Probe sets from 28,132 genes (Ensembl) or from 19,734 putative full-length transcripts (GenBank

Probe sets from 28,132 genes (Ensembl) or from 19,734 Autophagy putative full-length transcripts (GenBank and Ref Seq). Briefly, for miRNA expression profiling, the RNA was labeled with FlashTag 10781694 Biotin HSR (Genisphere) and then hybridized to Affymetrix miRNA array. After hybridization, staining and washing were performed according to the user guide. For mRNA expression profiling, the RNA was reverse transcribed to doublestranded cDNA, fragmented and labeled with Biotin labeling kit (Genisphere), and then hybridized to Affymetrix gene 1.0 array as recommended. Standard Affymetrix array cassette staining, washing, and scanning were then performed. The last step was2.8 qRT-PCR of miRNAsThe microarray data were validated by qRT-PCR. Specific Autophagy bulge-loopTM miRNA qRT-PCR primer sets (1 reverse transcription primer and a pair of quantitative PCR primers for each set) were designed by RiboBio (Guangzhou, China). RNU6B (Guangzhou RiboBio Co., Ltd) was used as the internal control. RNU6B is a small nuclear RNA that is frequently used as reference RNA for miRNA quantification. RT-PCR reactions were conducted according to the manufacturer’s recommendation. In brief, reverse transcriptase reactions contained purified total RNA, RT primers for each miRNA and U6 small nuclear RNA, RT buffer, dNTPs, RNase inhibitor, DTT, and M-MLV reverse transcriptase. qRT-PCR was performed using SYBR-Green PCR Master Mix (Takara) and real-time cyclers (Strata Gene MX3000P qPCR system). The PCR cycling conditions were as follows: 95uC for 10 min, followed by 40 cycles of denaturation at 95uC for 15 s and a combined annealing/extension step at 60uC for 60 s. The reaction was conducted using the real-time thermal cycler Mx3005p from Agilent Technologies (Agilent Technologies,Integrated miRNA-mRNA Analysis of ChordomasIntegrated miRNA-mRNA Analysis of ChordomasFigure 1. Identification of chordoma and notochord tissues. H E stained section of a chordoma (A) showing moderately atypical physaliphorous (intracellular, bubble-like vacuoles) cells set within a myxoid matrix. The tumor cells demonstrated positive immunostaining for cytokeratin (B), S100 protein (C), and brachyury (D). H E stained section of a notochord tissue (E) showed a clear boundary between the notochord and the surrounding tissue. The notochord cells demonstrated positive immunostaining for brachyury (F). doi:10.1371/journal.pone.0066676.gWaldbronn, Germany). All parameters were measured in triplicate.3.2 mRNA Array Analysis and Integrative Identification of miRNA TargetsThe mRNA array showed that 2,791 mRNAs were differentially expressed, including 577 mRNAs that were downregulated and 2,214 mRNAs that were upregulated in chordomas relative to the fetal notochords (Figure 2B, Table S4). Among these genes, 911 overlapped with putative target genes of differentially expressed miRNAs, including 87 downregulated mRNAs and 824 upregulated mRNAs (Table S5). These 911 intersecting genes were subjected to bioinformatics analysis.Results 3.1 miRNA Array Analysis and Target PredictionIn our study, 33 (20 upregulated and 13 downregulated) of the 1,105 analyzed miRNAs were significantly dysregulated in the chordoma group relative to the fetal notochord group (Figure 2A, Table S2). To further determine the biological functions of these miRNAs, TargetScan was used to predict the target genes of the 33 miRNAs, which resulted in the identification of 6,045 putative target genes (Table S3).3.3 GO AnalysisGO enrichment analyses indi.Probe sets from 28,132 genes (Ensembl) or from 19,734 putative full-length transcripts (GenBank and Ref Seq). Briefly, for miRNA expression profiling, the RNA was labeled with FlashTag 10781694 Biotin HSR (Genisphere) and then hybridized to Affymetrix miRNA array. After hybridization, staining and washing were performed according to the user guide. For mRNA expression profiling, the RNA was reverse transcribed to doublestranded cDNA, fragmented and labeled with Biotin labeling kit (Genisphere), and then hybridized to Affymetrix gene 1.0 array as recommended. Standard Affymetrix array cassette staining, washing, and scanning were then performed. The last step was2.8 qRT-PCR of miRNAsThe microarray data were validated by qRT-PCR. Specific bulge-loopTM miRNA qRT-PCR primer sets (1 reverse transcription primer and a pair of quantitative PCR primers for each set) were designed by RiboBio (Guangzhou, China). RNU6B (Guangzhou RiboBio Co., Ltd) was used as the internal control. RNU6B is a small nuclear RNA that is frequently used as reference RNA for miRNA quantification. RT-PCR reactions were conducted according to the manufacturer’s recommendation. In brief, reverse transcriptase reactions contained purified total RNA, RT primers for each miRNA and U6 small nuclear RNA, RT buffer, dNTPs, RNase inhibitor, DTT, and M-MLV reverse transcriptase. qRT-PCR was performed using SYBR-Green PCR Master Mix (Takara) and real-time cyclers (Strata Gene MX3000P qPCR system). The PCR cycling conditions were as follows: 95uC for 10 min, followed by 40 cycles of denaturation at 95uC for 15 s and a combined annealing/extension step at 60uC for 60 s. The reaction was conducted using the real-time thermal cycler Mx3005p from Agilent Technologies (Agilent Technologies,Integrated miRNA-mRNA Analysis of ChordomasIntegrated miRNA-mRNA Analysis of ChordomasFigure 1. Identification of chordoma and notochord tissues. H E stained section of a chordoma (A) showing moderately atypical physaliphorous (intracellular, bubble-like vacuoles) cells set within a myxoid matrix. The tumor cells demonstrated positive immunostaining for cytokeratin (B), S100 protein (C), and brachyury (D). H E stained section of a notochord tissue (E) showed a clear boundary between the notochord and the surrounding tissue. The notochord cells demonstrated positive immunostaining for brachyury (F). doi:10.1371/journal.pone.0066676.gWaldbronn, Germany). All parameters were measured in triplicate.3.2 mRNA Array Analysis and Integrative Identification of miRNA TargetsThe mRNA array showed that 2,791 mRNAs were differentially expressed, including 577 mRNAs that were downregulated and 2,214 mRNAs that were upregulated in chordomas relative to the fetal notochords (Figure 2B, Table S4). Among these genes, 911 overlapped with putative target genes of differentially expressed miRNAs, including 87 downregulated mRNAs and 824 upregulated mRNAs (Table S5). These 911 intersecting genes were subjected to bioinformatics analysis.Results 3.1 miRNA Array Analysis and Target PredictionIn our study, 33 (20 upregulated and 13 downregulated) of the 1,105 analyzed miRNAs were significantly dysregulated in the chordoma group relative to the fetal notochord group (Figure 2A, Table S2). To further determine the biological functions of these miRNAs, TargetScan was used to predict the target genes of the 33 miRNAs, which resulted in the identification of 6,045 putative target genes (Table S3).3.3 GO AnalysisGO enrichment analyses indi.