases ◽  
Dna Sequencing ◽  
Lung Adenocarcinoma ◽  
Rna Sequencing ◽  
Cell Lines ◽  
Differentially Expressed Genes ◽  
Primary Tumor ◽  
The Brain

Lung adenocarcinoma has a strong propensity to metastasize to the brain. The brain metastases are difficult to treat and can cause significant morbidity and mortality. Identifying patients with increased risk of developing brain metastasis can assist medical decision-making, facilitating a closer surveillance or justifying a preventive treatment. We analyzed 27 lung adenocarcinoma patients who received a primary lung tumor resection and developed metastases within 5 years after the surgery. Among these patients, 16 developed brain metastases and 11 developed non-brain metastases only. We performed targeted DNA sequencing, RNA sequencing and immunohistochemistry to characterize the difference between the primary tumors. We also compared our findings to the published data of brain-tropic and non-brain-tropic lung adenocarcinoma cell lines. The results demonstrated that the targeted tumor DNA sequencing did not reveal a significant difference between the groups, but the RNA sequencing identified 390 differentially expressed genes. A gene expression signature including CDKN2A could identify 100% of brain-metastasizing tumors with a 91% specificity. However, when compared to the differentially expressed genes between brain-tropic and non-brain-tropic lung cancer cell lines, a different set of genes was shared between the patient data and the cell line data, which include many genes implicated in the cancer-glia/neuron interaction. Our findings indicate that it is possible to identify lung adenocarcinoma patients at the highest risk for brain metastasis by analyzing the primary tumor. Further investigation is required to elucidate the mechanism behind these associations and to identify potential treatment targets.

scholarly journals Transcriptional profiling of bovine muscle-derived satellite cells during differentiation in vitro by high throughput RNA sequencing

2015 ◽  
Vol 20 (3) ◽  
Author(s):  
Hui Li Tong ◽  
Hong Yan Yin ◽  
Wei Wei Zhang ◽  
Qian Hu ◽  
Shu Feng Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Sequencing ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
High Throughput ◽  
Satellite Cells ◽  
Muscle Development ◽  
Future Research ◽  
Pathway Enrichment Analysis

AbstractIn this study, we utilized high throughput RNA sequencing to obtain a comprehensive gene expression profile of muscle-derived satellite cells (MDSCs) upon induction of differentiation. MDSCs were cultured in vitro and RNA was extracted for sequencing prior to differentiation (MDSC-P), and again during the early and late differentiation (MDSC-D1, and MDSC-D3, respectively) stages. Sequence tags were assembled and analyzed by digital gene expression profile to screen for differentially expressed genes, Gene Ontology annotation, and pathway enrichment analysis. Quantitative real-time PCR was used to confirm the results of RNA sequencing. Our results indicate that certain of genes were changed during skeletal muscle cell development, cell cycle progression, and cell metabolism during differentiation of bovine MDSCs. Furthermore, we identified certain genes that could be used as novel candidates for future research of muscle development. Additionally, the sequencing results indicated that lipid metabolism might be the predominant cellular process that occurs during MDSC differentiation.

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