Extended Data Fig. 3: Immunofluorescence screen for differential levels of epigenetic marks.
From: NSD2 targeting reverses plasticity and drug resistance in prostate cancer
a, Immunostaining of indicated epigenetic marks in NPPO-1 organoids. Images are shown in pairs, with and without co-staining for Vimentin (VIM). CHGA, Chromogranin A; SYP, Synaptophysin. Scale bars, 50 µm. b, Scatter plots show quantitation of epigenetic mark levels, comparing fluorescence intensity in neuroendocrine (NE) and non-neuroendocrine (nonNE) cells in three replicate experiments. Data points indicate mean ± s.d. (biological replicates for NE and nonNE cells: H2AK119Ub n = 45, 37; H2BK120Ub n = 32, 32; H3K4me1 n = 74, 36; H3K4me3 n = 40, 23; H3K9me2 n = 65, 28; H3K9me3 n = 31, 27; H3K18Ac n = 30, 25; H3K27Ac n = 50, 24; H3K27me3 n = 34, 22; H3K36me3 n = 41, 26; H3K79me2 n = 39, 23; 5-Methylcytosine n = 38, 27; 5-Hydroxymethylcytosine n = 25, 25). Mean fluorescence intensities were compared by unpaired t-tests (two-tailed); comparisons lacking p-values were not significant. c, Box and whiskers plots show NSD1, NSD2, and NSD3 expression levels (log10 transformed count/million (CPM)) in samples of CRPC-adeno (n = 34) and CRPC-NE (n = 15) based on data from20. Data are expressed as median and interquartile (IQR) ranges (n = 15 biological replicates, CRPC-NE; n = 34 biological replicates, CRPC-Adeno); whiskers show Min to Max, and all points are shown. Unpaired t test (two-tailed) was used for comparison between two groups. d,e, Violin plots show NSD1, NSD2, and NSD3 expression in the single-cell RNA-seq dataset from25. Pairwise statistical comparisons between subtypes were performed using the non-parametric Mann-Whitney U test (two-sided).
