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Two distinct extracellular RNA signatures released by a single cell type identified by microarray and next-generation
Cecilia Lässer1, Ganesh Vilas Shelke1, Ashish Yeri2
1a Krefting Research Center, Department of Internal Medicine and Clinical Nutrition , University of Gothenburg , Gothenburg , Sweden.
RNA Biology
|October 30, 2016
Summary
Cells release distinct high-density (HD) and low-density (LD) extracellular RNA (exRNA) profiles. These distinct exRNA signatures, differing in RNA content and associated proteins, are separated by density gradients, offering new insights into exRNA function.
Area of Science:
- Molecular Biology
- Cell Biology
- Biochemistry
Background:
- Extracellular RNA (exRNA) is secreted by cells into the environment and found in various body fluids.
- Conflicting results exist regarding the precise nature and composition of exRNA.
- Mast cells release exRNA, but the heterogeneity of these released molecules is not fully understood.
Purpose of the Study:
- To separate and characterize distinct extracellular RNA (exRNA) profiles released by mast cells.
- To investigate the differences in RNA species and protein content between these distinct exRNA fractions.
- To determine the cellular origins and potential packaging mechanisms of different exRNA types.
Main Methods:
- Separation of exRNA into high-density (HD) and low-density (LD) fractions using density gradient flotation.
- Characterization of exRNA content using microarray and next-generation sequencing.
- Proteomic analysis of HD and LD fractions via LC-MS/MS and Gene Ontology term finding.
- Electron microscopy to visualize exRNA-associated structures.
Main Results:
- Two distinct exRNA profiles, HD and LD, were successfully separated from mast cells.
- HD exRNA was enriched in lincRNA, antisense RNA, vault RNA, snoRNA, and snRNA, with limited rRNA.
- LD exRNA was enriched in mitochondrial rRNA, tRNA, piRNA, Y RNA, and full-length 18S/28S rRNA.
- Both fractions contained proteins associated with extracellular vesicles, with HD proteins linked to nucleus/ribosomes and LD proteins to mitochondria.
- HD mRNA correlated poorly with cellular mRNA, while LD mRNA showed a strong correlation.
Conclusions:
- Mast cells release at least two distinct types of exRNA with significantly different RNA species content.
- These exRNA populations can be separated based on their density, suggesting different origins or packaging mechanisms.
- The distinct proteomes suggest differential association with cellular compartments like the nucleus, ribosomes, or mitochondria.
- Understanding these distinct exRNA signatures is crucial for future studies on exRNA function and cell-to-cell communication.
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