Abstract
Long non-coding RNAs (lncRNAs) have been demonstrated to be involved in the pathogenesis of neuropsychiatric disorders such as epilepsy. In the current study, we evaluated expression of eight lncRNAs in 80 epileptic patients (40 refractory and 40 non-refractory ones) and 40 normal individual using quantitative real-time PCR. Bayesian regression model showed significant higher expression of UCA1 in both refractory and non-refractory groups compared with controls (posterior beta of relative expression (RE) = 2.03, P value = 0.003, and posterior beta of RE = 4.05, P value < 0.0001, respectively). Besides, expression of UCA1 was higher in non-refractory patients compared with refractory ones (posterior beta of RE = 2.008, P value = 0.019). When repeating statistical analyses in a gender-based manner, differences in expression of UCA1 were significant in all subgroup analyses except for male non-refractory vs. refractory subgroups analysis. Expression levels of NKILA and ANRIL were higher in both refractory and non-refractory groups compared with controls (posterior beta of RE = 1.565, P value = 0.018, and posterior beta of RE = 1.902, P value = 0.006 for NKILA; posterior beta of RE = 1.304, P value < 0.0001, and posterior beta of RE = 1.603, P value = 0.019 for ANRIL, respectively). However, expression levels of these two lncRNAs were not different between refractory and non-refractory groups. Gender-based analysis for these two lncRNAs revealed similar results except for lack of difference in ANRIL expression between male refractory group and controls. Expression of THRIL was significantly lower in both refractory and non-refractory groups compared with controls (posterior beta of RE = − 0.842, P value = 0.044 and posterior beta of RE = − 1.969, P value < 0.0001, respectively). Furthermore, expression of this lncRNA was lower in non-refractory patients compared with refractory ones (posterior beta of RE = − 1.129, P value = 0.002). However, no significant difference was detected between non-refractory and refractory patients either in males or females. The interactions between gender and relative expressions of PACER, DILC, and MALAT1 were significant, so the results were assessed in gender-based manner. In females, expression of DILC was higher in non-refractory patients compared with refractory ones (posterior beta of RE = 0.959, P value = 0.044). Expression of MALAT1 was lower in female non-refractory patients compared with controls and in female non-refractory patients compared with refractory ones (posterior beta of RE = − 1.35, P value = 0.002, and posterior beta of RE = − 0.942, P value = 0.045, respectively). Finally, expression of PACER was higher in refractory patients vs. controls and non-refractory patients vs. controls in both male and female subgroups. However, comparison between non-refractory and refractory patients revealed significant results only among females. Expression of none of the assessed lncRNAs was correlated with age of study participants. There were robust correlations between expression levels of lncRNAs. The most robust correlations were detected between UCA1 and PACER (r = 0.84, P < 0.0001) and between UCA1 and ANRIL (r = 0.75, P < 0.0001). Taken together, our study demonstrated dysregulation of lncRNAs in peripheral blood of epileptic patients and potentiated them as biomarkers for this neurologic condition.
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References
Bernard D, Prasanth KV, Tripathi V, Colasse S, Nakamura T, Xuan ZY, Zhang MQ, Sedel F, Jourdren L, Coulpier F, Triller A, Spector DL, Bessis A (2010) A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression. EMBO J 29:3082–3093
Chen Y, Zhou J (2017) LncRNAs: macromolecules with big roles in neurobiology and neurological diseases. Metab Brain Dis 32:281–291
Cordero-Arreola J, West RM, Mendoza-Torreblanca J, Mendez-Hernandez E, Salas-Pacheco J, Menendez-Gonzalez M, Freire RC, Machado S, Murillo-Rodriguez E, Nardi AE, Arias-Carrion O (2017) The role of innate immune system receptors in epilepsy research. CNS Neurol Disord Drug Targets 16:749–762
Geng JF, Liu X, Zhao HB, Fan WF, Geng JJ, Liu XZ (2018) LncRNA UCA1 inhibits epilepsy and seizure-induced brain injury by regulating miR-495/Nrf2-ARE signal pathway. Int J Biochem Cell Biol 99:133–139
Hashemian F, Ghafouri-Fard S, Arsang-Jang S, Mirzajani S, Fallah H, Mehvari Habibabadi J, Sayad A, Taheri M (2019) Epilepsy is associated with dysregulation of long non-coding RNAs in the peripheral blood. Front Mol Biosci 6:113
Hayden MS, Ghosh S (2014) Regulation of NF-kappaB by TNF family cytokines. Semin Immunol 26:253–266
Huang L-G, Wang X-X, Zou J, Li J-J, Lu Q-C (2017) Dysregulation of miR-1304-3p in hippocampus and serum of patients with intractable epilepsy. Int J Clin Exp Pathol 10:4263
Jiang M, Lee CL, Smith KL, Swann JW (1998) Spine loss and other persistent alterations of hippocampal pyramidal cell dendrites in a model of early-onset epilepsy. J Neurosci 18:8356–8368
Jiang G, Zhou R, He X, Shi Z, Huang M, Yu J, Wang X (2016) Expression levels of microRNA-199 and hypoxia-inducible factor-1 alpha in brain tissue of patients with intractable epilepsy. Int J Neurosci 126:326–334
Klein SL, Flanagan KL (2016) Sex differences in immune responses. Nat Rev Immunol 16:626
Krawczyk M, Emerson BM (2014) p50-associated COX-2 extragenic RNA (PACER) activates COX-2 gene expression by occluding repressive NF-kappaB complexes. Elife 3:e01776
Lan WG, Xu DH, Xu C, Ding CL, Ning FL, Zhou YL, Ma LB, Liu CM, Han X (2016) Silencing of long non-coding RNA ANRIL inhibits the development of multidrug resistance in gastric cancer cells. Oncol Rep 36:263–270
Lazarowski A, Czornyj L, Lubienieki F, Girardi E, Vazquez S, D’giano C (2007) ABC transporters during epilepsy and mechanisms underlying multidrug resistance in refractory epilepsy. Epilepsia 48(Suppl 5):140–149
Lee DY, Moon J, Lee ST, Jung KH, Park DK, Yoo JS, Sunwoo JS, Byun JI, Lim JA, Kim TJ, Jung KY, Kim M, Jeon D, Chu K, Lee SK (2015) Dysregulation of long non-coding RNAs in mouse models of localization-related epilepsy. Biochem Biophys Res Commun 462:433–440
Li Z, Chao TC, Chang KY, Lin N, Patil VS, Shimizu C, Head SR, Burns JC, Rana TM (2014) The long noncoding RNA THRIL regulates TNFalpha expression through its interaction with hnRNPL. Proc Natl Acad Sci U S A 111:1002–1007
Liu B, Sun L, Liu Q, Gong C, Yao Y, Lv X, Lin L, Yao H, Su F, Li D, Zeng M, Song E (2015) A cytoplasmic NF-kappaB interacting long noncoding RNA blocks IkappaB phosphorylation and suppresses breast cancer metastasis. Cancer Cell 27:370–381
Lubin FD, Ren Y, Xu X, Anderson AE (2007) Nuclear factor-kappa B regulates seizure threshold and gene transcription following convulsant stimulation. J Neurochem 103:1381–1395
Mazdeh M, Ghafouri-Fard S, Hatami M, Eftekharian MM, Ganji M, Sayad A, Arsang-Jang S, Taheri M, Omrani MD (2018a) Expression analysis of vitamin D signaling pathway genes in epileptic patients. J Mol Neurosci 64:551–558
Mazdeh M, Komaki A, Omrani MD, Gharzi V, Sayad A, Taheri M, Ghafouri-Fard S (2018b) Expression analysis of beta-secretase 1 (BACE1) and its naturally occurring antisense (BACE1-AS) in blood of epileptic patients. Neurol Sci 39:1565–1569
Mazdeh M, Zamani M, Eftekharian MM, Komaki A, Arsang-Jang S, Taheri M, Ghafouri-Fard S (2019) Expression analysis of vitamin D receptor-associated lncRNAs in epileptic patients. Metab Brain Dis 34:1457–1465
Miller-Delaney SFC, Bryan K, Das S, Mckiernan RC, Bray IM, Reynolds JP, Gwinn R, Stallings RL, Henshall DC (2015) Differential DNA methylation profiles of coding and non-coding genes define hippocampal sclerosis in human temporal lobe epilepsy. Brain 138:616–631
Mirzajani S, Ghafouri-Fard S, Habibabadi JM, Arsang-Jang S, Omrani MD, Fesharaki SSH, Sayad A, Taheri M (2019) Peripheral expression of Rubicon like autophagy enhancer is reduced in epileptic patients. Gene Rep 17:100539
Patel, D. C., Wallis, G., Dahle, E. J., Mcelroy, P. B., Thomson, K. E., Tesi, R. J., Szymkowski, D. E., West, P. J., Smeal, R. M., Patel, M., Fujinami, R. S., White, H. S. & Wilcox, K. S. (2017) Hippocampal TNFalpha signaling contributes to seizure generation in an infection-induced mouse model of limbic epilepsy. eNeuro 4
Plata-Salaman CR, Ilyin SE, Turrin NP, Gayle D, Flynn MC, Romanovitch AE, Kelly ME, Bureau Y, Anisman H, Mcintyre DC (2000) Kindling modulates the IL-1beta system, TNF-alpha, TGF-beta1, and neuropeptide mRNAs in specific brain regions. Brain Res Mol Brain Res 75:248–258
Rana A, Musto AE (2018) The role of inflammation in the development of epilepsy. J Neuroinflammation 15:144
Rojas A, Jiang J, Ganesh T, Yang MS, Lelutiu N, Gueorguieva P, Dingledine R (2014) Cyclooxygenase-2 in epilepsy. Epilepsia 55:17–25
Swann JW, Al-Noori S, Jiang M, Lee CL (2000) Spine loss and other dendritic abnormalities in epilepsy. Hippocampus 10:617–625
Wang X, Sun W, Shen W, Xia M, Chen C, Xiang D, Ning B, Cui X, Li H, Li X, Ding J, Wang H (2016) Long non-coding RNA DILC regulates liver cancer stem cells via IL-6/STAT3 axis. J Hepatol 64:1283–1294
Wang HK, Yan H, Wang K, Wang J (2017) Dynamic regulation effect of long non-coding RNA-UCA1 on NF-kB in hippocampus of epilepsy rats. Eur Rev Med Pharmacol Sci 21:3113–3119
Wang J, Ye C, Liu J, Hu Y (2018) UCA1 confers paclitaxel resistance to ovarian cancer through miR-129/ABCB1 axis. Biochem Biophys Res Commun 501:1034–1040
Wu Q, Yi X (2018) Down-regulation of long noncoding RNA MALAT1 protects hippocampal neurons against excessive autophagy and apoptosis via the PI3K/Akt signaling pathway in rats with epilepsy. J Mol Neurosci 65:234–245
Wu P, Zuo X, Deng H, Liu X, Liu L, Ji A (2013) Roles of long noncoding RNAs in brain development, functional diversification and neurodegenerative diseases. Brain Res Bull 97:69–80
Xue M, Li X, Li Z, Chen W (2014) Urothelial carcinoma associated 1 is a hypoxia-inducible factor-1alpha-targeted long noncoding RNA that enhances hypoxic bladder cancer cell proliferation, migration, and invasion. Tumour Biol 35:6901–6912
Zhou X, Han X, Wittfeldt A, Sun J, Liu C, Wang X, Gan LM, Cao H, Liang Z (2016) Long non-coding RNA ANRIL regulates inflammatory responses as a novel component of NF-kappaB pathway. RNA Biol 13:98–108
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The current study was supported by a grant from Shahid Beheshti University of Medical Sciences.
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MT and SGF wrote the draft and revised it. SAA and MDO analyzed the data. AS, JMF, and SSHF supervised the study. All the authors contributed equally and are aware of submission.
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Mirzajani, S., Ghafouri-Fard, S., Habibabadi, J.M. et al. Expression Analysis of lncRNAs in Refractory and Non-Refractory Epileptic Patients. J Mol Neurosci 70, 689–698 (2020). https://doi.org/10.1007/s12031-019-01477-8
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DOI: https://doi.org/10.1007/s12031-019-01477-8