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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. 7 — Reactivation of silenced tumor suppressor genes by CRISPRa correlates with phenotypic reprogramming in Hep3B HCC cells. A, B Transcriptional reactivation of four silenced tumor suppressor genes (TSGs), HHIP, MT1M, PZP, and TTC36, targeted individually and simultaneously (MIX 4 genes) by SpdCas9-VPR stably expressed along with the corresponding TSG-gRNA in Hep3B HCC cells. A Data shown as fold log10 change in TSG mRNA levels, evaluated by qRT-PCR, relative to SpdCas9-VPR with no gRNA (NO G). Data presented as means ± SEM (n = 3) and P values were determined by one-way ANOVA with Dunnett's multiple comparisons test (****P < 0.0001, *P = 0.0107). B Heatmap comparing the fold change in mRNA regulation evaluated by qRT-PCR. The TSG-gRNAs are arranged in rows, and the genes in columns. Data presented as means (n = 3). C–F Immunofluorescence of HHIP, MT1M, PZP, TTC36, SpdCas9-VPR, and Hoechst-stained cell-nuclei in stable Hep3B cells expressing SpdCas9-VPR alone (NO G), SpdCas9-VPR targeting HHIP with G4, MT1M with G1, PZP with G2, TTC36 with G3, or SpdCas9-VPR co-targeting all four TSGs (MIX 4 genes). G–I Phenotypic reprogramming in Hep3B cells lentivirally transduced with SpdCas9-VPR targeting and upregulating HHIP with G4, TTC36 with G3, the MIX 4 genes, or with NO G as control. G Cell proliferation assessed by α-Ki-67 immunostaining (green), superimposed on nuclear Hoechst 33258 staining (blue). Data normalized to SpdCas9-VPR NO G, presented as means ± SEM (n = 3), and P values were determined by unpaired t-test (****P < 0.0001, ***P = 0.0003). H Cell viability determined using a luminescence assay (CellTiter-Glo^®). Data shown as fold change compared to SpdCas9-VPR NO G at 24, 48, and 72 h, presented as means ± SEM (n = 3), and P values were determined by unpaired t-test with Welch's correction (****P < 0.0001). I Inhibition of cell migration assessed by the Boyden chamber assay. Data normalized to SpdCas9-VPR NO G, presented as means ± SEM (n = 3), and P values were determined by unpaired t-test (*P = 0.0390, ****P < 0.0001, ***P = 0.0008)