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Detection of circulating extracellular mRNAs by modified small-RNA-sequencing analysis
Kemal M. Akat, … , Martin Borggrefe, Thomas Tuschl
Kemal M. Akat, … , Martin Borggrefe, Thomas Tuschl
Published April 11, 2019
Citation Information: JCI Insight. 2019;4(9):e127317. https://doi.org/10.1172/jci.insight.127317.
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Resource and Technical Advance Cardiology Vascular biology

Detection of circulating extracellular mRNAs by modified small-RNA-sequencing analysis

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Abstract

Extracellular mRNAs (ex-mRNAs) potentially supersede extracellular miRNAs (ex-miRNAs) and other RNA classes as biomarkers. We performed conventional small-RNA-sequencing (sRNA-seq) and sRNA-seq with T4 polynucleotide kinase (PNK) end treatment of total extracellular RNAs (exRNAs) isolated from serum and platelet-poor EDTA, acid citrate dextrose (ACD), and heparin plasma to study the effect on ex-mRNA capture. Compared with conventional sRNA-seq, PNK treatment increased the detection of informative ex-mRNAs reads up to 50-fold. The exRNA pool was dominated by RNA originating from hematopoietic cells and platelets, with additional contribution from the liver. About 60% of the 15- to 42-nt reads originated from the coding sequences, in a pattern reminiscent of ribosome profiling. Blood sample type had a considerable influence on the exRNA profile. On average approximately 350–1100 distinct ex-mRNA transcripts were detected depending on plasma type. In serum, additional transcripts from neutrophils and hematopoietic cells increased this number to near 2300. EDTA and ACD plasma showed a destabilizing effect on ex‑mRNA and noncoding RNA ribonucleoprotein complexes compared with other plasma types. In a proof-of-concept study, we investigated differences between the exRNA profiles of patients with acute coronary syndrome and healthy controls. The improved tissue resolution of ex‑mRNAs after PNK treatment enabled us to detect a neutrophil signature in ACS that escaped detection by ex‑miRNA analysis.

Authors

Kemal M. Akat, Youngmin A. Lee, Arlene Hurley, Pavel Morozov, Klaas E.A. Max, Miguel Brown, Kimberly Bogardus, Anuoluwapo Sopeyin, Kai Hildner, Thomas G. Diacovo, Markus F. Neurath, Martin Borggrefe, Thomas Tuschl

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Figure 1

Treatment of total extracellular RNA with T4 polynucleotide kinase followed by small-RNA-sequencing.

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Treatment of total extracellular RNA with T4 polynucleotide kinase follo...
(A) Total RNA was isolated from 450 μl serum or platelet-depleted EDTA, acid citrate dextrose (ACD), and heparin plasma from 6 healthy individuals and purified using silica-based spin columns. Half of the RNA was treated with T4 polynucleotide kinase (T4 PNK) and repurified (PNK treated), and multiplexed small-RNA-sequencing (sRNA-seq) libraries were prepared separately for the untreated (libraries 1 and 3) and PNK-treated RNA (libraries 2 and 4). (B) Differences in read annotation in the 4 sample types for untreated RNA and PNK-treated RNA using initial annotation settings (reads 12–42 nt, up to 2 mismatches, multimapping). (C) Differences in ex‑mRNA capture between untreated and PNK-treated RNA using final annotation criteria (reads >15 nt, no mismatch and up to 2 mapping locations). Box plots show the median and first and third quartiles (bottom and top hinges). Whiskers extend at most ×1.5 interquartile range from the hinges; any data outside this are shown as individual outlier points. Shown are results from n = 6 individual samples per condition.

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