Abstract
BackgroundAlthough advances in sequencing technologies have popularized the use of microRNA (miRNA) sequencing (miRNA-seq) for the quantification of miRNA expression, questions remain concerning the optimal methodologies for analysis and utilization of the data. The construction of a miRNA sequencing library selects RNA by length rather than type. However, as we have previously described, miRNAs represent only a subset of the species obtained by size selection. Consequently, the libraries obtained for miRNA sequencing also contain a variety of additional species of small RNAs. This study looks at the prevalence of these other species obtained from bone marrow aspirate specimens and explores the predictive value of these small RNAs in the determination of response to therapy in myelodysplastic syndromes (MDS).MethodsPaired pre and post treatment bone marrow aspirate specimens were obtained from patients with MDS who were treated with either azacytidine or decitabine (24 pre-treatment specimens, 23 post-treatment specimens) with 22 additional non-MDS control specimens. Total RNA was extracted from these specimens and submitted for next generation sequencing after an additional size exclusion step to enrich for small RNAs. The species of small RNAs were enumerated, single nucleotide variants (SNVs) identified, and finally the differential expression of tRNA-derived species (tDRs) in the specimens correlated with diseasestatus and response to therapy.ResultsUsing miRNA sequencing data generated from bone marrow aspirate samples of patients with known MDS (N = 47) and controls (N = 23), we demonstrated that transfer RNA (tRNA) fragments (specifically tRNA halves, tRHs) are one of the most common species of small RNA isolated from size selection. Using tRNA expression values extracted from miRNA sequencing data, we identified six tRNA fragments that are differentially expressed between MDS and normal samples. Using the elastic net method, we identified four tRNAs-derived small RNAs (tDRs) that together can explain 67 % of the variation in treatment response for MDS patients. Similar analysis of specifically mitochondrial tDRs (mt-tDRs) identified 13 mt-tDRs which distinguished disease status in the samples and a single mt-tDR which predited response. Finally, 14 SNVs within the tDRs were found in at least 20 % of the MDS samples and were not observed in any of the control specimens.DiscussionThis study highlights the prevalence of tDRs in RNA-seq studies focused on small RNAs. The potential etiologies of these species, both technical and biologic, are discussed as well as important challenges in the interpretation of tDR data.ConclusionsOur analysis results suggest that tRNA fragments can be accurately detected through miRNA sequencing data and that the expression of these species may be useful in the diagnosis of MDS and the prediction of response to therapy.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1929-y) contains supplementary material, which is available to authorized users.
Highlights
Advances in sequencing technologies have popularized the use of microRNA sequencing for the quantification of miRNA expression, questions remain concerning the optimal methodologies for analysis and utilization of the data
We found that for the reads obtained using a standard miRNA-seq protocol, the number of reads aligned to tRNA-derived small RNAs (tDRs) (78.81 % of reads) vastly outnumbered those aligning to miRNAs (4.43 % of reads) (Fig. 1a)
The peak at 33 bases indicates the abundance of transfer RNA (tRNA) species that have been cleaved in the anticodon loop from their full length of 73–94 nucleotides [10, 19]
Summary
Advances in sequencing technologies have popularized the use of microRNA (miRNA) sequencing (miRNA-seq) for the quantification of miRNA expression, questions remain concerning the optimal methodologies for analysis and utilization of the data. During miRNA-seq library preparation, small RNAs are selected by electrophoresis on a size typically ranging from 20 to 50 nucleotides (nts). One of the major byproducts of size selection for miRNAs is tRNA-derived small RNAs (tDRs) [13, 16]. This may be the result of either active cleavage or an artifact of the miRNA-seq library construction. D loop cleavage results in a 19 nt tRNA-derived fragment (tRF), and cleavage of the anticodon loop before the anti-codon affords a 33 nt tRH [10, 19] These 5’ tDR products, in particular the 33-base tRH, may be captured by miRNA-seq
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