Fig. 1: Characterization of lncRNA expression in the TCGA data set and in an institutional data set, with a specific focus on ZFAS1. | Cell Death Discovery

Fig. 1: Characterization of lncRNA expression in the TCGA data set and in an institutional data set, with a specific focus on ZFAS1.

From: Long non-coding RNA ZFAS1 is a major regulator of epithelial-mesenchymal transition through miR-200/ZEB1/E-cadherin, vimentin signaling in colon adenocarcinoma

Fig. 1

a Example of a hematoxylin and eosin slide that was used as a guide for laser capture microdissection of the tissue from the University of Louisville Biorepository. b Fold regulaton of each of the seven selected lncRNAs examined by RTqPCR from LCM tissue from the University of Louisville Biorepository; FAM83H-AS1 (FR = −3.68, *p < 0.001), FER1L4 (FR = −2.22 p = 0.12), GAS5 (FR = 1.70, **p = 0.021), H19 (FR = −1.67, p = 0.84), PVT1 (FR = 2.75, ***p = 0.003), UCA1 (FR = −4.85, *p < 0.001), ZFAS1 (FR = 3.06, *p < 0.001), (n = 23 paired samples). c Scatter plot of ZFAS1 expression in colon cancer compared to paired normal colon epithelium examined by RTqPCR from LCM tissue from the University of Louisville Biorepository (n = 23 paired institutional samples) (FC = 3.06, *p < 0.001). d Heatmap comparing the differential expression (RSEM quantification) between paired colon adenocarcinoma and normal colon epithelium of the seven lncRNAs using RNAseq expression data from the Cancer Genome Atlas (n = 40 paired samples). e Increased ZFAS1 expression in cancer compared to paired normal colon epithelium in the GEO GSE95132 RNA-seq dataset (n = 10 paired samples, RNA-seq expression, units=TPM) (Ϯp = 0.009). f Increased expression of ZFAS1 in cancer compared to paired normal colon epithelium in the GEO GSE104836 RNA-seq dataset (n = 10 paired samples, units = normalized RNAseq expression) (Ϯp = 0.009). g Increased expression of ZFAS1 in colon cancer compared to unpaired colon epithelium in the GEO GSE103512 array dataset (n = 70 Affymetrix array expression, units = normalized Affymetrix array) (*p < 0.001). h There is increased ZFAS1 expression with copy number gain and copy number amplification compared to diploid in the RNAseq TCGA data set (n = 388) (*p < 0.001, Ϯp < 0.009). i There is no difference in the overall clinical patient survival between high and low ZFAS1 expression in the RNAseq TCGA data set (n = 192) (RNA-seq expression data dichotomized on basis of median expression) (p = 0.11). All RTqPCR experiments were run in duplicate.

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