A Novel Five-Node Feed-Forward Loop Unravels miRNA-Gene-TF Regulatory Relationships in Ischemic Stroke

Abstract

The complex and interlinked cascade of events regulated by microRNAs (miRNAs), transcription factors (TF), and target genes highlight the multifactorial nature of ischemic stroke pathology. The complexity of ischemic stroke requires a wider assessment than the existing experimental research that deals with only a few regulatory components. Here, we assessed a massive set of genes, miRNAs, and transcription factors to build a miRNA-gene-transcription factor regulatory network to elucidate the underlying post-transcriptional mechanisms in ischemic stroke. Feed-forward loops (three-node, four-node, and novel five-node) were converged to establish regulatory relationships between miRNAs, TFs, and genes. The synergistic function of miRNAs in ischemic stroke was predicted and incorporated into a novel five-node feed-forward loop. Significant miRNA-TF pairs were identified using cumulative hypergeometric distribution. Two subnetworks were derived from the extensive miRNA-TF regulatory network and analyzed to predict the molecular mechanism relating the regulatory components. NFKB and STAT were identified to be the chief regulators of innate inflammatory and neuronal survival mechanisms, respectively. Exclusive novel interactions between miR-9 and miR-124 with TLX, BCL2, and HDAC4 were identified to explain the post-stroke induced neurogenesis mechanism. Therefore, this network-based approach to delineate miRNA, TF, and gene interactions might promote the development of effective therapeutics against ischemic stroke.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7

References

  1. 1.

    Ladecola C, Anrather J (2011) Stroke research at a crossroad: asking the brain for directions. Nat Neurosci 14:1363–1368

    Article  Google Scholar 

  2. 2.

    Jeyaseelan K, Lim KY, Armugam A (2008) MicroRNA expression in the blood and brain of rats subjected to transient focal ischemia by middle cerebral artery occlusion. Stroke 39:959–966

    CAS  Article  Google Scholar 

  3. 3.

    Saugstad JA (2010) MicroRNAs as effectors of brain function with roles in ischemia and injury, neuroprotection, and neurodegeneration. J Cereb Blood Flow Metab 30:1564–1576

    CAS  Article  Google Scholar 

  4. 4.

    Nampoothiri SS, Menon HV, Das D, G K R (2016) ISCHEMIRs: finding a way through the obstructed cerebral arteries. Curr Drug Targets 17:800–810

    CAS  Article  Google Scholar 

  5. 5.

    Lavrik IN, Zhivotovsky B (2014) Systems biology: a way to make complex problems more understandable. Cell Death Dis 5:e1256

    CAS  Article  Google Scholar 

  6. 6.

    Werner HM, Mills GB, Ram PT (2014) Cancer systems biology: a peek into the future of patient care? Nat Rev Clin Oncol 11:167–176

    Article  Google Scholar 

  7. 7.

    Mangan S, Alon U (2003) Structure and function of the feed-forward loop network motif. Proc Natl Acad Sci U S A 100:11980–11985

    CAS  Article  Google Scholar 

  8. 8.

    Sun J, Gong X, Purow B, Zhao Z (2012) Uncovering microRNA and transcription factor mediated regulatory networks in glioblastoma. PLoS Comput Biol 8:e1002488

    CAS  Article  Google Scholar 

  9. 9.

    Safran M, Dalah I, Alexander, Rosen N, Iny Stein T, Shmoish M, Nativ N, Bahir I et al (2010) GeneCards Version 3: the human gene integrator. Database (Oxford) 2010:baq020

    Article  Google Scholar 

  10. 10.

    Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K et al (2000) Gene ontology: tool for the unification of biology. Nat Genet 25:25–29

    CAS  Article  Google Scholar 

  11. 11.

    The Gene Ontology Consortium (2015) Gene ontology consortium: going forward. Nucleic Acids Res 43:D1049–D1056

    Article  Google Scholar 

  12. 12.

    Jiang Q, Wang Y, Hao Y, Juan L, Teng M, Zhang X (2009) miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res 37:D98–D104

    CAS  Article  Google Scholar 

  13. 13.

    Ruepp A, Kowarsch A, Theis F (2012) PhenomiR: microRNAs in human diseases and biological processes. Methods Mol Biol 822:249–260

    CAS  Article  Google Scholar 

  14. 14.

    Li Y, Qiu C, Tu J, Geng B, Yang J, Jiang T, Cui Q (2014) HMDD v2.0: a database for experimentally supported human microRNA and disease associations. Nucleic Acids Res 42:D1070–D1074

    CAS  Article  Google Scholar 

  15. 15.

    Yang JH, Li JH, Jiang S, Zhou H, Qu LH (2013) ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data. Nucleic Acids Res 41:D177–D187

    CAS  Article  Google Scholar 

  16. 16.

    Jiang C, Xuan Z, Zhao F, Zhang MQ (2007) TRED: a transcriptional regulatory element database, new entries and other development. Nucleic Acids Res 35:D137–D140

    CAS  Article  Google Scholar 

  17. 17.

    Hsu SD, Tseng YT, Shrestha S, Lin YL, Khaleel A, Chou CH, Chu CF, Huang HY et al (2014) miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions. Nucleic Acids Res 42:D78–D85

    CAS  Article  Google Scholar 

  18. 18.

    Warde-Farley D, Donaldson SL, Comes O, Zuberi K, Badrawi R, Chao P, Franz M, Grouios C et al (2010) The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res 38:W214–W220

    CAS  Article  Google Scholar 

  19. 19.

    Xu J, Li CX, Li YS, Lv JY, Ma Y, Shao TT, Xu LD, Wang YY et al (2011) MiRNA-miRNA synergistic network: construction via co-regulating functional modules and disease miRNA topological features. Nucleic Acids Res 39:825–836

    CAS  Article  Google Scholar 

  20. 20.

    Kanehisa M, Goto S (2000) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28:27–30

    CAS  Article  Google Scholar 

  21. 21.

    Chen EY, Tan CM, Kou Y, Duan Q, Wang Z, Meirelles GV, Clark NR, Ma'ayan A (2013) Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics 14:128

    Article  Google Scholar 

  22. 22.

    Martinou JC, Dubois-Dauphin M, Staple JK, Rodriguez I, Frankowski H, Missotten M, Albertini P, Talabot D et al (1994) Overexpression of BCL-2 in transgenic mice protects neurons from naturally occurring cell death and experimental ischemia. Neuron 13:1017–1030

    CAS  Article  Google Scholar 

  23. 23.

    Hata R, Gillardon F, Michaelidis TM, Hossmann KA (1999) Targeted disruption of the bcl-2 gene in mice exacerbates focal ischemic brain injury. Metab Brain Dis 14:117–124

    CAS  Article  Google Scholar 

  24. 24.

    Chen J, Simon RP, Nagayama T, Zhu R, Loeffert JE, Watkins SC, Graham SH (2000) Suppression of endogenous bcl-2 expression by antisense treatment exacerbates ischemic neuronal death. J Cereb Blood Flow Metab 20:1033–1039

    CAS  Article  Google Scholar 

  25. 25.

    Webster KA, Graham RM, Thompson JW, Spiga MG, Frazier DP, Wilson A, Bishopric NH (2006) Redox stress and the contributions of BH3-only proteins to infarction. Antioxid Redox Signal 8:1667–1676

    CAS  Article  Google Scholar 

  26. 26.

    Yin KJ, Deng Z, Huang H, Hamblin M, Xie C, Zhang J, Chen YE (2010) miR-497 regulates neuronal death in mouse brain after transient focal cerebral ischemia. Neurobiol Dis 38:17–26

    CAS  Article  Google Scholar 

  27. 27.

    Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, Tuschl T (2002) Identification of tissue-specific microRNAs from mouse. Curr Biol 12:735–739

    CAS  Article  Google Scholar 

  28. 28.

    Devlin C, Greco S, Martelli F, Ivan M (2011) miR-210: more than a silent player in hypoxia. IUBMB Life 63:94–100

    CAS  PubMed  PubMed Central  Google Scholar 

  29. 29.

    Sun Y, Gui H, Li Q, Luo ZM, Zheng MJ, Duan JL, Liu X (2013) MicroRNA-124 protects neurons against apoptosis in cerebral ischemic stroke. CNS Neurosci Ther 19:813–819

    CAS  Article  Google Scholar 

  30. 30.

    Ouyang YB, Lu Y, Yue S, Giffard RG (2012) miR-181 targets multiple Bcl-2 family members and influences apoptosis and mitochondrial function in astrocytes. Mitochondrion 12:213–219

    CAS  Article  Google Scholar 

  31. 31.

    Jin K, Zhu Y, Sun Y, Mao XO, Xie L, Greenberg DA (2002) Vascular endothelial growth factor (VEGF) stimulates neurogenesis in vitro and in vivo. Proc Natl Acad Sci U S A 99:11946–11950

    CAS  Article  Google Scholar 

  32. 32.

    Selvamani A, Sathyan P, Miranda RC, Sohrabji F (2012) An antagomir to microRNA Let7f promotes neuroprotection in an ischemic stroke model. PLoS One 7:e32662

    CAS  Article  Google Scholar 

  33. 33.

    Buller B, Liu X, Wang X, Zhang RL, Zhang L, Hozeska-Solgot A, Chopp M, Zhang ZG (2010) MicroRNA-21 protects neurons from ischemic death. FEBS J 277:4299–4307

    CAS  Article  Google Scholar 

  34. 34.

    Ji R, Cheng Y, Yue J, Yang J, Liu X, Chen H, Dean DB, Zhang C (2007) MicroRNA expression signature and antisense-mediated depletion reveal an essential role of microRNA in vascular neointimal lesion formation. Circ Res 100:1579–1588

    CAS  Article  Google Scholar 

  35. 35.

    Liu XS, Chopp M, Wang XL, Zhang L, Hozeska-Solgot A, Tang T, Kassis H, Zhang RL et al (2013) MicroRNA-17-92 cluster mediates the proliferation and survival of neural progenitor cells after stroke. J Biol Chem 288:12478–12488

    CAS  Article  Google Scholar 

  36. 36.

    Yin KJ, Deng Z, Hamblin M, Xiang Y, Huang H, Zhang J, Jiang X, Wang Y et al (2010) Peroxisome proliferator-activated receptor delta regulation of miR-15a in ischemia-induced cerebral vascular endothelial injury. J Neurosci 30:6398–6408

    CAS  Article  Google Scholar 

  37. 37.

    Harari OA, Liao AK (2010) NF-κB and innate immunity in ischemic stroke. Ann N Y Acad Sci 1207:32–40

    CAS  Article  Google Scholar 

  38. 38.

    Shi H (2009) Hypoxia inducible factor 1 as a therapeutic target in ischemic stroke. Curr Med Chem 16:4593–4600

    CAS  Article  Google Scholar 

  39. 39.

    Liu J, Xu Q, Wang H, Wang R, Hou XY (2013) Neuroprotection of ischemic postconditioning by downregulating the postsynaptic signaling mediated by kainate receptors. Stroke 44:2031–2035

    Article  Google Scholar 

  40. 40.

    Taganov KD, Boldin MP, Chang KJ, Baltimore D (2006) NF-kappaB-dependent induction of microRNA miR-146, an inhibitor targeted to signaling proteins of innate immune responses. Proc Natl Acad Sci U S A 103:12481–12486

    CAS  Article  Google Scholar 

  41. 41.

    Li T, Morgan MJ, Choksi S, Zhang Y, Kim YS, Liu ZG (2010) MicroRNAs modulate the noncanonical NF-κB pathway by regulating IKKα expression during macrophage differentiation. Nat Immunol 11:799–805

    CAS  Article  Google Scholar 

  42. 42.

    Jin R, Yang G, Li G (2010) Inflammatory mechanisms in ischemic stroke: role of inflammatory cells. J Leukoc Biol 87:779–789

    CAS  Article  Google Scholar 

  43. 43.

    Dziennis S, Alkayed NJ (2008) Role of signal transducer and activator of transcription 3 in neuronal survival and regeneration. Rev Neurosci 19:341–361

    CAS  Article  Google Scholar 

  44. 44.

    Ahn YH, Lee G, Kang SK (2006) Molecular insights of the injured lesions of rat spinal cords: Inflammation, apoptosis, and cell survival. Biochem Biophys Res Commun 22:560–570

    Article  Google Scholar 

  45. 45.

    Bhalala OG, Pan L, Sahni V, McGuire TL, Gruner K, Tourtellotte WG, Kessler JA (2012) microRNA-21 regulates astrocytic response following spinal cord injury. J Neurosci 32:17935–17947

    CAS  Article  Google Scholar 

  46. 46.

    Kohanbash G, Okada H (2012) MicroRNAs and STAT interplay. Semin Cancer Biol 22:70–75

    CAS  Article  Google Scholar 

  47. 47.

    Sepramaniam S, Armugam A, Lim KY, Karolina DS, Swaminathan P, Tan JR, Jeyaseelan K (2010) MicroRNA 320a functions as a novel endogenous modulator of aquaporins 1 and 4 as well as a potential therapeutic target in cerebral ischemia. J Biol Chem 285:29223–29230

    CAS  Article  Google Scholar 

  48. 48.

    Rashidian J, Iyirhiaro G, Aleyasin H, Rios VI, Callaghan S, Bland RJ, Slack RS, During MJ et al (2005) Multiple cyclin-dependent kinases signals are critical mediators of ischemia/ hypoxic neuronal death in vitro and in vivo. Proc Natl Acad Sci U S A 102:14080–14085

    CAS  Article  Google Scholar 

  49. 49.

    Li Y, Chopp M, Powers C, Jiang N (1997) Immunoreactivity of cyclin D1/cdk4 in neurons and oligodendrocytes after focal cerebral ischemia in rat. J Cereb Blood Flow Metab 17:846–856

    CAS  Article  Google Scholar 

  50. 50.

    Liu XS, Chopp M, Zhang RL, Tao T, Wang XL, Kassis H, Hozeska-Solgot A, Zhang L et al (2011) MicroRNA profiling in subventricular zone after stroke: MiR-124a regulates proliferation of neural progenitor cells through Notch signaling pathway. PLoS One 6:e23461

    CAS  Article  Google Scholar 

  51. 51.

    Wei N, Xiao L, Xue R, Zhang D, Zhou J, Ren H, Guo S, Xu J (2016) MicroRNA-9 mediates the cell apoptosis by targeting Bcl2l11 in ischemic stroke. Mol Neurobiol 53:6809–6817

    CAS  Article  Google Scholar 

  52. 52.

    Zhao C, Sun G, Li S, Shi Y (2009) A feedback regulatory loop involving microRNA-9 and nuclear receptor TLX in neural stem cell fate determination. Nat Struct Mol Biol 16:365–371

    CAS  Article  Google Scholar 

Download references

Funding

This study was funded by (a) the Department of Biotechnology, Government of India “Bioinformatics Infrastructure Facility for Biology Teaching through Bioinformatics (BIF-BTBI)” (grant number: BT/BI/25/001/2006 dated 25 March 2011) and (b) the Kerala State Council for Science, Technology and Environment, Science Research Scheme (grant number: 018/SRSLS/2014/CSTE).

Author information

Affiliations

Authors

Contributions

RKG, NSS, and FSM contributed to all components of the work (design, experimentation, analysis, and writing).

Corresponding author

Correspondence to G. K. Rajanikant.

Ethics declarations

Conflict of Interest

The authors declare that they have no conflict of interests.

Electronic Supplementary Material

ESM 1

(PDF 2100 kb).d

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Nampoothiri, S.S., Fayaz, S.M. & Rajanikant, G.K. A Novel Five-Node Feed-Forward Loop Unravels miRNA-Gene-TF Regulatory Relationships in Ischemic Stroke. Mol Neurobiol 55, 8251–8262 (2018). https://doi.org/10.1007/s12035-018-0963-6

Download citation

Keywords

  • Ischemic stroke
  • Network biology
  • miRNA
  • Genes
  • Transcription factor
  • Feed-forward loop
  • Neurogenesis