title: Poly(A)-specific ribonuclease and Nocturnin in squamous cell lung cancer: prognostic value and impact on gene expression.
abstract: BACKGROUND
  Lung cancer is the leading cause of cancer mortality worldwide, mainly due to late diagnosis, poor prognosis and tumor heterogeneity. Thus, the need for biomarkers that will aid classification, treatment and monitoring remains intense and challenging and depends on the better understanding of the tumor pathobiology and underlying mechanisms. The deregulation of gene expression is a hallmark of cancer and a critical parameter is the stability of mRNAs that may lead to increased oncogene and/or decreased tumor suppressor transcript and protein levels. The shortening of mRNA poly(A) tails determines mRNA stability, as it is usually the first step in mRNA degradation, and is catalyzed by deadenylases. Herein, we assess the clinical significance of deadenylases and we study their role on gene expression in squamous cell lung carcinoma (SCC).
  
  
  METHODS
  Computational transcriptomic analysis from a publicly available microarray was performed in order to examine the expression of deadenylases in SCC patient samples. Subsequently we employed real-time PCR in clinical samples in order to validate the bioinformatics results regarding the gene expression of deadenylases. Selected deadenylases were silenced in NCI-H520 and Hep2 human cancer cell lines and the effect on gene expression was analyzed with cDNA microarrays.
  
  
  RESULTS
  The in silico analysis revealed that the expression of several deadenylases is altered in SCC. Quantitative real-time PCR showed that four deadenylases, PARN, CNOT6, CNOT7 and NOC, are differentially expressed in our SCC clinical samples. PARN overexpression correlated with younger patient age and CNOT6 overexpression with non-metastatic tumors. Kaplan-Meier analysis suggests that increased levels of PARN and NOC correlate with significantly increased survival. Gene expression analysis upon PARN and NOC silencing in lung cancer cells revealed gene expression deregulation that was functionally enriched for gene ontologies related to cell adhesion, cell junction, muscle contraction and metabolism.
  
  
  CONCLUSIONS
  Our results highlight the clinical significance of PARN and NOC on the survival in SCC diagnosed patients. We demonstrate that the enzymes are implicated in important phenotypes pertinent to cancer biology and provide information on their role in the regulation of gene expression in SCC. Overall, our results support an emerging role for deadenylases in SCC and contribute to the understanding of their role in cancer biology.
authors.affiliation: Department of Biochemistry and Biotechnology, University of Thessaly, Ploutonos 26, Larissa, 412 21, Greece. pmarago@med.uth.gr.|Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, Biopolis, Larissa, 415 00, Greece. pmarago@med.uth.gr.
authors.forename: Panagiotis
authors.initials: P
authors.lastname: Maragozidis
authors.affiliation: Department of Biochemistry and Biotechnology, University of Thessaly, Ploutonos 26, Larissa, 412 21, Greece. epapanastasi@yahoo.gr.
authors.forename: Eirini
authors.initials: E
authors.lastname: Papanastasi
authors.affiliation: Department of Biochemistry and Biotechnology, University of Thessaly, Ploutonos 26, Larissa, 412 21, Greece. ditha2007@hotmail.com.
authors.forename: Diana
authors.initials: D
authors.lastname: Scutelnic
authors.affiliation: Department of Biochemistry and Biotechnology, University of Thessaly, Ploutonos 26, Larissa, 412 21, Greece. athinatotomi@gmail.com.
authors.forename: Athina
authors.initials: A
authors.lastname: Totomi
authors.affiliation: Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, Biopolis, Larissa, 415 00, Greece. kouirouxis@hotmail.gr.|Department of Pneumonology - Oncology, Theagenio Cancer Hospital, Al. Symeonidi 2, Thessaloniki, 540 07, Greece. kouirouxis@hotmail.gr.
authors.forename: Ioanna
authors.initials: I
authors.lastname: Kokkori
authors.affiliation: Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, Biopolis, Larissa, 415 00, Greece. szarog@med.uth.gr.|Department of Physiology, Faculty of Medicine, University of Thessaly, Biopolis, Larissa, 415 00, Greece. szarog@med.uth.gr.
authors.forename: Sotirios G
authors.initials: SG
authors.lastname: Zarogiannis
authors.affiliation: Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, Biopolis, Larissa, 415 00, Greece. noraker@gmail.com.
authors.forename: Theodora
authors.initials: T
authors.lastname: Kerenidi
authors.affiliation: Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, Biopolis, Larissa, 415 00, Greece. kgourg@med.uth.gr.
authors.forename: Konstantinos I
authors.initials: KI
authors.lastname: Gourgoulianis
authors.affiliation: Department of Biochemistry and Biotechnology, University of Thessaly, Ploutonos 26, Larissa, 412 21, Greece. balatsos@bio.uth.gr.
authors.forename: Nikolaos A A
authors.initials: NA
authors.lastname: Balatsos
mesh_terms: D002294:Carcinoma, Squamous Cell / Q000201:enzymology* / Q000235:genetics / Q000473:pathology; D045744:Cell Line, Tumor; D019295:Computational Biology / Q000379:methods*; D005095:Exoribonucleases / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D053208:Kaplan-Meier Estimate; D008175:Lung Neoplasms / Q000201:enzymology* / Q000235:genetics / Q000473:pathology; D009687:Nuclear Proteins / Q000235:genetics / Q000378:metabolism*; D011379:Prognosis; D020871:RNA Stability / Q000235:genetics; D012097:Repressor Proteins; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*
chemical_list: D005095:Exoribonucleases; D009687:Nuclear Proteins; D012097:Repressor Proteins; D014157:Transcription Factors; C102804:nocturnin; C545829:CNOT7 protein, human; C534418:cNOT6 protein, human