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


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.

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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).

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

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Correspondence to G. K. Rajanikant.

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The authors declare that they have no conflict of interests.

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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

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