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. 2023 Apr 29;15:73. doi: 10.1186/s13148-023-01482-0

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© The Author(s) 2023

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 2 — Epi-drugs reactivate a subset of tumor suppressor genes in Hep3B and HuH-7 HCC cell lines. A Heatmap of the 12-tumor suppressor gene (TSG) panel comparing the mRNA expression in Hep3B and HuH-7 HCC cell lines versus normal hepatocytes. Gene expression was evaluated by qRT-PCR. Red color indicates the least expressed (cycle threshold 40) and blue color the highest expressed (cycle threshold 20) genes. Data are means (n = 3). B, C Transcriptional regulation of the 12-TSG panel 72 h after 5-aza treatment at different concentrations, indicated by color, in Hep3B and HuH-7 cells, respectively. The data show the fold log10 change in TSG mRNA levels relative to vehicle-treated cells. From left to right, for Hep3B cells: BCO2: *P = 0.000017, 0.000189, 0.000237, 0.000041, 0.000036; CDKN2A: *P = 0.001726, 0.000067, 0.000965, 0.000064, 0.000066; CPS1: *P = 0.000004, 0.000004, 0.000009, 0.000004, 0.000005; HHIP: *P = 0.001481, 0.032448, 0.003285; miR-122-5p: *P = 0.000884, 0.009364, 0.009338, 0.021386; MT1E: *P = 0.013894, 0.000860, 0.008483, 0.001014, 0.021049; MT1M: *P = 0.001025, 0.000295, 0.004843, 0.007027, 0.000230; PSAT1: *P = 0.011710, 0.020228, 0.004350; PTGR1: *P = 0.000021, 0.000004, 0.000007, 0.000130, 0.000010; PZP: *P = 0.000595, 0.018607, 0.000256, 0.006314; TMEM106A: *P = 0.000067, 0.000002, 0.000175, < 0.000001, 0.002216; and TTC36: *P = 0.003576, 0.001630, 0.001968, < 0.000001. For HuH-7 cells: BCO2: *P = 0.000234, 0.000074, 0.009780, 0.002345, 0.000073; CDKN2A: *P = 0.002474, 0.002569, 0.004410, 0.001787, 0.000041; CPS1: *P = 0.000012, 0.000018, 0.000023, 0.000031, 0.000052; HHIP: *P = 0.011967, 0.008680, 0.000309, 0.000009; miR-122-5p: *P = 0.002266, 0.001959, 0.002015, 0.001671, 0.002592; PSAT1: *P = 0.009506, 0.012759, 0.022472, 0.020526; PTGR1: *P = 0.008993, 0.000421, 0.002261, 0.000051; PZP: *P = 0.000718, 0.012523, 0.000963, 0.000180, 0.001813; TMEM106A: *P = 0.000001, 0.000003, 0.000603, 0.000005, 0.000717; and TTC36: *P = 0.012646, 0.000005, 0.002686, < 0.000001, 0.000026. D, E Transcriptional regulation of the 12-TSG panel 48 h after SAHA treatment at different concentrations, indicated by color, in Hep3B and HuH-7 cells, respectively. The data show the fold log10 change in TSG mRNA levels relative to vehicle-treated cells. From left to right, for Hep3B cells: BCO2: *P = 0.000006, < 0.000001, 0.000511; CPS1: *P = 0.000209, 0.000020, 0.000003; HHIP: *P = 0.003836, 0.000015; MT1E: *P = 0.004923, 0.005036; MT1M: *P = 0.001981, 0.001938, 0.003620; PSAT1: *P = 0.000809; PTGR1: *P = 0.000052, 0.000013, 0.000023; TMEM106A: *P = 0.001558, 0.002973; and TTC36: *P = 0.000448. For HuH-7 cells: BCO2: *P = 0.000019, 0.000023, 0.000054; CDKN2A: *P = 0.000785, 0.000030, 0.000190; CPS1: *P = 0.000156, < 0.000001; HHIP: *P = 0.005756; miR-122-5p: *P = 0.000968, 0.001295; MT1E: *P = 0.002001; PTGR1: *P = 0.000127; and TMEM106A: *P = 0.000221, 0.001073, 0.001910. The data presented as means ± SEM (n = 3), and P values were determined by multiple unpaired t-test comparisons with a two-stage linear step-up procedure of Benjamini, Krieger, and Yekutieli