Fig. 4: Characterization of NFYC-AS1 knockdown phenotype by Gapmer ASOs. | Cell Death & Disease

Fig. 4: Characterization of NFYC-AS1 knockdown phenotype by Gapmer ASOs.

From: The pancancer overexpressed NFYC Antisense 1 controls cell cycle mitotic progression through in cis and in trans modes of action

Fig. 4

A Bar plot showing NFYC-AS1 expression measured through qRT-PCR using primer 4 (Pr4) and primer 6 (Pr6) at 48 h after 5 nM Gapmer transfection in H520 RB1-wt cells. Data are NEG-normalized and reported as mean ± sd as from multiple independent biological replicates (n indicated in Supplementary Table S11). B Cell counts at different timepoints after NFYC-AS1 Gapmer-knockdown, normalized against the NEG at 72 h in H520 cells. Data reported as mean ± se, as from n = 3 independent biological replicates. C Bar plot showing NFYC-AS1 and CCND1 expression levels (qRT-PCR) in H520 cells seeded at different cell densities, normalized against the lowest confluency. Data reported as mean ± sd, as from n = 3 independent biological replicates. Jonckheere-Terpstra test p-values are shown. D Heatmap reporting NES (FDR < 0.10 for all three Gapmers) of cancer hallmarks (GSEA) for genes differentially expressed in Gapmer-transfected H520 cells (allGap = all Gapmers vs NEG). E Heatmap reporting NES (FDR < 0.10) of cancer hallmarks (GSEA) for genes ranked for correlation with NFYC-AS1 in LUSC cells (CCLE). F GSEA plots of genes related to lung cancer vulnerabilities [34] or G synthetic lethal in RB1-mut cells [35] in genes modulated upon NFYC-AS1 Gapmer-silencing. H Bar plot showing NFYC-AS1 expression (qRT-PCR) at 48 h after 25 nM Gapmer transfection in H82 RB1-mut cells. Data are NEG-normalized and reported as mean ± sd, as from n = 4 independent biological replicates. I Cell counts at different time points after NFYC-AS1 Gapmer-knockdown, normalized against NEG at 72 h in H82 cells. Data reported as mean ± se, as from n = 6 independent biological replicates. J Progression-free survival curve stratified according to Cutoff Finder-determined threshold (63.72) for NFYC-AS1 in LUSC patients (TCGA). Log-rank test p-value and hazard risk (HR) are shown. *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001, ns (non-significant). One sample t-test p-values are reported for panels A, B, H, and I.

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