Fig. 4: Depletion of NKX6.3 leads to DNA copy number alterations.
A Cumulative copy-number frequencies for HFE-145shNKX6.3#1 and HFE-145shNKX6.3#2 compared to HFE-145shCtrl cells. Numbers above the graph (x-axis) denote chromosomes, while frequency (y-axis) denotes the proportion of gain (red) or loss (blue) at the respective chromosomal position. B Whole-genome evaluation of CNAs in HFE-145shNKX6.3#1 and HFE-145shNKX6.3#2 compared to HFE-145shCtrl cells is ordered sequentially by chromosomes represented by different colors. In the Log2 gene frequency graph, noticeable copy number gains and losses are displayed in red boxes. C Copy number gains (left) or losses (right) gene signatures were involved in 15 or 14 hallmark enrichments, respectively. D Loss of DNA copy number in chromosome 4, including SORBS2 and SPACL1, in HFE-145shNKX6.3#1 and HFE-145shNKX6.3#2 compared to HFE-145shCtrl cells (left). In FISH assay, loss of SORBS2 and SPACL1 gene was detected in HFE-145shNKX6.3#1 and HFE-145shNKX6.3#2 cells (right). E Gain of DNA copy number in chromosome 14, including DLGAP5 and CDKN3, in HFE-145shNKX6.3#1 and HFE-145shNKX6.3#2 compared to HFE-145shCtrl cells (left). Gain of DLGAP5 and CDKN3 gene was detected in HFE-145shNKX6.3#1 and HFE-145shNKX6.3#2 cells using FISH assay (right). F, G Depletion of NKX6.3 reduced DNA copy number and mRNA expression of SORBS2 and SPARCL1 (F) but increased DNA copy number and mRNA expression of DLGAP5 and CDKN3 (G) (n = 3). H Immunoblot of SORBS2, SPARCL1, DLGAP5, and CDKN3 in NKX6.3-depleted cells.
