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Co-expression Network of mRNAs and lncRNAs Regulated by Stress-Linked Behavioral Assays

  • Jianghong Zhang
  • Meiying Xue
  • Yue Mei
  • Zhigang Li
  • Zeng Ceng
  • Yuanyuan Li
  • Yi Zhang
  • Na Li
  • Huajing TengEmail author
  • Zhong Sheng SunEmail author
  • Yan WangEmail author
Original Investigation

Abstract

Rationale

Mood-related behavioral assays, designed typically on rodents’ natural aversion to certain threats, are useful in studying the mechanisms of mood and in discovering effective treatments for neuropsychiatric disorders.

Objectives

Although reasonable attention has been paid to the conducted sequence, few studies address the argument whether a behavioral assay itself affects the intrinsic signaling, gene expression, and the subsequent performance of mice.

Methods

We examined the short- (1 day) and long-term effects (7 and 14 days) of commonly used behavioral assays for anxiety and depression, including the elevated plus maze test (EPM), forced swimming test (FST), and tail suspension test (TST), on behaviors. We also investigated the effects of repeated behavioral assays on behaviors. The alterations in the expression profiles in the hippocampus experienced behavioral assays were explored via the integrative analysis of mRNA and lncRNA transcriptomes generated by RNA sequencing.

Results

We found that one FST or TST can induce anxiety-related behaviors, while repeated FST or TST resulted in depression-related behaviors in mice. The altered behaviors were associated with extensive transcriptional alterations in the FST and TST hippocampus of mice. KEGG pathway analyses indicated that differentially expressed genes (DEGs) in the FST and TST hippocampus were enriched in anxiety- and metabolic-related pathways, respectively. Moreover, differentially expressed lncRNAs, showing correlations with DEGs, were linked to anxiety-related pathways in the FST hippocampus and metabolic-related pathways in the TST hippocampus.

Conclusions

Our study identified the unique and shared mRNAs and lncRNAs regulated by mood-related behavioral assays, emphasizing the importance of the sequence of and intervals between them.

Keywords

Stress Behavioral assays Anxiety RNA-Seq lncRNAs 

Notes

Author contributions

YW and ZS supervised the study and analyses. YW, ZS, and JZ wrote the manuscript. JZ, YM, ZL, ZC, and YL performed the behavioral assays and statistical analysis of the data. MX, YZ, NL, and HT performed the bioinformatics analyses of RNA-Seq data.

Funding information

This work was supported by the National Natural Science Foundation of China (grant numbers 31571301, 31601027, 31872237, and 81000559).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

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References

  1. Andrus BM, Blizinsky K, Vedell PT, Dennis K, Shukla PK, Schaffer DJ, Radulovic J, Churchill GA, Redei EE (2012) Gene expression patterns in the hippocampus and amygdala of endogenous depression and chronic stress models. Mol Psychiatry 17:49–61PubMedCrossRefPubMedCentralGoogle Scholar
  2. Bannon MJ, Savonen CL, Jia H, Dachet F, Halter SD, Schmidt CJ, Lipovich L, Kapatos G (2015) Identification of long noncoding RNAs dysregulated in the midbrain of human cocaine abusers. J Neurochem 135:50–59PubMedPubMedCentralCrossRefGoogle Scholar
  3. Barry G, Briggs JA, Vanichkina DP, Poth EM, Beveridge NJ, Ratnu VS, Nayler SP, Nones K, Hu J, Bredy TW, Nakagawa S, Rigo F, Taft RJ, Cairns MJ, Blackshaw S, Wolvetang EJ, Mattick JS (2014) The long non-coding RNA Gomafu is acutely regulated in response to neuronal activation and involved in schizophrenia-associated alternative splicing. Mol Psychiatry 19:486–494PubMedCrossRefPubMedCentralGoogle Scholar
  4. Briggs JA, Wolvetang EJ, Mattick JS, Rinn JL, Barry G (2015) Mechanisms of long non-coding RNAs in mammalian nervous system development, plasticity, disease, and evolution. Neuron 88:861–877PubMedCrossRefPubMedCentralGoogle Scholar
  5. Can A, Dao DT, Arad M, Terrillion CE, Piantadosi SC, and Gould TD (2012a) The mouse forced swim test. J Vis Exp: e3638Google Scholar
  6. Can A, Dao DT, Terrillion CE, Piantadosi SC, Bhat S, and Gould TD (2012b) The tail suspension test. J Vis Exp: e3769Google Scholar
  7. Cao X, Yeo G, Muotri AR, Kuwabara T, Gage FH (2006) Noncoding RNAs in the mammalian central nervous system. Annu Rev Neurosci 29:77–103PubMedCrossRefPubMedCentralGoogle Scholar
  8. Cesana M, Cacchiarelli D, Legnini I, Santini T, Sthandier O, Chinappi M, Tramontano A, Bozzoni I (2011) A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell 147:358–369PubMedPubMedCentralCrossRefGoogle Scholar
  9. Chen Y, Dube CM, Rice CJ, Baram TZ (2008) Rapid loss of dendritic spines after stress involves derangement of spine dynamics by corticotropin-releasing hormone. J Neurosci 28:2903–2911PubMedPubMedCentralCrossRefGoogle Scholar
  10. Cryan JF, Mombereau C, Vassout A (2005) The tail suspension test as a model for assessing antidepressant activity: review of pharmacological and genetic studies in mice. Neurosci Biobehav Rev 29:571–625PubMedCrossRefPubMedCentralGoogle Scholar
  11. Cui X, Niu W, Kong L, He M, Jiang K, Chen S, Zhong A, Li W, Lu J, Zhang L (2017) Long noncoding RNA expression in peripheral blood mononuclear cells and suicide risk in Chinese patients with major depressive disorder. Brain Behav 7:e00711PubMedPubMedCentralCrossRefGoogle Scholar
  12. Dansie LE, Ethell IM (2011) Casting a net on dendritic spines: the extracellular matrix and its receptors. Dev Neurobiol 71:956–981PubMedPubMedCentralCrossRefGoogle Scholar
  13. DeCarolis NA, Eisch AJ (2010) Hippocampal neurogenesis as a target for the treatment of mental illness: a critical evaluation. Neuropharmacology 58:884–893PubMedPubMedCentralCrossRefGoogle Scholar
  14. Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, Lagarde J, Veeravalli L, Ruan X, Ruan Y, Lassmann T, Carninci P, Brown JB, Lipovich L, Gonzalez JM, Thomas M, Davis CA, Shiekhattar R, Gingeras TR, Hubbard TJ, Notredame C, Harrow J, Guigó R (2012) The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 22:1775–1789PubMedPubMedCentralCrossRefGoogle Scholar
  15. Diamond DM, Rose GM (1994) Stress impairs LTP and hippocampal-dependent memory. Ann N Y Acad Sci 746:411–414PubMedCrossRefPubMedCentralGoogle Scholar
  16. Faghihi MA, Modarresi F, Khalil AM, Wood DE, Sahagan BG, Morgan TE, Finch CE, St Laurent G 3rd, Kenny PJ, Wahlestedt C (2008) Expression of a noncoding RNA is elevated in Alzheimer’s disease and drives rapid feed-forward regulation of beta-secretase. Nat Med 14:723–730PubMedPubMedCentralCrossRefGoogle Scholar
  17. Godoy LD, Rossignoli MT, Delfino-Pereira P, Garcia-Cairasco N, de Lima Umeoka EH (2018) A comprehensive overview on stress neurobiology: basic concepts and clinical implications. Front Behav Neurosci 12:127PubMedPubMedCentralCrossRefGoogle Scholar
  18. Gormanns P, Mueller NS, Ditzen C, Wolf S, Holsboer F, Turck CW (2011) Phenome-transcriptome correlation unravels anxiety and depression related pathways. J Psychiatr Res 45:973–979PubMedCrossRefPubMedCentralGoogle Scholar
  19. Gray JD, Rubin TG, Hunter RG, McEwen BS (2014) Hippocampal gene expression changes underlying stress sensitization and recovery. Mol Psychiatry 19:1171–1178PubMedCrossRefPubMedCentralGoogle Scholar
  20. Herman JP, Cullinan WE (1997) Neurocircuitry of stress: central control of the hypothalamo-pituitary-adrenocortical axis. Trends Neurosci 20:78–84PubMedCrossRefPubMedCentralGoogle Scholar
  21. Hodes GE, Kana V, Menard C, Merad M, Russo SJ (2015) Neuroimmune mechanisms of depression. Nat Neurosci 18:1386–1393PubMedPubMedCentralCrossRefGoogle Scholar
  22. Jacobson L, Sapolsky R (1991) The role of the hippocampus in feedback regulation of the hypothalamic-pituitary-adrenocortical axis. Endocr Rev 12:118–134PubMedCrossRefPubMedCentralGoogle Scholar
  23. Kerrisk ME, Cingolani LA, Koleske AJ (2014) ECM receptors in neuronal structure, synaptic plasticity, and behavior. Prog Brain Res 214:101–131PubMedPubMedCentralCrossRefGoogle Scholar
  24. Kim JJ, Diamond DM (2002) The stressed hippocampus, synaptic plasticity and lost memories. Nat Rev Neurosci 3:453–462PubMedCrossRefPubMedCentralGoogle Scholar
  25. Kocerha J, Dwivedi Y, Brennand KJ (2015) Noncoding RNAs and neurobehavioral mechanisms in psychiatric disease. Mol Psychiatry 20:677–684PubMedPubMedCentralCrossRefGoogle Scholar
  26. Komada M, Takao K, and Miyakawa T (2008) Elevated plus maze for mice. J Vis Exp: e1088Google Scholar
  27. Lamb AN, Rosenfeld JA, Neill NJ, Talkowski ME, Blumenthal I, Girirajan S, Keelean-Fuller D, Fan Z, Pouncey J, Stevens C, Mackay-Loder L, Terespolsky D, Bader PI, Rosenbaum K, Vallee SE, Moeschler JB, Ladda R, Sell S, Martin J, Ryan S, Jones MC, Moran R, Shealy A, Madan-Khetarpal S, McConnell J, Surti U, Delahaye A, Heron-Longe B, Pipiras E, Benzacken B, Passemard S, Verloes A, Isidor B, le Caignec C, Glew GM, Opheim KE, Descartes M, Eichler EE, Morton CC, Gusella JF, Schultz RA, Ballif BC, Shaffer LG (2012) Haploinsufficiency of SOX5 at 12p12.1 is associated with developmental delays with prominent language delay, behavior problems, and mild dysmorphic features. Hum Mutat 33:728–740PubMedPubMedCentralCrossRefGoogle Scholar
  28. Latos PA, Pauler FM, Koerner MV, Senergin HB, Hudson QJ, Stocsits RR, Allhoff W, Stricker SH, Klement RM, Warczok KE et al (2012) Airn transcriptional overlap, but not its lncRNA products, induces imprinted Igf2r silencing. Science 338:1469–1472PubMedCrossRefGoogle Scholar
  29. Liu Z, Li X, Sun N, Xu Y, Meng Y, Yang C, Wang Y, Zhang K (2014) Microarray profiling and co-expression network analysis of circulating lncRNAs and mRNAs associated with major depressive disorder. PLoS One 9:e93388PubMedPubMedCentralCrossRefGoogle Scholar
  30. Magarinos AM, McEwen BS (1995) Stress-induced atrophy of apical dendrites of hippocampal CA3c neurons: comparison of stressors. Neuroscience 69:83–88PubMedCrossRefPubMedCentralGoogle Scholar
  31. McIlwain KL, Merriweather MY, Yuva-Paylor LA, Paylor R (2001) The use of behavioral test batteries: effects of training history. Physiol Behav 73:705–717PubMedCrossRefPubMedCentralGoogle Scholar
  32. Mercer TR, Mattick JS (2013) Structure and function of long noncoding RNAs in epigenetic regulation. Nat Struct Mol Biol 20:300–307PubMedCrossRefPubMedCentralGoogle Scholar
  33. Mercer TR, Dinger ME, Sunkin SM, Mehler MF, Mattick JS (2008) Specific expression of long noncoding RNAs in the mouse brain. Proc Natl Acad Sci U S A 105:716–721PubMedPubMedCentralCrossRefGoogle Scholar
  34. Miao Z, Mao F, Liang J, Szyf M, Wang Y, Sun ZS (2018) Anxiety-related behaviours associated with microRNA-206-3p and BDNF expression in pregnant female mice following psychological social stress. Mol Neurobiol 55:1097–1111PubMedCrossRefPubMedCentralGoogle Scholar
  35. Miao Z, Zhang J, Li Y, Li X, Song W, Sun ZS, and Wang Y (2019) Presence of the pregnant partner regulates microRNA-30a and BDNF levels and protects male mice from social defeat-induced abnormal behaviors. NeuropharmacologyGoogle Scholar
  36. Nasca C, Bigio B, Zelli D, Nicoletti F, McEwen BS (2015) Mind the gap: glucocorticoids modulate hippocampal glutamate tone underlying individual differences in stress susceptibility. Mol Psychiatry 20(6):755–763PubMedCrossRefPubMedCentralGoogle Scholar
  37. Olejniczak M, Kotowska-Zimmer A, Krzyzosiak W (2018) Stress-induced changes in miRNA biogenesis and functioning. Cell Mol Life Sci 75(2):177–191PubMedCrossRefPubMedCentralGoogle Scholar
  38. Parikshak NN, Swarup V, Belgard TG, Irimia M, Ramaswami G, Gandal MJ, Hartl C, Leppa V, Ubieta LT, Huang J, Lowe JK, Blencowe BJ, Horvath S, Geschwind DH (2016) Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism. Nature 540:423–427PubMedCrossRefPubMedCentralGoogle Scholar
  39. Paylor R, Spencer CM, Yuva-Paylor LA, Pieke-Dahl S (2006) The use of behavioral test batteries, II: effect of test interval. Physiol Behav 87:95–102PubMedCrossRefPubMedCentralGoogle Scholar
  40. Petazzi P, Sandoval J, Szczesna K, Jorge OC, Roa L, Sayols S, Gomez A, Huertas D, Esteller M (2013) Dysregulation of the long non-coding RNA transcriptome in a Rett syndrome mouse model. RNA Biol 10:1197–1203PubMedPubMedCentralCrossRefGoogle Scholar
  41. Petit-Demouliere B, Chenu F, Bourin M (2005) Forced swimming test in mice: a review of antidepressant activity. Psychopharmacology 177:245–255PubMedCrossRefPubMedCentralGoogle Scholar
  42. Qureshi IA, Mattick JS, Mehler MF (2010) Long non-coding RNAs in nervous system function and disease. Brain Res 1338:20–35PubMedCrossRefPubMedCentralGoogle Scholar
  43. Radley J, Morilak D, Viau V, Campeau S (2015) Chronic stress and brain plasticity: mechanisms underlying adaptive and maladaptive changes and implications for stress-related CNS disorders. Neurosci Biobehav Rev 58:79–91PubMedPubMedCentralCrossRefGoogle Scholar
  44. Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139–140PubMedPubMedCentralCrossRefGoogle Scholar
  45. Santarelli L, Saxe M, Gross C, Surget A, Battaglia F, Dulawa S, Weisstaub N, Lee J, Duman R, Arancio O, Belzung C, Hen R (2003) Requirement of hippocampal neurogenesis for the behavioral effects of antidepressants. Science 301:805–809PubMedCrossRefPubMedCentralGoogle Scholar
  46. Spadaro PA, Flavell CR, Widagdo J, Ratnu VS, Troup M, Ragan C, Mattick JS, Bredy TW (2015) Long noncoding RNA-directed epigenetic regulation of gene expression is associated with anxiety-like behavior in mice. Biol Psychiatry 78:848–859PubMedPubMedCentralCrossRefGoogle Scholar
  47. Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25:1105–1111PubMedPubMedCentralCrossRefGoogle Scholar
  48. Uhr M, Tontsch A, Namendorf C, Ripke S, Lucae S, Ising M, Dose T, Ebinger M, Rosenhagen M, Kohli M, Kloiber S, Salyakina D, Bettecken T, Specht M, Pütz B, Binder EB, Müller-Myhsok B, Holsboer F (2008) Polymorphisms in the drug transporter gene ABCB1 predict antidepressant treatment response in depression. Neuron 57:203–209PubMedCrossRefPubMedCentralGoogle Scholar
  49. Wan P, Su W, Zhuo Y (2017) The role of long noncoding RNAs in neurodegenerative diseases. Mol Neurobiol 54:2012–2021PubMedCrossRefPubMedCentralGoogle Scholar
  50. Wang Y, Zeng C, Li J, Zhou Z, Ju X, Xia S, Li Y, Liu A, Teng H, Zhang K et al (2018) PAK2 haploinsufficiency results in synaptic cytoskeleton impairment and autism-related behavior. Cell Rep 24:2029–2041PubMedCrossRefPubMedCentralGoogle Scholar
  51. Watanabe Y, Gould E, McEwen BS (1992) Stress induces atrophy of apical dendrites of hippocampal CA3 pyramidal neurons. Brain Res 588:341–345PubMedCrossRefPubMedCentralGoogle Scholar
  52. Yu G, Wang LG, Han Y, He QY (2012) clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS 16:284–287PubMedPubMedCentralCrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Beijing Institutes of Life ScienceChinese Academy of SciencesBeijingChina
  2. 2.University of Chinese Academy of ScienceBeijingChina
  3. 3.Laboratory of Environmental Criteria and Risk Assessment & Environmental Standards InstituteChinese Research Academy of Environmental SciencesBeijingChina
  4. 4.Institute of Genomic MedicineWenzhou Medical UniversityWenzhouChina

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