Fig 2: Evaluation of Hepatic Differentiation in HCC Cells after DNMT1 Knockdown(A) Expression of DNMT1 in clinical liver samples. The expression levels of DNMT1 in 20 primary HCC tumors and their corresponding paired non-tumorous tissues were determined by RT-qPCR. The Wilcoxon signed-rank test was used to evaluate the p value. DNMT1 and ALB protein levels in (B) epigenetically reconditioned and (C) DNMT1-knockdown HepG2 cells. Proteins were extracted 8 days after transfection. ß-Tubulin was used as a loading control for immunoblots. Two distinct siRNAs were used to specifically target DNMT1 (siDNMT1_A and siDNMT1_B), and two scrambled siRNAs were used as negative controls (siCtrl_A and siCtrl_B). (D) CYP3A4 and CYP1A2 activity assay in the DNMT1-knockdown cells. Five days after transfection, HepG2 cells were treated with 25 µM dexamethasone for 72 hr, and the induced activities were measured. (E) Relative expression of ALB, NTCP, CYP3A4, and miR-122 following DNMT1 silencing in HepG2 and Hep3B cells. Gene expression levels were measured 6 and 8 days after transfection. (F) COBRA analysis of the ALB, NTCP, CYP3A4, and miR-122 genes after DNMT1 knockdown. Genomic DNA was extracted from HepG2 and Hep3B cells 6 and 8 days after cell transfection. Representative data from three COBRA experiments are shown for each gene. The data represent the mean ± SD. Statistical significance relative to the siCtrl-transfected cells: *p < 0.05; **p < 0.01; ***p < 0.001 (t test). M, methylated; U, unmethylated.

Fig 3: Characterization of HSA-DKK2C2 variants. (A) Reducing SDS-PAGE stained with SimplyBlue SafeStain examining purified HSA-DKK2C2 variants. Lanes 1 and 20: molecular weight standards; Lane 2: wild type HSA-DKK2C2 ACE464; Lane 3: BKM225; Lane 4: BKM226; Lane 5: BKM227; Lane 6: BKM228; Lane 7: BKM229; Lane 8: BKM230; Lane 9: BKM231; Lane 10: BKM232; Lane 11: BKM233; Lane 12: ACE502; Lane 13: ACE504; Lane 14: ACE505; Lane 15: ACE506—pH 5.5 purification; Lane 16: ACE506—pH 6.5 purification; Lane 17: ACE507—pH 5.5 purification, glycosylated form; Lane 18: ACE507—pH 5.5 purification, hypo-glycosylated form; Lane 19: ACE507—pH 6.5 purification. (B) Approximately 4 µg of wild-type HSA-DKK2C2 and each of the variants were analyzed by native PAGE under non-reducing conditions and stained with SimplyBlue SafeStain. Lane 1: wild type HSA-DKK2C2 ACE464; Lane 2: BKM225; Lane 3: BKM226; Lane 4: BKM227; Lane 5: BKM228; Lane 6: BKM229; Lane 7: BKM230; Lane 8: BKM231; Lane 9: BKM232; Lane 10: BKM233; Lane 11: ACE502; Lane 12: ACE504; Lane 13: ACE505; Lane 14: ACE506—pH 5.5 purification; Lane 15: ACE506—pH 6.5 purification; Lane 16: ACE507—pH 5.5 purification, glycosylated form; Lane 17: ACE507—pH 5.5 purification, hypo-glycosylated form; Lane 18: ACE507—pH 6.5 purification. Direction of anode (-) and cathode (+) is indicated. (C) A graphical depiction of the DSF profiles of selected HSA-DKK2C2 mutants. Thermal denaturation profiles for the six mutants BKM229 (brown); ACE505 (magenta); BKM228 (cyan); ACE504 (green); ACE506 (orange); and BKM233 (blue), and wild type HSA-DKK2C2 ACE464 (red), from 25°C to 95°C. (D) A graphical depiction of the results of heparin–biotin ELISA for selected HSA-DKK2C2 mutants. Titrations curve for biotin–heparin binding to HSA-DKK2C2 mutants plated at 15 µg/ml. Detection was at 450 nm with streptavidin-horseradish peroxidase. Illustrated is a representative of duplicate experiments for these variants. (E) A graphical depiction of the results of HSA-DKK2C2 mutant competition with anti-LRP6 antibody for binding to LRP6. LRP6 binding curves for HSA-DKK2C2 molecules impaired for either heparin or LRP6 binding (BKM195 and BKM199), following competition with anti-LRP6 monoclonal antibody. (F) A graphical depiction of percent canonical Wnt pathway activation in STF assay by Wnt3a in response to varying concentrations of wild type HSA-DKK2C2 ACE464 (red) and selected HSA-DKK2C2 variants. Plotted are the average values from triplicate experiments. (G) Bar graph depicting the ratio of phosphorylated LRP6 to total LRP6 detected by Western blotting for cells treated with each of the six HSA-DKK2C2 variants. This experiment was performed at three concentrations of DKK2C2 molecule (250, 500 or 1000 nM). Plotted values are depicting values generated from incubation with 1000 nM. (H) PK analysis of HSA-DKK2C2 variants. A bar graph depicting average serum levels from 2 or 3 mice intravenously dosed with 10 mg/kg of HSA-DKK2C2 molecules 24 h postinjection. Variants were detected by quantitative western blotting and quantified against a standard curve of wild type HSA-DKK2C2 ACE464 in serum. In D–H wild type refers to ACE464.

Fig 4: Hepatospecific Gene Expression and Drug-Metabolizing Activity in Epigenetically Reconditioned HCC Cells(A) Expression levels of four characteristic liver marker genes (ALB, SLC10A1, CYP3A4, and miR-122) in clinical samples. Boxplots illustrate the differential gene expression between 20 primary HCC samples (T) and their corresponding paired non-tumor tissues (NT). Mann-Whitney U tests were used to calculate p values. (B) Experimental design for evaluating liver gene expression and drug-metabolizing activity in HCC cells after epigenetic reconditioning. (C) Expression levels of selected hepatospecific genes in epigenetically reconditioned HepG2 and Hep3B cells. Total RNA was extracted after reconditioning with 2 µM 5-AZA for 12 days and 3 and 5 days of culture without 5-AZA (T1 and T2, respectively). The relative mRNA expression levels were determined by RT-qPCR. Non-reconditioned HCC cells were used as controls. (D) Relative levels of the AFP, CDH1, G6Pc, TAT, CYP1A2, and HNF4A mRNAs measured by RT-qPCR in the control and reconditioned HCC cells. (E) Evaluation of CYP3A4 and CYP1A2 enzyme activity. CYP activities were induced by treatment with 25 µM dexamethasone for 72 hr before assessment. All data shown in the figure represent the mean ± SD. Statistically significant differences in gene expression and CYP activity levels were achieved at *p < 0.05, **p < 0.01, and ***p < 0.001 (t test).

Fig 5: Colocalization of AGE-albumin and activated microglial cells in substantia nigra (SN) and cortex of human Parkinson’s disease (PD).Notes: (A) Triple immunostaining of AGE (blue), albumin (green), and Iba1 (red, activated microglial cell marker) in SN of normal and human PD patients. Merged image shows that AGE, ALB, and Iba1 were colocalized mostly in human PD patient brain. Fluorescence expression level (B) and colocalization coefficient (C) analyzed by densitometric analysis software using Zen software (Carl Zeiss Meditec AG). (D) Triple immunostaining of AGE (blue), albumin (green), and Iba1 (red) in cerebral cortex of PD patients. Merged image shows that the labeling of AGE, ALB, and Iba1 was similarly localized in cerebral cortex of human PD brain. Fluorescence expression level (E) and colocalization coefficient (F) were analyzed by densitometric analysis software using Zen software. Scale bar =50 µm. *P<0.05, **P<0.01, and ***P<0.001.Abbreviations: AGE, advanced glycation end product; ALB, albumin; Iba1, ionized calcium binding adaptor molecule 1.