Expanding the repertoire of miRNAs and miRNA-offset RNAs expressed in multiple myeloma by small RNA deep sequencing

Luca Agnelli, Andrea Bisognin, Katia Todoerti, Martina Manzoni, Elisa Taiana, Serena Galletti, Giovanna Cutrona, Enrico Gaffo, Stefania Bortoluzzi, Antonino Neri

Research output: Contribution to journalArticle

Abstract

Microarray analysis of the multiple myeloma (MM) miRNome has unraveled the differential expression of miRNAs in cytogenetic subgroups, their involvement in the tumor biology and their effectiveness in prognostic models. Herein, the small RNA transcriptional landscape in MM has been investigated exploiting the possibilities offered by small RNA-seq, including accurate quantification of known mature species, discovery and characterization of isomiRs, and miRNA-offset RNAs (moRNAs). Matched small RNA-seq and miRNA GeneChip ® microarray expression profiles were obtained in a representative panel of 30 primary MM tumors, fully characterized for genomic aberrations and mutations. RNA-seq and microarray gave concordant estimations of known species. Enhanced analysis of RNA-seq data with the miR&moRe pipeline led to the characterization of 655 known and 17 new mature miRNAs and of 74 moRNAs expressed in the considered cohort, 5 of which (moR-150-3p, moR-24-2-5p, moR-421-5p, moR-21-5p, and moR-6724-5p) at high level. Ectopic expression of miR-135a-3p in t(4;14) patients, upregulation of moR-150-3p and moR-21-5p in t(14;16)/t(14;20) samples, and of moR-6724-1-5p in patients overexpressing CCND1 were uncovered and validated by qRT-PCR. Overall, RNA-seq offered a more complete overview of small non-coding RNA in MM tumors, indicating specific moRNAs that demand further investigations to explore their role in MM biology.

Original languageEnglish
Article number21
JournalBlood Cancer Journal
Volume9
Issue number3
DOIs
Publication statusPublished - Mar 1 2019

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RNA Sequence Analysis
High-Throughput Nucleotide Sequencing
Multiple Myeloma
MicroRNAs
RNA
Small Untranslated RNA
Neoplasms
Microarray Analysis
Cytogenetics
Up-Regulation
Polymerase Chain Reaction
Mutation

ASJC Scopus subject areas

  • Hematology
  • Oncology

Cite this

Expanding the repertoire of miRNAs and miRNA-offset RNAs expressed in multiple myeloma by small RNA deep sequencing. / Agnelli, Luca; Bisognin, Andrea; Todoerti, Katia; Manzoni, Martina; Taiana, Elisa; Galletti, Serena; Cutrona, Giovanna; Gaffo, Enrico; Bortoluzzi, Stefania; Neri, Antonino.

In: Blood Cancer Journal, Vol. 9, No. 3, 21, 01.03.2019.

Research output: Contribution to journalArticle

Agnelli, Luca ; Bisognin, Andrea ; Todoerti, Katia ; Manzoni, Martina ; Taiana, Elisa ; Galletti, Serena ; Cutrona, Giovanna ; Gaffo, Enrico ; Bortoluzzi, Stefania ; Neri, Antonino. / Expanding the repertoire of miRNAs and miRNA-offset RNAs expressed in multiple myeloma by small RNA deep sequencing. In: Blood Cancer Journal. 2019 ; Vol. 9, No. 3.
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