Combined expression of miR-122a, miR-1, and miR-200b can differentiate degraded RNA samples from liver, pancreas, and stomach.
The effect of RNA degradation on the diagnostic utility of microRNA has not been systematically evaluated in clinical samples. We asked if the microRNA profile is preserved in degraded RNA samples derived from mouse and human tissue. We selected tissue-specific microRNA candidates from published human microarray data, and validated them using quantitative reverse transcription polymerase chain reaction (QRTPCR) analyses on flash-frozen, normal mouse liver, pancreas, and stomach tissue samples. MiR-122a, miR-1, and miR-200b were identified as tissue-specific, and the 3-microRNA-based QRTPCR could predict the tissue origin for mouse tissue samples that were left at room temperature for 2 h with an accuracy of 91.7%. When we applied this 3-microRNA predictor to clinical specimens with various degree of RNA degradation, the predictor differentiated degraded RNA samples from liver, pancreas, and stomach with an accuracy of 90% (26/29). Expression levels of miR-122a, miR-1, and miR-200b were modestly changed after the extended (2-4 h) storage at room temperature, but the magnitudes of expression changes were small compared to the expression differences between various tissues of origin. This proof-of-principle study demonstrates that RNA degradation due to extended storage at room temperature does not affect the predictive power of tissue-specific microRNA QRTPCR predictor.
National Cancer Center, Goyang, Republic of Korea.
Joseph
J
Kim
Na Eun
NE
Choi
Su Jin
SJ
Oh
Sang Jae
SJ
Park
Hark Kyun
HK
Kim
D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D000818:Animals; D005260:Female; D015870:Gene Expression; D006801:Humans; D008099:Liver / Q000737:chemistry*; D008297:Male; D051379:Mice; D016688:Mice, Inbred NOD; D016513:Mice, SCID; D035683:MicroRNAs / Q000032:analysis*; D008875:Middle Aged; D010179:Pancreas / Q000737:chemistry*; D020871:RNA Stability; D012334:RNA, Neoplasm / Q000032:analysis; D020133:Reverse Transcriptase Polymerase Chain Reaction; D013270:Stomach / Q000737:chemistry*
C544547:MIRN1 microRNA, human; C531907:MIRN122 microRNA, human; C533896:MIRN200 microRNA, human; D035683:MicroRNAs; D012334:RNA, Neoplasm