Identification of Dysregulated microRNAs in Glioma Using RNA-sequencing

Abstract

Glioma is the most common malignant brain tumor in central nervous system. Despite advances in the treatment of glioma such as surgery and chemoradiotherapy, most patients are easy to relapse, resulting in adverse clinical outcomes. Hence, effective molecular-targeting treatment may be one of attractive strategies for glioma therapy. The dysregulated microRNAs (miRNAs), one of the candidates of therapeutic targets, are believed to play an important role in the progression of glioma. In this study, we aimed to examine the expression profile of miRNAs in glioma and provide a reference for glioma therapy. Firstly, expression profile of miRNAs in 5 normal brain tissues, 5 low-grade glioma (LGG) tissues and 5 glioblastoma (GBM) tissues was detected by RNA sequencing (RNA-seq). Next, the target genes of differentially expressed miRNAs (DEmiRNAs) were predicted and then GO enrichment and KEGG pathway analysis performed by bioinformatics. Finally, 10 miRNAs which were significantly up- or down-regulated both in GBM and LGG were validated by real-time quantitative PCR (qRT-PCR). RNA-seq results indicated a number of DEmiRNAs in glioma. There were 64 up-regulated miRNAs and 17 down-regulated miRNAs in LGG, and 181 up-regulated miRNAs and 124 down-regulated miRNAs in GBM, respectively. Bioinformatics analysis showed that the target genes of these DEmiRNAs were enriched in various biological processes and signaling pathways such as cell metabolic and developmental process. Selected DEmiRNAs were further confirmed by qRT-PCR. miRNA-10b-5p, miRNA-92b-3p and miRNA-455-5p were significantly up-regulated in both GBM and LGG; while miRNA-542-3p was significantly up-regulated in LGG; miRNA-184 and miRNA-206 were significantly down-regulated in both GBM and LGG; miRNA-766-5p and miRNA-1-3p were significantly down-regulated in GBM. The subject of our study demonstrated several dysregulated miRNAs may serve as a potential therapeutic target for glioma.

Keywords

glioma / microRNA / RNA-sequencing

References

[1] OstromQT, GittlemanH, LiaoP, et al.. CBTRUS Statistical Report: Primary brain and other central nervous system tumors diagnosed in the United States in 2010–2014. Neuro Oncol, 2017, 19(suppl_5): v1-v88

[2] WellerM, van den BentM, HopkinsK, et al.. European Association for Neuro-Oncology (EANO) Task Force on Malignant Glioma. EANO guideline for the diagnosis and treatment of anaplastic gliomas and glioblastoma. Lancet Oncol, 2014, 15(9): e395-403

[3] ClausEB, WalshKM, WienckeJK, et al.. Survival and low-grade glioma: the emergence of genetic information. Neurosurg Focus, 2015, 38(1): E6

[4] AnestisDM, TsitsopoulosPP, BleCA, et al.. Congenital Glioblastoma Multiforme: An Unusual and Challenging Tumor. Neuropediatrics, 2017, 48(6): 403-412

[5] DuffauH. Les glioblastomes en 2017 [Glioblastoma in 2017]. Rev Infirm, 2017, 66(228): 16-18

[6] WirschingHG, GalanisE, WellerM. Glioblastoma. Handb Clin Neurol, 2016, 134: 381-397

[7] PetrescuGED, SaboAA, TorsinLI, et al.. MicroRNA based theranostics for brain cancer: basic principles. J Exp Clin Cancer Res, 2019, 38(1): 231

[8] Lagos-QuintanaM, RauhutR, LendeckelW, et al.. Identification of novel genes coding for small expressed RNAs. Science, 2001, 294(5543): 853-858

[9] CaldasC, BrentonJD. Sizing up miRNAs as cancer genes. Nat Med, 2005, 11(7): 712-714

[10] GulluogluS, TuysuzEC, SahinM, et al.. Simultaneous miRNA and mRNA transcriptome profiling of glioblastoma samples reveals a novel set of OncomiR candidates and their target genes. Brain Res, 2018, 1700: 199-210

[11] SaadatpourL, FadaeeE, FadaeiS, et al.. Glioblastoma: exosome and microRNA as novel diagnosis biomarkers. Cancer Gene Ther, 2016, 23(12): 415-418

[12] BalacescuO, SurD, CainapC, et al.. The Impact of miRNA in Colorectal Cancer Progression and Its Liver Metastases. Int J Mol Sci, 2018, 19(12): 3711

[13] SartoriusK, SartoriusB, WinklerC, et al.. The biological and diagnostic role of miRNA’s in hepatocellular carcinoma. Front Biosci (Landmark Ed), 2018, 23: 1701-1720

[14] WuM, WangG, TianW, et al.. MiRNA-based Therapeutics for Lung Cancer. Curr Pharm Des, 2018, 23(39): 5989-5996

[15] LiC, HashimiSM, GoodDA, et al.. Apoptosis and microRNA aberrations in cancer. Clin Exp Pharmacol Physiol, 2012, 39(8): 739-746

[16] LuY, QinT, LiJ, et al.. MicroRNA-140-5p inhibits invasion and angiogenesis through targeting VEGF-A in breast cancer. Cancer Gene Ther, 2017, 24(9): 386-392

[17] YuJ, LeiR, ZhuangX, et al.. MicroRNA-182 targets SMAD7 to potentiate TGFβ-induced epithelialmesenchymal transition and metastasis of cancer cells. Nat Commun, 2016, 7: 13884

[18] HummelR, MaurerJ, HaierJ. MicroRNAs in brain tumors: a new diagnostic and therapeutic perspective?. Mol Neurobiol, 2011, 44(3): 223-234

[19] LiW, LiC, XiongQ, et al.. MicroRNA-10b-5p downregulation inhibits the invasion of glioma cells via modulating homeobox B3 expression. Exp Ther Med, 2019, 17(6): 4577-4585

[20] NixJS, YuanM, ImadaEL, et al.. Global microRNA profiling identified miR-10b-5p as a regulator of neurofibromatosis 1 (NF1)-glioma migration. Neuropathol Appl Neurobiol, 2021, 47(1): 96-107

[21] AgrawalR, PandeyP, JhaP, et al.. Hypoxic signature of microRNAs in glioblastoma: insights from small RNA deep sequencing. BMC Genomics, 2014, 15(1): 686

[22] CaiJ, ZhaoJ, ZhangN, et al.. MicroRNA-542-3p Suppresses Tumor Cell Invasion via Targeting AKT Pathway in Human Astrocytoma. J Biol Chem, 2015, 290(41): 24678-24688

[23] DuL, HuangGH, MouKJ, et al.. MiR-206 is down-regulated and suppresses cell proliferation by targeting FOXP1 in brain gliomas. Int J Clin Exp Pathol, 2018, 11(7): 3405-3415

[24] CuiQK, LiuWD, ZhuJX, et al.. MicroRNA-184 promotes proliferation ability of glioma cells by regulating FOXO3. Asian Pac J Trop Med, 2014, 7(10): 776-779

[25] EmdadL, JanjicA, AlzubiMA, et al.. Suppression of miR-184 in malignant gliomas upregulates SND1 and promotes tumor aggressiveness. Neuro Oncol, 2015, 17(3): 419-429

[26] DuL, HuangGH, MouKJ, et al.. MiR-206 is down-regulated and suppresses cell proliferation by targeting FOXP1 in brain gliomas. Int J Clin Exp Pathol, 2018, 11(7): 3405-3415

[27] ZhouF, CaoW, XuR, et al.. MicroRNA-206 attenuates glioma cell proliferation, migration, and invasion by blocking the WNT/β-catenin pathway via direct targeting of Frizzled 7 mRNA. Am J Transl Res, 2019, 11(7): 4584-4601

[28] MaoY, ShenG, SuZ, et al.. RAD21 inhibited transcription of tumor suppressor MIR4697HG and led to glioma tumorigenesis. Biomed Pharmacother, 2020, 123: 109759

[29] MaY, ZhouG, LiM, et al.. Long noncoding RNA DANCR mediates cisplatin resistance in glioma cells via activating AXL/PI3K/Akt/NF-κB signaling pathway. Neurochem Int, 2018, 118: 233-241