Identification of microRNAs associated with hyperthermia-induced cellular stress response

MicroRNAs (miRNAs) are a class of small RNAs that play a critical role in the coordination of fundamental cellular processes. Recent studies suggest that miRNAs participate in the cellular stress response (CSR), but their specific involvement remains unclear. In this study, we identify a group of thermally regulated miRNAs (TRMs) that are associated with the CSR. Using miRNA microarrays, we show that dermal fibroblasts differentially express 123 miRNAs when exposed to hyperthermia. Interestingly, only 27 of these miRNAs are annotated in the current Sanger registry. We validated the expression of the annotated miRNAs using qPCR techniques, and we found that the qPCR and microarray data was in well agreement. Computational target-prediction studies revealed that putative targets for the TRMs are heat shock proteins and Argonaute-2—the core functional unit of RNA silencing. These results indicate that cells express a specific group of miRNAs when exposed to hyperthermia, and these miRNAs may function in the regulation of the CSR. Future studies will be conducted to determine if other cells lines differentially express these miRNAs when exposed to hyperthermia.

[1]  V. Ambros,et al.  The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14 , 1993, Cell.

[2]  K. Albermann,et al.  Nuclear Factor Kb: An Oxidative Stress-Responsive Transcription Factor of Eukaryotic Cells (A Review) , 1992 .

[3]  V. Ambros microRNAs Tiny Regulators with Great Potential , 2001, Cell.

[4]  D. Kültz,et al.  Molecular and evolutionary basis of the cellular stress response. , 2005, Annual review of physiology.

[5]  Stijn van Dongen,et al.  miRBase: tools for microRNA genomics , 2007, Nucleic Acids Res..

[6]  Kenneth R Diller,et al.  Stress protein expression kinetics. , 2006, Annual review of biomedical engineering.

[7]  Sun-Mi Park,et al.  microRNAs and death receptors. , 2008, Cytokine & growth factor reviews.

[8]  N. Rajewsky microRNA target predictions in animals , 2006, Nature Genetics.

[9]  A. Hovnanian,et al.  LEKTI fragments specifically inhibit KLK5, KLK7, and KLK14 and control desquamation through a pH-dependent interaction. , 2007, Molecular biology of the cell.

[10]  Ivo L. Hofacker,et al.  Vienna RNA secondary structure server , 2003, Nucleic Acids Res..

[11]  Sam Griffiths-Jones,et al.  The microRNA Registry , 2004, Nucleic Acids Res..

[12]  C. Croce,et al.  miR-15 and miR-16 induce apoptosis by targeting BCL2. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[13]  G. Hannon,et al.  Control of translation and mRNA degradation by miRNAs and siRNAs. , 2006, Genes & development.

[14]  Phillip A. Sharp,et al.  microRNAs: A Safeguard against Turmoil? , 2007, Cell.

[15]  C. Burge,et al.  Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets , 2005, Cell.

[16]  C. Burge,et al.  The microRNAs of Caenorhabditis elegans. , 2003, Genes & development.

[17]  Stijn van Dongen,et al.  miRBase: microRNA sequences, targets and gene nomenclature , 2005, Nucleic Acids Res..

[18]  D. Bartel MicroRNAs Genomics, Biogenesis, Mechanism, and Function , 2004, Cell.

[19]  V. Ambros,et al.  The Cold Shock Domain Protein LIN-28 Controls Developmental Timing in C. elegans and Is Regulated by the lin-4 RNA , 1997, Cell.

[20]  G. Ruvkun,et al.  Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans , 1993, Cell.

[21]  D. Bartel,et al.  MicroRNA-Directed Cleavage of HOXB8 mRNA , 2004, Science.

[22]  Imran Babar,et al.  MicroRNAs as potential agents to alter resistance to cytotoxic anticancer therapy. , 2007, Cancer research.

[23]  Michael Kertesz,et al.  The role of site accessibility in microRNA target recognition , 2007, Nature Genetics.

[24]  F. Slack,et al.  The let-7 microRNA represses cell proliferation pathways in human cells. , 2007, Cancer research.

[25]  John Yu,et al.  Human TRIM71 and its nematode homologue are targets of let-7 microRNA and its zebrafish orthologue is essential for development. , 2007, Molecular biology and evolution.

[26]  G. Wakabayashi,et al.  Downregulation of miR‐138 is associated with overexpression of human telomerase reverse transcriptase protein in human anaplastic thyroid carcinoma cell lines , 2008, Cancer science.

[27]  George A Calin,et al.  Downregulation of microRNA expression in the lungs of rats exposed to cigarette smoke , 2009, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[28]  F. Slack,et al.  miRNA modulation of the cellular stress response. , 2008, Future oncology.

[29]  Brian S. Roberts,et al.  The colorectal microRNAome. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[30]  R. Place,et al.  MicroRNA-373 induces expression of genes with complementary promoter sequences , 2008, Proceedings of the National Academy of Sciences.

[31]  D. Kültz,et al.  Evolution of the cellular stress proteome: from monophyletic origin to ubiquitous function , 2003, Journal of Experimental Biology.

[32]  C. Kappen,et al.  Morpholino-mediated knockdown in primary chondrocytes implicates Hoxc8 in regulation of cell cycle progression. , 2009, Bone.

[33]  Burton B. Yang,et al.  MicroRNA-378 promotes cell survival, tumor growth, and angiogenesis by targeting SuFu and Fus-1 expression , 2007, Proceedings of the National Academy of Sciences.

[34]  Robert A. H. White,et al.  Positional cloning of the Ttc7 gene required for normal iron homeostasis and mutated in hea and fsn anemia mice. , 2005, Genomics.

[35]  L. Dillon Gene Expression Changes in Cyclic Functions , 1983 .

[36]  George A. Calin,et al.  A MicroRNA Signature of Hypoxia , 2006, Molecular and Cellular Biology.

[37]  Jian Gu,et al.  PI3K signaling and miRNA expression during the response of quiescent human fibroblasts to distinct proliferative stimuli , 2006, Genome Biology.

[38]  K. Taira,et al.  MicroRNA-196 inhibits HOXB8 expression in myeloid differentiation of HL60 cells. , 2004, Nucleic acids symposium series.

[39]  P. A. Mason,et al.  Gene Expression Changes in the Skin of Rats Induced by Prolonged 35 GHz Millimeter-Wave Exposure , 2008, Radiation research.

[40]  S. Gullans,et al.  Regulation of expression of the stress response gene, Osp94: identification of the tonicity response element and intracellular signalling pathways. , 2004, The Biochemical journal.

[41]  R. Morimoto,et al.  Cells in stress: transcriptional activation of heat shock genes. , 1993, Science.

[42]  M. Feder,et al.  Heat-shock proteins, molecular chaperones, and the stress response: evolutionary and ecological physiology. , 1999, Annual review of physiology.

[43]  W. Filipowicz,et al.  Relief of microRNA-Mediated Translational Repression in Human Cells Subjected to Stress , 2006, Cell.

[44]  J. Steitz,et al.  Switching from Repression to Activation: MicroRNAs Can Up-Regulate Translation , 2007, Science.

[45]  Martin Reczko,et al.  The database of experimentally supported targets: a functional update of TarBase , 2008, Nucleic Acids Res..

[46]  Anita Mahadevan-Jansen,et al.  Molecular imaging-assisted optimization of hsp70 expression during laser-induced thermal preconditioning for wound repair enhancement. , 2009, The Journal of investigative dermatology.

[47]  Ligang Wu,et al.  MicroRNAs direct rapid deadenylation of mRNA. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[48]  R. Place,et al.  Small dsRNAs induce transcriptional activation in human cells , 2006, Proceedings of the National Academy of Sciences.

[49]  W. Filipowicz,et al.  Repression of protein synthesis by miRNAs: how many mechanisms? , 2007, Trends in cell biology.

[50]  Joshua T. Beckham,et al.  Assessing laser-tissue damage with bioluminescent imaging. , 2006, Journal of biomedical optics.

[51]  A. Hatzigeorgiou,et al.  TarBase: A comprehensive database of experimentally supported animal microRNA targets. , 2005, RNA.

[52]  R. Morimoto,et al.  The transcriptional regulation of heat shock genes: a plethora of heat shock factors and regulatory conditions. , 1996, EXS.

[53]  T. Tuschl,et al.  Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. , 2004, Molecular cell.

[54]  A. Rougvie,et al.  Intrinsic and extrinsic regulators of developmental timing: from miRNAs to nutritional cues , 2005, Development.

[55]  R. Aharonov,et al.  Identification of hundreds of conserved and nonconserved human microRNAs , 2005, Nature Genetics.

[56]  K. Lindblad-Toh,et al.  Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals , 2005, Nature.

[57]  Y. Benjamini,et al.  Controlling the false discovery rate in behavior genetics research , 2001, Behavioural Brain Research.

[58]  Anthony K. L. Leung,et al.  Quantitative analysis of Argonaute protein reveals microRNA-dependent localization to stress granules , 2006, Proceedings of the National Academy of Sciences.

[59]  C. Burge,et al.  Prediction of Mammalian MicroRNA Targets , 2003, Cell.

[60]  H. Kampinga,et al.  Stressful preconditioning and HSP70 overexpression attenuate proteotoxicity of cellular ATP depletion. , 2002, American journal of physiology. Cell physiology.

[61]  Karl T Kelsey,et al.  MicroRNA responses to cellular stress. , 2006, Cancer research.

[62]  B. A. Miller,et al.  The Role of TRP Channels in Oxidative Stress-induced Cell Death , 2006, The Journal of Membrane Biology.