Project description:An integrative analysis of human biofluid data in the exRNA Atlas revealed the existence of distinct extracellular RNA cargo types. In order to detect differences in density between cargo types, cushioned density gradient ultracentrifugation (C-DGUC) of serum and plasma was performed using OptiPrem (TM) density gradient.
Project description:An integrative analysis of human biofluid data in the exRNA Atlas revealed the existence of distinct extracellular RNA cargo types. To gain further insight on the biological nature of these cargo types, we correlated exRNA Atlas cargo profiles with a variety of other RNA-seq profiles. This study focuses on lipoprotein particle (LPP) exRNA profiles obtained via sequential density ultracentrifugation (SD-UC) and fast protein liquid chromatography (FPLC).
Project description:We investigated the gene expression of the human TM. We isolated TM cells from healthy human donor eyes. Next, we performed RNA isolation, amplification, labeling and hybridization against 44k Agilent microarrays.
Project description:All cells secrete extracellular RNA (exRNA), however the roles of secreted RNAs are still not fully understood. Here, we are profiling the small RNAs secreted from Caco-2 cells. ExRNAs were isolated as different fractions: total extracellular, intravesicular, extravesicular, and nonvesicular (abitrarily named as Total ExRNA P40, P100, S100).
Project description:Cells secrete extracellular RNA (exRNA) to their surrounding environment and exRNA has been found in many body fluids such as blood, breast milk and cerebrospinal fluid. However, there are conflicting results regarding the nature of exRNA. Here, we have separated two distinct exRNA profiles released by mast cells, here termed high-density (HD) and low-density (LD) exRNA. The exRNA in both fractions was characterized by microarray and next-generation sequencing. Both exRNA fractions contained mRNA and miRNA, and the mRNAs in the LD exRNA correlated closely with the cellular mRNA, whereas the HD mRNA did not. Furthermore, the HD exRNA was enriched in lincRNA, antisense RNA, vault RNA, snoRNA, and snRNA with little or no evidence of full-length 18S and 28S rRNA. The LD exRNA was enriched in mitochondrial rRNA, mitochondrial tRNA, tRNA, piRNA, Y RNA, and full-length 18S and 28S rRNA. The proteomes of the HD and LD exRNA-containing fractions were determined with LC-MS/MS and analysed with Gene Ontology term finder, which showed that both proteomes were associated with extracellular vesicles. Additionally, the proteins in the HD fractions tended to be associated with the nucleus and ribosomes, whereas the LD fraction proteome tended to be associated with the mitochondrion. We show that the two exRNA signatures released by a single cell type can be separated by floatation on a density gradient. These results show that cells can release multiple types of exRNA with substantial differences in RNA species content. This is important for any future studies determining the nature and function of exRNA released from different cells under different conditions.
Project description:Circulating extracellular RNAs (exRNAs) have great promise as novel clinically plasma-based biomarkers for cancer diagnosis and prognosis. knowledge of the difference or association between these different sources of exRNAs is very limited. We performed a sequential physical and biochemical precipitation to receive 4 plasma fractions (platelets and cell debris, Thrombin-treated fraction, extracellular vesicles and supernatant) from each plasma sample. After total RNA extraction, we made ligation-free libraries and performed RNA-seq to evaluate full spectrum of RNA abundance in each fraction. All RNAs were included without size selection during the library preparation. We utilized a successive stepwise alignment strategy to map the RNA sequences to different RNA categories. We found that each plasma fraction had its own unique distribution of RNA species. Hierarchical cluster analysis showed similarity in samples with same fraction and significant differences between different fractions. In addition, we also observed abundance difference of unique transcript. Furthermore, a considerable proportion of exogenous RNAs and novel predicted miRNAs in all plasma fractions were detected. These results demonstrate that thorough inspection of all plasma fractions is necessary for exRNA-based biomarker study and appropriate sampling processes is needed for illustrating the complexity of plasma-based EVs study.