Journal: Nature Communications

Article Title: Epigenetic modulation with nanosatellite triggers tumoricidal immunity for hepatocellular carcinoma treatment

doi: 10.1038/s41467-025-61974-w

Figure Lengend Snippet: a A boxplot of YTHDF1 expression in HCC patients and healthy people isolated from TCGA and Genotype-Tissue Expression determined by Gene Expression Profiling Interactive Analysis. The data were transformed as log2(TPM + 1). Normal: maxima 4.7099, minima 2.0076, center 3.4694; Tumor: maxima 5.6854, minima 2.3564, center 3.9079. Color key: red, HCC tissues; blue, normal liver tissues. YTHDF1 displays negative associations with ( b ) disease-free survival in HCC patients. c The prognostic significance of YTHDF1 in HCC patients. Number at risk refers to the number of patients in each experimental group who remain event-free at the specified time points and are still at risk of reaching the study endpoint. d The correlation between YTHDF1 and immune score. e YTHDF1 expression at the mRNA and protein levels in Huh7 and Hepa1-6 cells, with hepatocytes freshly isolated from C57BL/6 mice serving as the control ( n = 3 independent experiments). f Schematic illustration of the role of the dynamic locking stEiNS in HCC tumor, which regulates the epigenetic modifications of both tumor cells and M2Φs to enhance the effectiveness of immunotherapy against HCC. Data are expressed as mean ± SD and were determined using one-way analysis of variance (ANOVA) followed by Tukey’s multiple comparisons test. **** P < 0.0001.

Article Snippet: Hepa1-6 and Huh7 cell lines were obtained from ATCC.

Techniques: Expressing, Isolation, Gene Expression, Transformation Assay, Control

Journal: Nature Communications

Article Title: Epigenetic modulation with nanosatellite triggers tumoricidal immunity for hepatocellular carcinoma treatment

doi: 10.1038/s41467-025-61974-w

Figure Lengend Snippet: a , b Confocal images and ( c ) flow cytometric analysis illustrating the in vitro internalization of s-Cy3EiNS after 12 h of incubation with Huh7 and Hepa1-6 cells, with siYTHDF1 labeled with Cy3 ( n = 3 independent experiments). Scale bar, 20 µm. d YTHDF1 Cy3+ ratio in Huh7 and Hepa1-6 cells treated with various formulations ( n = 3 independent experiments). e Mean fluorescence intensity (MFI) ratio of YTHDF1 Cy3+ in Huh7 and Hepa1-6 cells across different treatment groups ( n = 3 independent experiments). Confocal images showing subcellular localization in ( f ) Huh7 and ( g ) Hepa1-6 cells incubated with s-Cy3EiNS for 1, 3, and 6 h at 37 °C ( n = 3 independent experiments). Nuclei were stained with DAPI (blue), endo/lysosomes with LysoTracker Green (green), and siYTHDF1 with Cy3 (red). h , i Quantitative co-localization analysis of S-Cy3 with endo/lysosomes labeled by LysoTracker Green ( n = 3 independent experiments). j Schematic illustration of deep tumor penetration of s-Cy3EiNS in 3D tumorspheres. Created in BioRender. Y.Q. (2025) https://BioRender.com/r8jogdb . k Representative CLSM images showing enhanced penetration of sEiNS compared to Lipo/s in Huh7 and Hepa1-6 tumorspheres ( n = 3 independent experiments). Scale bar, 100 µm. l The IVIS imaging and ( m ) fluorescence intensity quantification at various time points in mice with subcutaneous Hepa1-6 tumors (tumors marked with white circles, n = 3 mice per group). EiNS(-M2Φpep), EiNS without M2Φpep modification. Data are expressed as mean ± SD. Statistical significance was determined using one-way ANOVA followed by Tukey’s multiple comparisons test ( d , e , h , i ), or two-way ANOVA ( m ). * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001.

Article Snippet: Hepa1-6 and Huh7 cell lines were obtained from ATCC.

Techniques: In Vitro, Incubation, Labeling, Fluorescence, Staining, Imaging, Modification

Journal: Nature Communications

Article Title: Epigenetic modulation with nanosatellite triggers tumoricidal immunity for hepatocellular carcinoma treatment

doi: 10.1038/s41467-025-61974-w

Figure Lengend Snippet: a YTHDF1 mRNA expression levels in Huh7 and Hepa1-6 cells following treatment with diverse nanomedicines ( n = 3 independent experiments). b YTHDF1 protein expression levels in Huh7 and Hepa1-6 cells after exposure to various nanomedicines ( n = 3 independent experiments). Cell viability of ( c ) Huh 7 and ( d ) Hepa1-6 cells assessed by MTT assay following treatment with various formulations ( n = 3 independent experiments). e Representative images and ( f ) quantification of clonal assay in Huh7 and hepa1-6 cells with treatment of various formulations were presented ( n = 3 independent experiments). g , h Apoptosis analysis and statistical evaluation of apoptosis rates in Huh7 and Hepa1-6 cells treated with sPPN, sEiNS, and Lipo/s for 24 h ( n = 3 independent experiments). i Treatments of HCC patients-derived PDOs in different treatment groups ( n = 3 independent experiments). Scale bar, 100 µm. Data are expressed as mean ± SD. Statistical significance was determined using one-way ANOVA followed by Tukey’s multiple comparisons test ( a , f , g ), or two-way ANOVA ( c , d ). * P < 0.05, ** P < 0.01, *** P < 0.001, **** P < 0.0001.

Article Snippet: Hepa1-6 and Huh7 cell lines were obtained from ATCC.

Techniques: Expressing, MTT Assay, Clone Assay, Derivative Assay

Journal: Nature Communications

Article Title: Epigenetic modulation with nanosatellite triggers tumoricidal immunity for hepatocellular carcinoma treatment

doi: 10.1038/s41467-025-61974-w

Figure Lengend Snippet: a KEGG analysis of the differential expression genes under TYHDF1 deletion in HCC cells. b GSEA showing the association between YTHDF1 expression and NF-κB pathway activity in HCC. c Effects of YTHDF1 on the NF-κB/caspase 3 signaling pathway ( n = 3 independent experiments). d , e Immunofluorescence showing YTHDF1 (pink) and p-p65 (green) localization in PDOs ( n = 3 independent experiments). Nuclei were stained with DAPI (blue). Scale bar, 50 µm. f The sequence logo plot showed the sequence conservation of NF-κB, as well as predicted score and binding sequences of five chemokines with NF-κB. Quantitative analysis of the CCL2, CCL5, CCL20, CXCL2, and CXCL12 secreted by ( g ) Huh7 and ( h ) Hepa1-6 cells in the medium after treatment with different formulations for 24 h ( n = 4 independent experiments). i CUT&RUN-qPCR analysis confirmed that NF-κB could bind to CCL2 promoter region in Huh7 and Hepa1-6 cells ( n = 3 independent experiments). Data are expressed as mean ± SD and were determined using two-tailed Student’s t test. ns P ≥ 0.05, * P < 0.05, ** P < 0.01.

Article Snippet: Hepa1-6 and Huh7 cell lines were obtained from ATCC.

Techniques: Quantitative Proteomics, Expressing, Activity Assay, Immunofluorescence, Staining, Sequencing, Binding Assay, Two Tailed Test