Profiling of small nucleolar RNAs by next generation sequencing: potential new players for breast cancer prognosis

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dc.contributor.authorKrishnan, Preethi
dc.contributor.authorGhosh, Sunita
dc.contributor.authorWang, Bo
dc.contributor.authorHeyns, Mieke
dc.contributor.authorGraham, Kathryn
dc.contributor.authorMackey, John R.
dc.contributor.authorKovalchuk, Olga
dc.contributor.authorDamaraju, Sambasivarao
dc.date.accessioned2018-12-17T05:23:08Z
dc.date.available2018-12-17T05:23:08Z
dc.date.issued2016
dc.descriptionSherpa Romeo green journal. Open access article. Creative Commons Attribution 4.0 International (CC BY 4.0) appliesen_US
dc.description.abstractOne of the most abundant,yet least explored,classes of RNA is the small nucleolar RNAs (snoRNAs), which are well known for their involvement in post-transcriptional modifications of other RNAs. Although snoRNAs were only considered to perform housekeeping functions for a long time, recent studies have highlighted their importance as regulators of gene expression and as diagnostic/prognostic markers.However, the prognostic potential of these RNAs has not been interrogated for breast cancer(BC). The objective of the current study was to identify snoRNAs as prognostic markers for BC. Small RNA sequencing (Illumina Genome Analyzer IIx) was performed for 104BC cases and 11 normal breast tissues. Partek Genomics Suite was used for analyzing the sequencing files.Two independent and proven approaches were used to identify prognostic markers: case-control(CC) and case only(CO). For both approaches, snoRNAs significant in the permutation test following univariate Cox proportional hazards regression model were used for constructing risks cores. Risk scores were subsequently adjusted for potential confounders in a multivariate Cox model. For both approaches, thirteen snoRNAs were associated with overall survival and/or recurrence free survival.Patients belonging to the high-risk group were associated with poor outcomes, and the risk score was significant after adjusting for confounders. Validation of representatives no RNAs (SNORD46andSNORD89) using qRT-PCR confirmed the observations from sequencing experiments.We also observed 64 snoRNAs harboring piwi interacting RNAs and/or micro RNAs that were predicted to target genes (mRNAs) involved in tumor igenesis.Our results demonstrate the potential of snoRNAs to serve (i) as novel prognostic markers for BC and (ii) as indirect regulators of gene expressionen_US
dc.description.peer-reviewYesen_US
dc.identifier.citationKrishnan, P., Ghosh, S., Wang, B., Heyns, M., Graham, K., Mackey, J.R. ... Damaraju, S. (2016). Profiling of small nucleolar RNAs by next generation sequencing: Potential new players for breast cancer prognosis. PLoS ONE, 11(9), e0162622. doi:10.1371/journal.pone.0162622en_US
dc.identifier.urihttps://hdl.handle.net/10133/5262
dc.language.isoen_USen_US
dc.publisherPublic Library of Scienceen_US
dc.publisher.departmentDepartment of Biological Sciencesen_US
dc.publisher.facultyArts and Scienceen_US
dc.publisher.institutionUniversity of Lethbridgeen_US
dc.publisher.urlhttps://dx.doi.org/10.1371/journal.pone.0162622
dc.subjectsnoRNAsen_US
dc.subjectPrognostic markersen_US
dc.subjectDiagnostic markersen_US
dc.subjectGene expressionen_US
dc.subjectSequencing experimentsen_US
dc.titleProfiling of small nucleolar RNAs by next generation sequencing: potential new players for breast cancer prognosisen_US
dc.typeArticleen_US
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