No for Pten mice, and Dr. Lisa Chantz for ODC anti-body.Author ContributionsConceived and designed the experiments: YK BT KH WDK. Performed the experiments: YK BT TAS LW. Analyzed the data: YK BT MS KH WDK. Contributed reagents/materials/analysis tools: KH. Wrote the paper: WDK KH.
Chordomas are rare, slow-growing, primary malignant neoplasms of the axial skeleton and arise from the remnant notochord [1?], and surgery remains the best standard treatment [3,4]. However, these tumors are difficult to be eradicated because they are often adjacent to vital structures. Accordingly, the prognosis of patients with chordomas is often poor; many patients develop fatal local recurrence [5], and the overall median survival is 6.29 years [1]. Therapeutic advances are therefore urgently required for improving the outcome. MicroRNAs (miRNAs) are a class of short (18?5 nucleotides) noncoding RNAs that suppress translation, increase mRNA deadenylation and degradation, and/or sequester the mRNA of target genes [6]. It is estimated that up to 30 of human genes [7] and virtually all cellular processes are regulated by miRNAs [8]. Abnormal expression of several miRNAs has previously been shown to be associated with multiple cancer types [9], including chordomas [10]. However, no studies have applied integratedanalysis techniques, which can 16985061 be used to identify functional miRNA-target relationships with high precision to miRNA and mRNA profiles for chordomas. In this study, we applied an integrative molecular and bioinformatic approach by simultaneously profiling both miRNA and mRNA for chordomas and notochord tissues to investigate the mechanisms responsible for the progression and pathogenesis of chordomas. The microarray data were validated by quantitative real-time reverse transcription polymerase chain reaction (qRTPCR). The understanding of the molecular differences between chordoma and the notochord may shed light on the molecular pathogenesis of chordoma and offer new possibilities for systemic treatment.Integrated miRNA-mRNA Analysis of ChordomasMaterials and Methods 2.1 Ethics StatementOur study design received approval from the institutional review board of Peking University Third Hospital (Beijing, China) (No. IRB00006761?012039). Written informed consent was get CAL 120 obtained from the patients.to scan the signals and analyze the data. AffymetrixH Expression Console Software (version 1.2.1) was used for microarray analysis. Raw data (CEL files) were normalized at the transcript level by using a Thiazole Orange chemical information robust multi-average method (RMA workflow). MiRNA and mRNA expression data are available from the NCBI Gene Expression Omnibus (GEO), accession number GSE37372.2.2 Tissue SamplesThree pairs of paraformaldehyde-fixed, paraffin-embedded (PFPE) tissue samples were divided into 2 groups (Table S1). One group contained three primary classic chordoma tissues (obtained from men with a mean age of 43.3 years; chordoma group), and the other group contained three notochord samples obtained from the intervertebral discs of aborted fetuses with a gestational age of 24?7 weeks (notochord group). Paraffin sections from the fixed chordoma tissues were cut at 5 mm and stained with hematoxylin and eosin (H E) 1676428 as well as antibodies against cytokeratin, S100 and brachyury proteins [11?4] (Figure 1). The sections of fetal notochord were also stained with H E and received immunohistochemical study with brachyury proteins (Figure 1). These samples were confirmed by two experienced patho.No for Pten mice, and Dr. Lisa Chantz for ODC anti-body.Author ContributionsConceived and designed the experiments: YK BT KH WDK. Performed the experiments: YK BT TAS LW. Analyzed the data: YK BT MS KH WDK. Contributed reagents/materials/analysis tools: KH. Wrote the paper: WDK KH.
Chordomas are rare, slow-growing, primary malignant neoplasms of the axial skeleton and arise from the remnant notochord [1?], and surgery remains the best standard treatment [3,4]. However, these tumors are difficult to be eradicated because they are often adjacent to vital structures. Accordingly, the prognosis of patients with chordomas is often poor; many patients develop fatal local recurrence [5], and the overall median survival is 6.29 years [1]. Therapeutic advances are therefore urgently required for improving the outcome. MicroRNAs (miRNAs) are a class of short (18?5 nucleotides) noncoding RNAs that suppress translation, increase mRNA deadenylation and degradation, and/or sequester the mRNA of target genes [6]. It is estimated that up to 30 of human genes [7] and virtually all cellular processes are regulated by miRNAs [8]. Abnormal expression of several miRNAs has previously been shown to be associated with multiple cancer types [9], including chordomas [10]. However, no studies have applied integratedanalysis techniques, which can 16985061 be used to identify functional miRNA-target relationships with high precision to miRNA and mRNA profiles for chordomas. In this study, we applied an integrative molecular and bioinformatic approach by simultaneously profiling both miRNA and mRNA for chordomas and notochord tissues to investigate the mechanisms responsible for the progression and pathogenesis of chordomas. The microarray data were validated by quantitative real-time reverse transcription polymerase chain reaction (qRTPCR). The understanding of the molecular differences between chordoma and the notochord may shed light on the molecular pathogenesis of chordoma and offer new possibilities for systemic treatment.Integrated miRNA-mRNA Analysis of ChordomasMaterials and Methods 2.1 Ethics StatementOur study design received approval from the institutional review board of Peking University Third Hospital (Beijing, China) (No. IRB00006761?012039). Written informed consent was obtained from the patients.to scan the signals and analyze the data. AffymetrixH Expression Console Software (version 1.2.1) was used for microarray analysis. Raw data (CEL files) were normalized at the transcript level by using a robust multi-average method (RMA workflow). MiRNA and mRNA expression data are available from the NCBI Gene Expression Omnibus (GEO), accession number GSE37372.2.2 Tissue SamplesThree pairs of paraformaldehyde-fixed, paraffin-embedded (PFPE) tissue samples were divided into 2 groups (Table S1). One group contained three primary classic chordoma tissues (obtained from men with a mean age of 43.3 years; chordoma group), and the other group contained three notochord samples obtained from the intervertebral discs of aborted fetuses with a gestational age of 24?7 weeks (notochord group). Paraffin sections from the fixed chordoma tissues were cut at 5 mm and stained with hematoxylin and eosin (H E) 1676428 as well as antibodies against cytokeratin, S100 and brachyury proteins [11?4] (Figure 1). The sections of fetal notochord were also stained with H E and received immunohistochemical study with brachyury proteins (Figure 1). These samples were confirmed by two experienced patho.