Comprehensive MiRNA Expression Profiling in Human T-cell Acute Lymphoblastic Leukemia by Small RNA-sequencing

Overview

Journal Sci Rep

Specialty Science

Date 2017 Aug 13

PMID 28801656

Citations 32

Authors

Annelynn Wallaert

Wouter Van Loocke

Lucie Hernandez

Tom Taghon

Frank Speleman

Pieter Van Vlierberghe

Affiliations

Soon will be listed here.

Abstract

T-cell acute lymphoblastic leukemia (T-ALL) is a genetically heterogeneous disease that can be classified into different molecular genetic subtypes according to their mRNA gene expression profile. In this study, we applied RNA sequencing to investigate the full spectrum of miRNA expression in primary T-ALL patient samples, T-ALL leukemia cell lines and healthy donor thymocytes. Notably, this analysis revealed that genetic subtypes of human T-ALL also display unique miRNA expression signatures, which are largely conserved in human T-ALL cell lines with corresponding genetic background. Furthermore, small RNA-sequencing also unraveled the variety of isoforms that are expressed for each miRNA in T-ALL and showed that a significant number of miRNAs are actually represented by an alternative isomiR. Finally, comparison of CD34 and CD4CD8 healthy donor thymocytes and T-ALL miRNA profiles allowed identifying several novel miRNAs with putative oncogenic or tumor suppressor functions in T-ALL. Altogether, this study provides a comprehensive overview of miRNA expression in normal and malignant T-cells and sets the stage for functional evaluation of novel miRNAs in T-ALL disease biology.

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References

Taghon T, Waegemans E, Van de Walle I . Notch signaling during human T cell development. Curr Top Microbiol Immunol. 2012; 360:75-97. DOI: 10.1007/82_2012_230. View

Mavrakis K, Wolfe A, Oricchio E, Palomero T, De Keersmaecker K, McJunkin K . Genome-wide RNA-mediated interference screen identifies miR-19 targets in Notch-induced T-cell acute lymphoblastic leukaemia. Nat Cell Biol. 2010; 12(4):372-9. PMC: 2989719. DOI: 10.1038/ncb2037. View

Lee L, Zhang S, Etheridge A, Ma L, Martin D, Galas D . Complexity of the microRNA repertoire revealed by next-generation sequencing. RNA. 2010; 16(11):2170-80. PMC: 2957056. DOI: 10.1261/rna.2225110. View

Shaham L, Vendramini E, Ge Y, Goren Y, Birger Y, Tijssen M . MicroRNA-486-5p is an erythroid oncomiR of the myeloid leukemias of Down syndrome. Blood. 2014; 125(8):1292-301. PMC: 4335082. DOI: 10.1182/blood-2014-06-581892. View

Neilsen C, Goodall G, Bracken C . IsomiRs--the overlooked repertoire in the dynamic microRNAome. Trends Genet. 2012; 28(11):544-9. DOI: 10.1016/j.tig.2012.07.005. View

Durinck K, Wallaert A, Van de Walle I, Van Loocke W, Volders P, Vanhauwaert S . The Notch driven long non-coding RNA repertoire in T-cell acute lymphoblastic leukemia. Haematologica. 2014; 99(12):1808-16. PMC: 4258754. DOI: 10.3324/haematol.2014.115683. View

Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H . The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 2012; 22(9):1775-89. PMC: 3431493. DOI: 10.1101/gr.132159.111. View

Ferrando A, Neuberg D, Staunton J, Loh M, Huard C, Raimondi S . Gene expression signatures define novel oncogenic pathways in T cell acute lymphoblastic leukemia. Cancer Cell. 2002; 1(1):75-87. DOI: 10.1016/s1535-6108(02)00018-1. View

Burroughs A, Ando Y, de Hoon M, Tomaru Y, Nishibu T, Ukekawa R . A comprehensive survey of 3' animal miRNA modification events and a possible role for 3' adenylation in modulating miRNA targeting effectiveness. Genome Res. 2010; 20(10):1398-410. PMC: 2945189. DOI: 10.1101/gr.106054.110. View

10.

Tan G, Chan E, Molnar A, Sarkar R, Alexieva D, Isa I . 5' isomiR variation is of functional and evolutionary importance. Nucleic Acids Res. 2014; 42(14):9424-35. PMC: 4132760. DOI: 10.1093/nar/gku656. View

11.

Bianchi E, Bulgarelli J, Ruberti S, Rontauroli S, Sacchi G, Norfo R . MYB controls erythroid versus megakaryocyte lineage fate decision through the miR-486-3p-mediated downregulation of MAF. Cell Death Differ. 2015; 22(12):1906-21. PMC: 4816102. DOI: 10.1038/cdd.2015.30. View

12.

Wallaert A, Durinck K, Van Loocke W, Van de Walle I, Matthijssens F, Volders P . Long noncoding RNA signatures define oncogenic subtypes in T-cell acute lymphoblastic leukemia. Leukemia. 2016; 30(9):1927-30. DOI: 10.1038/leu.2016.82. View

13.

Ha M, Kim V . Regulation of microRNA biogenesis. Nat Rev Mol Cell Biol. 2014; 15(8):509-24. DOI: 10.1038/nrm3838. View

14.

Van Peer G, Lefever S, Anckaert J, Beckers A, Rihani A, Van Goethem A . miRBase Tracker: keeping track of microRNA annotation changes. Database (Oxford). 2014; 2014. PMC: 4142392. DOI: 10.1093/database/bau080. View

15.

Wu Z, Cai L, Lin S, Lu J, Yao Y, Zhou L . The miR-92b functions as a potential oncogene by targeting on Smad3 in glioblastomas. Brain Res. 2013; 1529:16-25. DOI: 10.1016/j.brainres.2013.07.031. View

16.

Esquela-Kerscher A, Slack F . Oncomirs - microRNAs with a role in cancer. Nat Rev Cancer. 2006; 6(4):259-69. DOI: 10.1038/nrc1840. View

17.

Wyman S, Knouf E, Parkin R, Fritz B, Lin D, Dennis L . Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity. Genome Res. 2011; 21(9):1450-61. PMC: 3166830. DOI: 10.1101/gr.118059.110. View

18.

Liu J, Shi W, Wu C, Ju J, Jiang J . miR-181b as a key regulator of the oncogenic process and its clinical implications in cancer (Review). Biomed Rep. 2014; 2(1):7-11. PMC: 3917097. DOI: 10.3892/br.2013.199. View

19.

Silva A, Yunes J, Cardoso B, Martins L, Jotta P, Abecasis M . PTEN posttranslational inactivation and hyperactivation of the PI3K/Akt pathway sustain primary T cell leukemia viability. J Clin Invest. 2008; 118(11):3762-74. PMC: 2556239. DOI: 10.1172/JCI34616. View

20.

Lu S, Sun Y, Chiang V . Adenylation of plant miRNAs. Nucleic Acids Res. 2009; 37(6):1878-85. PMC: 2665221. DOI: 10.1093/nar/gkp031. View