M. Fu, G. Huang, Z. Zhang, J. Liu, Z. Zhang, Z. Huang, B. Yu, F. Meng

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Presentation transcript:

Expression profile of long noncoding RNAs in cartilage from knee osteoarthritis patients M. Fu, G. Huang, Z. Zhang, J. Liu, Z. Zhang, Z. Huang, B. Yu, F. Meng Osteoarthritis and Cartilage Volume 23, Issue 3, Pages 423-432 (March 2015) DOI: 10.1016/j.joca.2014.12.001 Copyright © 2014 Osteoarthritis Research Society International Terms and Conditions

Fig. 1 LncRNA profile of microarray data. (A). Scatter-Plot of lncRNA expression. The lncRNAs above the top green line and below the bottom green line indicated more than 2.0 fold change of lncRNAs between OA cartilage and control normal samples. (B). Volcano Plot of the differentially expressed lncRNAs. The red points in the plot represent the differentially expressed lncRNAs with statistical significance. (C). Hierarchical Clustering shows a distinguishable lncRNA expression profile between the two groups and homogeneity within groups. RNA was extracted from cartilage samples obtained from six OA patients and five control subjects. Osteoarthritis and Cartilage 2015 23, 423-432DOI: (10.1016/j.joca.2014.12.001) Copyright © 2014 Osteoarthritis Research Society International Terms and Conditions

Fig. 2 mRNA profile of microarray data. (A). Scatter-Plot of mRNA expression. The mRNAs above the top green line and below the bottom green line indicated more than 2.0 fold change of mRNAs between OA cartilage and control normal samples. (B). Volcano Plot of the differentially expressed mRNAs. The red points in the plot represent the differentially expressed mRNAs with statistical significance. (C). Hierarchical Clustering shows a distinguishable mRNA expression profile between the two groups and homogeneity within groups. RNA was extracted from cartilage samples obtained from six OA patients and five control subjects. Osteoarthritis and Cartilage 2015 23, 423-432DOI: (10.1016/j.joca.2014.12.001) Copyright © 2014 Osteoarthritis Research Society International Terms and Conditions

Fig. 3 Comparison of lncRNAs expression level between microarray and qRT-PCR results. Three upregulated and three downregulated differentially expressed lncRNAs were validated by qRT-PCR in cartilage samples from six OA patients and five normal control subjects. Each sample was analyzed in triplicate. Gene expression was normalized to U6 expression and calculated by 2−ΔΔCt method. The heights of the columns in the chart represent the mean fold changes (C/N) in the expression between OA group and normal group. The qRT-PCR results are consistent with microarray data. ***P < 0.001 vs normal group in qRT-PCR validation. Osteoarthritis and Cartilage 2015 23, 423-432DOI: (10.1016/j.joca.2014.12.001) Copyright © 2014 Osteoarthritis Research Society International Terms and Conditions

Fig. 4 Predicted cis target genes of two differentially expressed lncRNAs (A. uc.343, B. HSP90AA4P). The X-axis represents genomic locations. The red points represent lncRNA and the number in the bracket is the length of the lncRNA. The blue points represent possible cis target genes. The Y-axis represents Pearson correlation of lncRNA-mRNA expression. Osteoarthritis and Cartilage 2015 23, 423-432DOI: (10.1016/j.joca.2014.12.001) Copyright © 2014 Osteoarthritis Research Society International Terms and Conditions

Fig. 5 Gene expression changes in human chondrogenic SW1353 cells stimulated with IL-1β. SW1353 cells were treated with IL-1β for 4 h, 12 h and 24 h, and the expression of COL2A1, MMP13 (A) and lncRNA uc.343, HOXC8 (B) was determined by qRT-PCR, compared to 0 h. Gene expression was normalized to GAPDH expression and calculated by 2−ΔΔCt method. Values are the mean ± SD of three different experiments. Data were analyzed using one-way ANOVA followed by Dunnett-t test. **P < 0.01, ***P < 0.001 vs 0 h. Osteoarthritis and Cartilage 2015 23, 423-432DOI: (10.1016/j.joca.2014.12.001) Copyright © 2014 Osteoarthritis Research Society International Terms and Conditions

Fig. S1 GO analysis for differentially expressed mRNAs. A–C. The top 10 highest enriched GO terms in three domains (A. biological process, B. cellular component, C. molecular function) targeted by upregulated transcripts. D–F. The top 10 highest enriched GO terms in three domains (D. biological process, E. cellular component, F. molecular function) targeted by downregulated transcripts. Osteoarthritis and Cartilage 2015 23, 423-432DOI: (10.1016/j.joca.2014.12.001) Copyright © 2014 Osteoarthritis Research Society International Terms and Conditions

Fig. S2 Pathway analysis for differentially expressed mRNAs. A–B. The top 10 highest enriched pathway corresponded to upregulated transcripts (A) and downregulated transcripts (B). C. The schematic diagram of Wnt signaling pathway which is associated with cartilage degeneration. The orange marked nodes are associated with upregulated or only whole dataset genes, yellow marked nodes are associated with downregulated genes, and green nodes have no significance. Osteoarthritis and Cartilage 2015 23, 423-432DOI: (10.1016/j.joca.2014.12.001) Copyright © 2014 Osteoarthritis Research Society International Terms and Conditions

Fig. S3 CNC network of differentially expressed lncRNAs and mRNAs. Only co-expression gene pairs with Pearson coefficient exceeded 0.995 were shown. The co-expression network consists of 106 lncRNAs and 291 mRNAs. The triangular node represents lncRNA and the round node represents a protein-coding RNA (mRNA). Solid lines between two nodes indicate positively correlated interactions between genes, and dotted lines indicate negatively correlated interactions. Osteoarthritis and Cartilage 2015 23, 423-432DOI: (10.1016/j.joca.2014.12.001) Copyright © 2014 Osteoarthritis Research Society International Terms and Conditions

Fig. S4 LncRNAs-TFs-Target Genes network. A number of lncRNAs were predicted to execute trans-regulation through collaboration with TF SP1. The lncRNAs with fold changes >6.0 and their respective trans-regulated target genes that had the highest Pearson correlation coefficients were chosen to construct the network. The red node represents lncRNA, the pink node represents target gene and the green node represents TF SP1. Osteoarthritis and Cartilage 2015 23, 423-432DOI: (10.1016/j.joca.2014.12.001) Copyright © 2014 Osteoarthritis Research Society International Terms and Conditions