Next-generation sequencing reveals differentially expressed small noncoding RNAs in uterine leiomyoma

The expression profile of sncRNAs was determined by next-generation sequencing and confirmed by qRT- PCR, indicating differential expression of selected snoRNAs, piRNAs, tRNA, and rRNA in leiomyoma.

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Volume 109, Issue 5, Pages 919–929

Authors:

Tsai-Der Chuang, Ph.D., Yeming Xie, Ph.D., Wei Yan, M.D., Ph.D., Omid Khorram, M.D., Ph.D.

Abstract:

Objective

To determine the expression profile of small noncoding RNAs (sncRNAs) in leiomyoma, which has not been investigated to date.

Design

Laboratory-based investigation.

Setting

Academic center.

Patient(s)

Women undergoing hysterectomy for benign indications.

Intervention(s)

Next-generation sequencing and screening of an sncRNA database with confirmatory analysis by quantitative reverse-transcription polymerase chain reaction (qRT-PCR).

Main Outcome Measure(s)

Expression profile of sncRNAs in leiomyoma and matched myometrium.

Result(s)

Screening our previously determined RNA sequencing data with the sncRNA database resulted in identification of 15 small nuclear (sn) RNAs, 284 small nucleolar (sno) RNAs, 98 Piwi-interacting (pi) RNAs, 152 transfer (t) RNAs, and 45 ribosomal (r) RNAs, of which 15 snoRNAs, 24 piRNAs, 7 tRNAs, and 6 rRNAs were differentially expressed at a 1.5-fold change cutoff in leiomyoma compared with myometrium. We selected 5 snoRNAs, 4 piRNAs, 1 tRNA, and 1 rRNA that were differentially expressed and confirmed their expression in paired tissues (n = 20) from both phases of the menstrual cycle with the use of qRT-PCR. The results indicated up-regulation of the snoRNAs (SNORD30, SNORD27, SNORA16A, SNORD46, and SNORD56) and down-regulation of the piRNAs (piR-1311, piR-16677, piR-20365, piR-4153), tRNA (TRG-GCC5–1), and rRNA (RNA5SP202) expression in leiomyoma compared with myometrium (P<.05). The pattern of expression of these sncRNAs was similar to RNA sequencing analysis, with no menstrual cycle–dependent differences detected except for SNORD30. Because Argonaute 2 (AGO2) is required for sncRNA-mediated gene silencing, we determined its expression and found greater abundance in leiomyoma.

Conclusion(s)

Our results provide the first evidence for the differential expression of additional classes of sncRNAs and AGO2 in leiomyoma, implicating their roles as a gene regulatory mechanism.


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