Background: Hypoxia is a pathophysiological condition which arises due to low oxygen
concentration in conditions like cardiovascular diseases, inflammation, ascent to higher altitude, malignancies,
deep sea diving, prenatal birth, etc. A number of microRNAs (miRNAs), Transcription
Factors (TFs) and genes have been studied separately for their role in hypoxic adaptation and controlling
cell-cycle progression and apoptosis during this stress.
Objective: We hypothesize that miRNAs and TFs may act in conjunction to regulate a multitude of
genes and play a crucial and combinatorial role during hypoxia-stress-responses and associated cellcycle
Method: We collected a comprehensive and non-redundant list of human hypoxia-responsive miRNAs
(also known as hypoxiamiRs). Their experimentally validated gene-targets were retrieved from
various databases and a comprehensive hypoxiamiR-gene regulatory network was built.
Results: Functional characterization and pathway enrichment of genes identified phospho-proteins as
enriched nodes. The phospho-proteins which were localized both in the nucleus and cytoplasm and
could potentially play important role as signaling molecules were selected; and further pathway enrichment
revealed that most of them were involved in NFkB signaling. Topological analysis identified
several critical hypoxiamiRs and network perturbations confirmed their importance in the network.
Feed Forward Loops (FFLs) were identified in the subnetwork of enriched genes, miRNAs and
TFs. Statistically significant FFLs consisted of four miRNAs (hsa-miR-182-5p, hsa- miR-146b-5p,
hsa-miR-96, hsa-miR-20a) and three TFs (SMAD4, FOXO1, HIF1A) both regulating two genes
(NFkB1A and CDKN1A).
Conclusion: Detailed BioCarta pathway analysis identified that these miRNAs and TFs together play
a critical and combinatorial role in regulating cell-cycle under hypoxia, by controlling mechanisms
that activate cell-cycle checkpoint protein, CDKN1A. These modules work synergistically to regulate
cell-proliferation, cell-growth, cell-differentiation and apoptosis during hypoxia. A detailed mechanistic
molecular model of how these co-regulatory FFLs may regulate the cell-cycle transitions during
hypoxic stress conditions is also put forth. These biomolecules may play a crucial and deterministic
role in deciding the fate of the cell under hypoxic-stress.