Extended Data Fig. 2: PROX1 induces chromatin closure and growth delays in mouse HCC cell lines.
a, PROX1 protein level in liver sections from patients with HCC (n ≥ 3). b,c, Inducible PROX1 overexpression (OE; b) and knockdown (shPROX1; c) in Hep3B cells at day 2 compared to control (Ctr) by qRT-PCR (n = 6 each). d, MA-plot of ATAC-seq differentially accessible regions (DARs) upon PROX1 OE in Hep3B cells at day 2 (n = 3). e, PCA of DARs in d labeled by condition and replicate. f, Genomic annotations of chromatin peaks closed upon PROX1 OE compared to control determined by GREAT. g, IGV tracks of PROX1 binding by CUT&RUN and ATAC-seq accessibility change at the MYC locus in Hep3B cells 2 days after PROX1 OE compared to control (n = 3 each). h, GSEA normalized enrichment scores (NES) for MYC targets and apoptosis upon inducible PROX1 OE for 7 days in Hep3B cells or 2 days in Myc/Trp53 HCC mouse models (day 16 collection; n = 3 each). i, Doxycycline dose-dependent Prox1 OE in mouse tumor-derived cell lines transformed with Trp53 KO with OE of Myc (Myc/Trp53; n = 2) or Kras(G12D) (Kras/Trp53; n = 3) determined by western blot at day 3. j, Quantification of PROX1 protein levels of cells treated as in i. k, Confluency of cells treated as in i normalized to uninduced controls. Scale bar = 100 µm (a). Bar graphs show mean with error bars = SD, boxplots show median and interquartile range (IQR), whiskers = 1.5× IQR, from indicated biological replicates. Two-sided t test (b,c), unpaired t test (j) or one-sample t test (k). P values are displayed.
