# Berberine Suppresses EMT in Liver and Gastric Carcinoma Cells through Combination with TGFβR Regulating TGF-β/Smad Pathway

Authors: Haiyan Du; Jiangyong Gu; Qin Peng; Xiaolan Wang; Lei Liu; Xuanyu Shu; Qiuying He; Yuhui Tan
Journal: Oxidative Medicine and Cellular Longevity
 (2021)

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## Abstract

Berberine (BBR), a natural alkaloid derived from Coptis, has anticancer activity. Some researchers have found that it could restrain epithelial-mesenchymal transition (EMT) of melanoma, neuroblastoma, and other tumor cells. However, it is unclear whether BBR can reverse EMT in hepatocellular carcinoma (HCC) and gastric carcinoma (GC). In our study, BBR inhibited the migration and invasion of HepG2, MGC803, and SGC7901 cells in a dose-dependent manner. Transcription sequencing assays showed that Vimentin, MMP, and Smad3 were downregulated, but Smad2, Smad6, TAB2, ZO-1, and claudin 7 were upregulated when treated with BBR. GO Enrichment analysis of KEGG pathway showed that BBR significantly inhibited TGF-β/Smad at 12 h, then, PI3K/Akt and Wnt/β-catenin signaling pathways at 24 h, which were closely related to the proliferation, migration, and EMT. The results of the transcriptome sequencing analysis were verified by Western Blot. It showed that the expression of epithelial marker E-cadherin and ZO-1 remarkably augmented with BBR treatment, as well as declined mesenchymal markers, including N-cadherin and Vimentin, decreased transcription factor Snail and Slug. The effects of BBR were similar to those of the PI3K inhibitor LY294002 and TGF-β receptor inhibitor SB431542. Furthermore, β-catenin and phosphorylation of AKT, Smad2, and Smad3 were changed dose-dependently by BBR treatment, which upregulated p-Smad2 and downregulated the others. Combined with LY or SB, respectively, BBR could enhance the effects of the two inhibitors. Simultaneously, IGF-1 and TGF-β, which is the activator of PI3K/AKT and TGF-β/Smad, respectively, could reverse the anti-EMT effect of BBR. The Molecular Docking results showed BBR had a high affinity with the TGF-β receptor I (TGFβR1), and the binding energy was -7.5 kcal/mol, which is better than the original ligand of TGFβR1. Although the affinity of BBR with TGF-β receptor II (TGFβR2) was lower than the original ligand of TGFβR2, the more considerable negative binding energy (−8.54 kcal/mol) was obtained. BBR upregulated p-Smad2, which was different from other reports, indicating that the function of Smad2 was relatively complex. Combination BBR with SB could enhance the effect of the inhibitor on EMT, and the results indicated that BBR binding to TGFβR was not competitive with SB to TGFβR since different binding amino acid sites. Our experiments demonstrated BBR increased p-Smad2 and decreased p-Smad3 by binding to TGFβR1 and TGβFR2 inhibiting TGF-β/Smad, then, PI3K/AKT and other signaling pathways to restrain EMT, metastasis, and invasion in tumor cells. The effect of BBR was similar on the three tumor cells.


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## Body

## 1. Introduction

HCC and GC are the most life-threatening tumor [1–3]. Advanced HCC and GC remain poor prognosis of patients, mainly due to cancer metastasis, of which the mechanism is unclear. Moreover, tumor metastasis is the leading cause of death in patients. When some malignant tumor were early diagnosed, the local invasion and metastasis have already occurred [4–6], and metastasis to vital organs such as the liver, lung, and brain, which is a significant cause of death from malignant tumor [7, 8].In general, epithelial-to-mesenchymal transition (EMT) is regarded as an essential process for metastasis and invasion of malignant tumor cells, downregulated tumor epithelial marker expression and upregulated mesenchymal marker expression, the connection between cells decreases, and cell vitality enhances. E-cadherin, ZO-1 (tight junction-associated protein 1), and Claudin 7 are proteins related to cell adhesion and connection, which are epithelial markers negatively related to EMT. N-cadherin, Vimentin, Snail, and Slug are mesenchymal markers with an increased expression. Furthermore, Snail and Slug are transcription factors positively related to EMT. It is demonstrated that tumor metastasis could be inhibited by reversing the EMT process and restraining EMT activation to improve the prognosis of cancer patients [9–14].BBR is a natural isoquinoline alkaloid and has pharmacological effects on anti-inflammation and antitumor [13–20]. BBR has been used in China longstanding to treat gastrointestinal tract diseases. A multicentre, double-blinded, randomised controlled, clinical study demonstrated that BBR could prevent the recurrence of colorectal adenoma [21]. More than 100 manuscripts of BBR-antitumor were searched by Pubmed, but most of them focus on inhibition of proliferation and inducing apoptosis of cancer cells. Only 24 articles researched BBR inhibiting EMT through PI3K, ERK, Wnt/β-catenin, and other signaling pathways in intestinal, lung, nasopharyngeal cancer cells, etc. [22–30], only 5 of them related to TGFβ/Smad pathway [31, 32]. Coptis is often used for liver and gastrointestinal diseases in TCM clinical practice [33]. Therefore, our manuscript is aimed at exploring whether BBR has the effect of reversing EMT, antimetastasis in HCC and GC, and the molecular mechanism of TGF-β/Smad pathway. TGF-β/Smad pathway has been widely divergent and puzzled. It was described as inhibiting tumor in early phase and promoting cancer in advanced phase [34]. It was unclear that Smad2 plays the roles in the signaling pathway. Some papers showed that Smad2 and Smad4 played opposite role to previous studies [35]. We selected liver and gastric cancer to study the effects of BBR on migration, invasion, EMT, and TGF-β/Smad signaling pathway, so as to provide a reference for clinical application.


## 2. Materials and Methods

### 2.1. Cell Culture and Drug Configuration

The human GC cell lines MGC803, SGC7901, and HCC cells HepG2 were donated by the Laboratory of Molecular Oncology, Guangzhou University of Chinese Medicine. The cells were grown in DMEM (high glucose), supplemented with 10% fetal bovine serum (FBS) (Excell Biol Inc., Shanghai, China) and 0.5% antibiotics, at 37°C with 5% CO2 incubator. The H-DMEM was purchased from Gibco (Carlsbad, CA, USA). BBR was dissolved in DMSO and diluted with culture medium to ensure the final containing DMSO was less than 0.1%. For BBR treatment, 40 mM BBR was prepared in DMSO and then diluted into the desired concentrations with the H-DMEM medium.


### 2.2. Cell Viability Assays

MTT assay was assessed to investigate the effect of BBR on cell viability. Cells were plated2×103 cells/well in a 96-well plate, then, cultured with concentrations BBR (10, 20, 40, 80, 160, and 320 μM). Cell growth was measured using an MTT assay for 24 h, 48 h, added with MTT (5 mg/ml, Sigma) for an additional 4 h. The supernatant was removed and added to 150 μl DMSO. The optical density (OD) was detected by using microplate spectrophotometer (Bio-Rad Laboratories, Inc.) at 490 nm. We evaluated the cell viability Cellviability=1−ODtreatment/ODcontrol100%.


### 2.3. Wound Healing Assay

Cells (60×105 cells/well) were seeded and cultured overnight, serum-starved for 6 h. The wound was manually scratched in the monolayer using a 20 μL pipette, washed with PBS, and digitally photographed for the 0 h time point using an inverted microscope equipped with a digital camera (Olympus, Hamburg, Germany). Next, cells were cultured in BBR (10, 20, and 40 μM) for 24 h. Image-Pro Plus software 6.0 (Bethesda, MD, USA) was used to measure the area ratio.


### 2.4. Transwell Assays

2×104 cells/well were planted in 200 μL of serum-free DMED in the upper chambers, 800 μL of DMEM (15% FBS) were added to the lower chambers. Incubation for overnight is treated with different concentrations of BBR on the upper chambers for 24 h. Cells on the upper chamber were meticulously wiped off with a cotton swab and invaded cells fixed with 4% paraformaldehyde for 30 min, last, 0.1% crystal violet stained with cells. The invading cells were enumerated by using a digital image analysis system (Image-Pro Plus 6.0, Media Cybernetics, Bethesda, MD, USA).


### 2.5. Transcriptome Sequencing Assay

HepG2 cells (2×105 cells/well) were seeded in plates overnight, treated with BBR (40 μM) 12 h and 24 h, respectively, then, added 1 ml of trizol 10 min, and collected in EP tube. Last, the samples were preserved in -80°C. Transcriptome sequencing technology performed by Shanghai Yasunari biotechnology company. They give the corresponding results GO analysis of RNA-seq data using the DAVID bioinformatics resource and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway in a month. Enrichment analysis was completed utilizing the DAVID program (https://david.ncifcrf.gov/).


### 2.6. Immunofluorescence Assay

Cells were planted3×104 cells/well in glass slides and incubated plate at 37°C atmosphere overnight. Then, treated with different concentrations of BBR for 24 h, the cells were fixed with 4% paraformaldehyde for 30 min, incubated in the blocking buffer 5% BSA and 1% Triton X-100 in PBS for 2 h, following incubated 4°C overnight with antivimentin antibody (Cell Signaling Technology, USA). After rinsing, the cell was incubated the fluorescent secondary antibody for 1 h, and nuclei were stained with 4 0,6-diamidino-2-phenylindole (DAPI) (Beyotime, Guangzhou, China) in the dark for 15 min. The cell imaging was performed on a Carl Zeiss fluorescence under laser confocal microscopy 880 (Carl Zeiss, Germany).


### 2.7. Western Blot Analysis

Cells were plated plates with2×105 cells/well overnight, followed, incubation BBR (10, 20, and 40 μM), PI3K/Akt inhibitor LY (10 μM, MedChem Express, NJ, USA), inhibitor SB (10 μM, Selleck company), agonist IGF-1 (PEPROTECH company 100 ng/L, MedChem Express), and TGF-β10 ng/mL for 12 h. Cultured cells were lysed in RIPA buffer (radio-immunoprecipitation assay buffer), and 1% PMSF (phenylmethanesulfony fluoride) was added. The total protein concentration of each sample was determined by using the Pierce bicinchoninic acid (BCA) protein assay (Keygen, Changchun, China). Equal amounts of proteins were separated by 10% SDS-PAGE and then transferred to polyvinylidene fluoride (PVDF) membranes (Millipore, Bedford, MA, USA). The membranes were cut using the molecular weight of proteins standards as guides to allow for blotting of protein of interest and loading controls on the same membrane. After blocking with 5% nonfat milk dissolved in TBST (0.1% Tween 20) for 6 h, the membrane was incubated with respective antisera at 1 : 1000 dilution at 4°C overnight. The antibodies were E-cadherin, N-cadherin, ZO-1, β-actin, vimentin, MMP-9, Snail, Slug, p-AKT, Smad2, p-Smad2, Smad3, p-Smad3, (CST, USA), p-Akt, Akt, PI3K, and β-catenin (ABclonal, Wuhan, China). After incubation with secondary antibody (1 : 4000 dilution, ABclonal, Wuhan, China) 2 h, the protein bands were visualized using enhanced chemiluminescence image analysis (Millipore, USA). The gray value was performed using the Tanon GIS system. Data were analyzed with Image J software (NIH Image, Bethesda, MD, USA).


### 2.8. Molecular Docking

The three-dimensional structure of berberine was obtained from the PubChem (CID: 2353). The crystal structures of TGF-β receptor I (PDB: 4X2F) and II (PDB: 5QIN) were downloaded from the RCSB PDB (http://www.rcsb.org/). The structure of TGF-β receptor III has not been reported. The interactions between berberine and TGF-β receptors were calculated by AutoDock v4.2.6. The center of the binding site of each receptor was defined as the center of the ligand which was cocrystallized with the receptor. The grid box was chosen to cover the residues in the binding site, and the grid spacing was set to 0.375 Å. The Lamarck’s genetic algorithm was used to optimize the conformations of berberine and the ligand in the binding pocket with the following parameters: the number of individuals in the population, the maximum number of energy evaluations, the maximum number of generations, and number of genetic algorithm runs were set as 150, 7.5×106, 2.7×104, and 50, respectively. Other parameters were set to default.


## 2.1. Cell Culture and Drug Configuration

The human GC cell lines MGC803, SGC7901, and HCC cells HepG2 were donated by the Laboratory of Molecular Oncology, Guangzhou University of Chinese Medicine. The cells were grown in DMEM (high glucose), supplemented with 10% fetal bovine serum (FBS) (Excell Biol Inc., Shanghai, China) and 0.5% antibiotics, at 37°C with 5% CO2 incubator. The H-DMEM was purchased from Gibco (Carlsbad, CA, USA). BBR was dissolved in DMSO and diluted with culture medium to ensure the final containing DMSO was less than 0.1%. For BBR treatment, 40 mM BBR was prepared in DMSO and then diluted into the desired concentrations with the H-DMEM medium.


## 2.2. Cell Viability Assays

MTT assay was assessed to investigate the effect of BBR on cell viability. Cells were plated2×103 cells/well in a 96-well plate, then, cultured with concentrations BBR (10, 20, 40, 80, 160, and 320 μM). Cell growth was measured using an MTT assay for 24 h, 48 h, added with MTT (5 mg/ml, Sigma) for an additional 4 h. The supernatant was removed and added to 150 μl DMSO. The optical density (OD) was detected by using microplate spectrophotometer (Bio-Rad Laboratories, Inc.) at 490 nm. We evaluated the cell viability Cellviability=1−ODtreatment/ODcontrol100%.


## 2.3. Wound Healing Assay

Cells (60×105 cells/well) were seeded and cultured overnight, serum-starved for 6 h. The wound was manually scratched in the monolayer using a 20 μL pipette, washed with PBS, and digitally photographed for the 0 h time point using an inverted microscope equipped with a digital camera (Olympus, Hamburg, Germany). Next, cells were cultured in BBR (10, 20, and 40 μM) for 24 h. Image-Pro Plus software 6.0 (Bethesda, MD, USA) was used to measure the area ratio.


## 2.4. Transwell Assays

2×104 cells/well were planted in 200 μL of serum-free DMED in the upper chambers, 800 μL of DMEM (15% FBS) were added to the lower chambers. Incubation for overnight is treated with different concentrations of BBR on the upper chambers for 24 h. Cells on the upper chamber were meticulously wiped off with a cotton swab and invaded cells fixed with 4% paraformaldehyde for 30 min, last, 0.1% crystal violet stained with cells. The invading cells were enumerated by using a digital image analysis system (Image-Pro Plus 6.0, Media Cybernetics, Bethesda, MD, USA).


## 2.5. Transcriptome Sequencing Assay

HepG2 cells (2×105 cells/well) were seeded in plates overnight, treated with BBR (40 μM) 12 h and 24 h, respectively, then, added 1 ml of trizol 10 min, and collected in EP tube. Last, the samples were preserved in -80°C. Transcriptome sequencing technology performed by Shanghai Yasunari biotechnology company. They give the corresponding results GO analysis of RNA-seq data using the DAVID bioinformatics resource and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway in a month. Enrichment analysis was completed utilizing the DAVID program (https://david.ncifcrf.gov/).


## 2.6. Immunofluorescence Assay

Cells were planted3×104 cells/well in glass slides and incubated plate at 37°C atmosphere overnight. Then, treated with different concentrations of BBR for 24 h, the cells were fixed with 4% paraformaldehyde for 30 min, incubated in the blocking buffer 5% BSA and 1% Triton X-100 in PBS for 2 h, following incubated 4°C overnight with antivimentin antibody (Cell Signaling Technology, USA). After rinsing, the cell was incubated the fluorescent secondary antibody for 1 h, and nuclei were stained with 4 0,6-diamidino-2-phenylindole (DAPI) (Beyotime, Guangzhou, China) in the dark for 15 min. The cell imaging was performed on a Carl Zeiss fluorescence under laser confocal microscopy 880 (Carl Zeiss, Germany).


## 2.7. Western Blot Analysis

Cells were plated plates with2×105 cells/well overnight, followed, incubation BBR (10, 20, and 40 μM), PI3K/Akt inhibitor LY (10 μM, MedChem Express, NJ, USA), inhibitor SB (10 μM, Selleck company), agonist IGF-1 (PEPROTECH company 100 ng/L, MedChem Express), and TGF-β10 ng/mL for 12 h. Cultured cells were lysed in RIPA buffer (radio-immunoprecipitation assay buffer), and 1% PMSF (phenylmethanesulfony fluoride) was added. The total protein concentration of each sample was determined by using the Pierce bicinchoninic acid (BCA) protein assay (Keygen, Changchun, China). Equal amounts of proteins were separated by 10% SDS-PAGE and then transferred to polyvinylidene fluoride (PVDF) membranes (Millipore, Bedford, MA, USA). The membranes were cut using the molecular weight of proteins standards as guides to allow for blotting of protein of interest and loading controls on the same membrane. After blocking with 5% nonfat milk dissolved in TBST (0.1% Tween 20) for 6 h, the membrane was incubated with respective antisera at 1 : 1000 dilution at 4°C overnight. The antibodies were E-cadherin, N-cadherin, ZO-1, β-actin, vimentin, MMP-9, Snail, Slug, p-AKT, Smad2, p-Smad2, Smad3, p-Smad3, (CST, USA), p-Akt, Akt, PI3K, and β-catenin (ABclonal, Wuhan, China). After incubation with secondary antibody (1 : 4000 dilution, ABclonal, Wuhan, China) 2 h, the protein bands were visualized using enhanced chemiluminescence image analysis (Millipore, USA). The gray value was performed using the Tanon GIS system. Data were analyzed with Image J software (NIH Image, Bethesda, MD, USA).


## 2.8. Molecular Docking

The three-dimensional structure of berberine was obtained from the PubChem (CID: 2353). The crystal structures of TGF-β receptor I (PDB: 4X2F) and II (PDB: 5QIN) were downloaded from the RCSB PDB (http://www.rcsb.org/). The structure of TGF-β receptor III has not been reported. The interactions between berberine and TGF-β receptors were calculated by AutoDock v4.2.6. The center of the binding site of each receptor was defined as the center of the ligand which was cocrystallized with the receptor. The grid box was chosen to cover the residues in the binding site, and the grid spacing was set to 0.375 Å. The Lamarck’s genetic algorithm was used to optimize the conformations of berberine and the ligand in the binding pocket with the following parameters: the number of individuals in the population, the maximum number of energy evaluations, the maximum number of generations, and number of genetic algorithm runs were set as 150, 7.5×106, 2.7×104, and 50, respectively. Other parameters were set to default.


## 3. Results

### 3.1. The Cell Viability Effect Changes of BBR on HepG2, MGC803, and SGC7901 Cells

To select the benefiting concentration in the following assays, the effects on cell viability of the candidate concentrations of BBR (10, 20, 40, 80, 160, and 320μM) in HepG2, MGC803, and SGC7901 cells were detected by MTT [3-(4,5-dimethythiazol-2-yl)-2,5-diphenyl tetrazoliumbromide] experiment. Treated with BBR for 24 hours, the IC50 (μM) values were 94.08±0.06, 154.4±0.05, and 102.9±0.04 in HepG2, MGC803, and SGC7901 cells, respectively. Treated with BBR for 48 hours, the IC50 (μM) values were 25.01±0.03, 34.47±0.02, and 33.84±0.03, respectively. BBR inhibited the cancer cell activity in a dose- and time-dependent manner (Figure 1). However, the ability of BBR inhibiting cancer cells was not significant compared with many reported compounds and clinical medication.Figure 1
BBR has a low cytotoxicity effect on HepG2, SGC7901, and MGC803 cells. HepG2, MGC803, and SGC7901 cells were treated with different concentrations of BBR (10, 20, 40, 80, 160, and 320μM). The cell viability was measured by MTT assay and showed at 24 h and 48 h (Figure 1), respectively. Data are presented as means standard deviation (SD) (∗p<0.05, ∗∗p<0.01 vs. ctrl group).


### 3.2. BBR Inhibited Invasion and Migration of HepG2, MGC803, and SGC7901 Cells

Wound healing assays and Transwell assays were conducted to determine whether BBR restrained metastasis and invasion of HepG2, MGC803, and SGC7901 cells. The consequence showed that the invasion and migration of BBR (10, 20, and 40μM for 24 h) groups were significantly inferior to control groups, decreased in a dose-dependent manner (Figures 2(a) and 2(b), p<0.05). Treated with BBR (40 μM) for 24 h, the relative migration inhibition rate (%) was 89.4±2.3, 93.3±2.5, and 78.0±3.0 in HepG2, MGC803, and SGC7901 cells, respectively (Figure 2(a), p<0.01), while the growth inhibition rate (%) was 36.0±2.7, 36.3±7.5, and 28.4±7.8, respectively (Figure 2(b), p<0.01). The relative migration and invasion inhibition rate was much higher than the growth inhibition rate. It indicated that BBR had higher inhibitory capacity of migration and invasion, which was not caused by growth inhibition.Figure 2
BBR inhibited migration and invasion of HepG2, MGC803 cells, and SGC7901. We used migration and transwell assays to evaluate the ability of migration and invasion in HepG2, SGC7901, and MGC803 cells. In the experiment, HepG2, SGC7901, and MGC803 cells were treated with different berberine concentrations for 24 h, followed by a taken picture for migration and transwell assays. Data were presented as means SD (∗p<0.05 vs. ctrl group).
(a)(b)


### 3.3. Transcriptome Sequencing Assays and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway and GO Enrichment Analysis

HepG2 cells were treated with BBR (40μM) in 12 and 24 hours, respectively, collected cells of each group, and extracted total RNA. Gene transcription levels of 12 samples (3 groups, n=4) were analyzed, subsequently, GO analysis of RNA-seq data (Figure 3(a)). A total of 10,000 transcripts were sequenced and detected 659 RNA fragments with significant differences in transcription levels. The genes were reported significant differences in transcription level by the ratio greater than 1.5 or less than 0.67, and p<0.05 in T-Test. The difference-expression genes that have been reported to be involved in EMT were shown in (Table 1(a)). TAB2, binding protein 2 of TGF-β activated Kinase1 (MAP3K7), Smad2, and Smad6 were significantly upregulated, while MMP28 and VIM were significantly downregulated in the 12 h group compared with 0 h group. Smad2, TJAP1(ZO-1), claudin 7, and Smad6 were significantly upregulated, while MMP28, VIM, and Smad3 were significantly downregulated in the 24 h group compared with the 0 h group. Claudin 7 was significantly upregulated, while VIM was significantly downregulated in the 24 h group compared with the 12 h group (Table 1(b)). The two transcripts of VIM-204 and VIM-209 were the same results. Remarkably, Smad2 and Vimentin had a significant difference degree. Mostly, fold change (different multiple) of Smad2 was greater than 6.7, when treated with BBR for both 12 h and 24 h. KEGG pathway enrichment analysis showed a significant difference in TGF-β signaling pathway among 0 h,12 h, and 24 h group (Figures 3(b) and 3(c)). There was a significant difference in the p53 pathway, IL-17 pathway, PI3K/Akt, Wnt/β-catenin, and JAK/Stat pathway only between 0 h and 24 h group (Figure 3(c)). In addition, some amino acid metabolism pathways showed a significant difference (Figure 3(b)). So, we supposed that berberine inhibited EMT via TGF-β/Smad, PI3K/Akt, and Wnt/β-catenin pathway, and TGF-β/Smad was a crucial procedure.Figure 3
Transcriptome sequencing assay in HepG2 cells with BBR treatment. HepG2 cells were treated with berberine. Furthermore, the transcriptome sequencing technology was performed by Shanghai Yasunari biotechnology company (a). The pathway analysis showed a significant difference in the TGF-β signaling pathway in 12 h and 24 h (b) and (c). The genes were reported closely related to EMT and have significant differences in transcription level (Tables 1 and 2). The top 20 with a lower p value was shown.
(a)(b)(c)Table 1
Analyze BBR treatment by transcriptome sequencing assay.
(a)
The target genes of BBR related to EMT were significantly upregulated
Gene_nameTrans_nameDescriptionFold_changep_value12 h/0 hSMAD2SMAD2-205SMAD family member 26.72230.03633SMAD2SMAD2-207SMAD family member 21.89560.0060TAB2TAB2-209TGF-beta activated kinase 1 (MAP3K7) binding protein 21.58110.0015SMAD6SMAD6SMAD family member 61.50900.000024 h/0 hSMAD2SMAD2-205SMAD family member 26.96330.0215TJAP1(ZO1)TJAP1-201Tight junction associated protein 12.20250.03990CLDN7CLDN7-201Claudin 71.88720.00161SMAD6SMAD6SMAD family member 61.55295.1607E-06JMYJMY-201Junction mediating and regulatory protein, p53 cofactor1.88397.4150E-09SMAD2SMAD2-207SMAD family member 21.53020.010024 h/12 hCLDN7CLDN7-207Claudin 71.81333.4290E-06CLDN7CLDN7-201Claudin 71.62260.0201CLDN7CLDN7-202Claudin 71.62040.0221(b)
EMT-related genes were significantly downregulated by berberine
Gene_nameTrans_nameDescriptionFold_changep_value12 h/0 hMMP28MMP28-201Matrix metallopeptidase 280.58870.0398VIMVIM-204Vimentin0.64860.0102TMEM42TMEM42-201Transmembrane protein 420.64860.010324 h/0 hSMAD3SMAD3-203SMAD family member 30.36960.0338VIMVIM-204Vimentin0.38770.0003EMP3EMP3-202Epithelial membrane protein 30.47370.0120VIMVIM-209Vimentin0.54470.0011MMP28MMP28-201Matrix metallopeptidase 280.55900.010124 h/12 hVIMVIM-204Vimentin0.59790.0115VIMVIM-209Vimentin0.63980.0036(a) and (b) The level of transcriptional was significantly upregulated and downregulated BBR treatment related to EMT genes (difference from large to small).


### 3.4. BBR Reversed EMT in HCC and Gastric Carcinoma Cells

Western blot method and immunofluorescence assays analyze the biomarker protein expression related to EMT in tumor cells. The results showed that the expression of N-cadherin, Vimentin, MMP-9, Snail, and Slug (mesenchymal marker) was obviously restrained with BBR (10, 20, and 40μM for 24 h) treatment (Figure 4(a)). On the contrary, E-cadherin and ZO-1 expression increased observably. Additionally, the BBR (40 μM) group markedly declined the fluorescence expression of vimentin compared to the control group (Figure 4(b)). The assay results indicated that BBR could effectively restrain EMT in HepG2, MGC803, and SGC7901 cells.Figure 4
Effects of BBR on epithelial-mesenchymal transition (EMT) in HCC cells and gastric carcinoma cells. (a) HepG2, SGC7901, and MGC803 cells were treated with BBR (10, 20, and 40μM) for 24 h. The level of EMT markers, including E-cadherin, ZO-1, N-cadherin, vimentin, Snail, and Slug, was assessed by Western blotting assays. (b) When treated with BBR (10, 20, and 40 μM), vimentin was determined by confocal microscopy in HepG2, SGC7901, and MGC803 cells, Vimentin-positive expression was indicated by green fluorescence, and blue fluorescence indicates 4′,6-diamidino-2-phenylindole- (DAPI-) labeled nuclei. Scale bars: 20 μm. Representative images and typical graphs (mean±SD) are shown, (n=3. ∗p<0.05, ∗∗p<0.01 versus the control group).
(a)(b)


### 3.5. The Inhibitory Effect of BBR on EMT in HepG2, MGC803, and SGC7901 Cells through TGF-β/Smad and PI3K/Akt

According to the previous result of 2.3, it was possible that BBR affects EMT related to TGF-β/Smad, PI3K/Akt, and Wnt/β-catenin pathways. So, we tested the conjecture by the Western Blot method. The band proteins intensities displayed that the proteins of p-Akt, p-Smad3, and β-catenin were remarkably downregulated but p-Smad2 was upregulated when added BBR (10, 20, and 40 μM for 24 h) in HepG2 and gastric cancer cells. Whereas total protein levels of Akt, PI3K, Smad2, and Smad3 were essentially unchanged (Figure 5(a)). The result showed that BBR downregulated PI3K/Akt and Wnt/β-catenin pathways and adjusted the TGF-β/Smad pathway by upregulated p-Smad2 and downregulated p-Smad3.Figure 5
Effects of BBR on the TGF-β/Smad, PI3K/Akt, and Wnt/β-catenin pathways in HepG2, MGC803, and SGC7901 cells by Western Blot. (a) HepG2, MGC803, and SGC7901 cells were treated with BBR (10, 20, and 40 μM) for 24 h. The pathway proteins of TGF-β/Smad, PI3K/Akt, and Wnt/β-catenin, including Smad2, p-Smad2, Smad3, p-Smad3, Akt, p-Akt, PI3K, and β-catenin, were measured. (b) HepG2 and MGC803 cells were treated alone or cotreated berberine (40 μM) and LY. Measured the proteins of E-cadherin, ZO-1, N-cadherin, vimentin, Snail, Slug, Akt, p-Akt, PI3K, and β-catenin. (c) Treated alone or cotreated BBR (40 μM) and SB (10 μM), the proteins of E-cadherin, ZO-1, N-cadherin, vimentin, Snail, Slug Smad2, p-Smad2, Smad3, and p-Smad3. (d) and (e) Treated alone or cotreated BBR (40 μM) and IGF-1 (100 ng/ml) or TGF-β (10 ng/ml) the proteins of relating to EMT, Smad2, Smad3, p-Smad2, and p-Smad3 and were measured. (f) To compare the effect of BBR (20 μM) and SB (20 μM) in TGF-β pathway, Smad2, Smad3, p-Smad2, and p-Smad3 protein expression level was detected. β-Actin was used as a loading control. Representative images and typical graphs (mean±SD) are shown, (n=3. ∗p<0.05, ∗∗p<0.01 versus the control group, #p<0.05, ##p<0.01 versus the inhibitors group).
(a)(b)(c)(d)(e)(f)We further detected the effect of BBR when function weaken or function intensify of TGF-β/Smad and PI3K/Akt by the corresponding inhibitor or agonist. TGF-β, a ligand of TGFβR, can regard as a specific activator of TGFβR and the initiating factor of the entire TGF-β/Smad pathway. Cells were preincubated with LY (PI3K/Akt inhibitor), or SB (TGFβR inhibitor), or IGF-1(PI3K/Akt agonist), or TGF β (TGFβR agonist) for 12 h, and treated alone or cotreated with BBR (40 μM) for 24 h, the proteins of EMT was similar to the result of 2.4 when treated with BBR alone. Similar and even more effective inhibition of EMT was obtained with the LY and SB treatment. The effect of BBR on Smad2/3 was extremely similar to SB, which brought a high level of p-Smad2 but decreased p-Smad3, whereas total protein of Akt, PI3K, Smad2, and Smad3 was essentially unchanged. Combination berberine with SB/LY was significantly better than BBR or SB/LY alone (Figures 5(b) and 5(c), ∗p<0.05, ∗∗p<0.01, vs. the ctrl group; #p<0.05, ##p<0.01, vs. the combined group). To compare BBR with SB on Smad2/3, we detected the proteins of Smad2/3, p-Smad2/3 with the same drug concentration (20 μM) treatment in MGC803 cells. The effect of BBR was slightly weaker than SB (Figure 5(d)).IGF-1 could enhance EMT andβ-catenin and reverse the effect of BBR on EMT and β-catenin. It did not affect either p-Smad2/Smad2 or p-Smad3/Smad3. IGF-1 did not reverse the regulation of BBR on p-Smad2 or p-Smad3 (Figure 5(e)). TGF-β could enhance the process of EMT and reversed the effect of BBR on EMT, p-Smad2, and p-Smad3 (Figure 5(f)). These results showed that BBR reduced EMT through TGF-β/Smad and PI3K/Akt, regulating TGF-β/Smad could influence PI3K/Akt, whereas activator IGF-1 of PI3K/Akt had little effects on the TGF-β/Smad pathway.


### 3.6. Target Prediction of BBR Based on Molecular Docking Method

The TGF-β/Smad pathway is probably the crucial pathway for BBR. To certify this assumption, we analyzed the interactions between the TGF-β receptor and BBR. The TGF-β receptor information were shown in Table 2. The ligand cocrystallized in TGFβR1 (4-amino -8-(4-aminophenyl) pyrido [2, 3-D] pyrimidin-5 (8H)-one) or TGFβR2 (N-{4-[3-(6-methoxypyridin-3-yl)-1H-pyrrolo [3,2-b]pyridin-2-yl]pyridin-2-yl}acetamide) was used as the control. The interaction diagrams between BBR and TGFβR were shown in Figures 6(a) and 6(b). BBR formed two conventional hydrogen bonds with TYR249 and SER287 of TGFβR1. It also had a Pi-Cation interaction with Lys232. BBR formed three conventional hydrogen bonds with ASN332 and THR325. The binding energy between TGFβR1 and BBR was -7.5 kcal/mol, compared with −6.62 kcal/mol between TGFβR1 and its ligand. The binding energy of TGFβR2 and BBR was −8.54 kcal/mol, compared with −10.16 kcal/mol between TGFβR2 and its ligand (Table 2). BBR had a high affinity with TGFβR1, which was higher than that of the original ligand. The binding energy between TGFβR2 and BBR was not as good as that between TGFβR2 and its ligand. However, the affinity between TGFβR2 and BBR was considerably high (The IC50 was 40 nM). Thus, it indicated that BBR would have a certain capacity of binding with TGFβR2.Table 2
Details experiment results showed in the molecular docking complex of the TGFβ R1 and TGFβR2 with BBR.
TGFβRUniProt IDPDBReferenceThe binding energy between TGFβR and berberineTGFβR1P368974X2FPubMed: 25437144-7.50 kcal/molTGFβR2P371735QINPubMed: 30429955-8.54 kcal/molFigure 6
Between TGF-β receptor proteins and BBR ligands. (a) TGF-βI receptors bound to BBR; (b) TGF-βII receptors bound to BBR.
(a)(b)


### 3.7. Relation of TGF-β and Smad2 on EMT, Proliferation in MGC803 Cells

Unfortunately, we have not found specific agonists and inhibitors that can directly target p-Smad2/3. So we used an inhibitor and agonist of TGFβR instead of overexpression or siRNA interference with Smad2/3, as p-Smad2/3 was more important than Smad2/3 in the pathway. Treated with TGF-β and SB to analyze the interrelationship of TGFβ and Smad2 and Smad3 on tumor proliferation and metastasis. TGF-β downregulated p-Smad2, upregulated p-Smad3, and promoted EMT and proliferation, and SB was on the opposite of TGF-β. The influence of SB was similar to BBR above (Figure 7(a)).Figure 7
Relation of TGF-β and Smad on EMT and proliferation in MGC803 cells. (a) Treated alone or cotreated SB (10 μM) and TGF-β (10 ng/ml) in 24 h; (10 μM) for 36 h in MGC803 cells by WB methods. (b) and (c) Treated alone or cotreated BBR (40 μM) and SB (10 μM) for 12 h and 36 h to detect relating proteins by WB method. (d) Treated with TGF-β (5, 10, 20, 40, 80, 160, and 320 ng/ml) in MGC803 cells to detect cell viability by MTT assays. (e) Treated with TGF-β (5, 10, 20, 40, and 80 ng/ml) in MGC803 cells to detect p-Smad2 by WB assay. (n=3. ∗p<0.05, ∗∗p<0.01 versus the control group, #p<0.05, ##p<0.01 versus the inhibitors group).
(a)(b)(c)(d)(e)Figure 8
A schematic representation showed the effect of BBR on EMT in tumor cells. BBR restrained the TGF-β/Smad, PI3K/Akt, and Wnt-/β-catenin pathways, and in the end, restrained the ability of migration and invasion in liver carcinoma and gastric tumor cells. “↓” indicates promotion; “⊥” indicates inhibition.As the relation of TGF-β and p-Smad2 was so different from the reported, we further analyzed whether the effect was changed due to different times treated with drugs. Treated with SB for 12 h, treated alone, or cotreated with BBR (40 μM) for 12 h and 36 h, respectively. The results were similar to drug treatment for 24 h above, both 12 h and 36 h (Figures 7(b) and 7(c)). These results indicated that BBR and SB upregulating p-Smad2 did not change with shortened or prolonged the action time. With the concentration of TGF-β (5, 10, 20, 40, 80, 160, and 320 ng/ml) in MGC803cells, TGF-β promoted the cell proliferation and downregulated p-Smad2 at 5 ~ 10 ng/mL, but TGF-β upregulated p-Smad2 at 20~ 40 ng/mL (Figures 7(d) and 7(e)). The results showed that the concentration of TGF-β affected the increase or decrease of p-Smad2.


## 3.1. The Cell Viability Effect Changes of BBR on HepG2, MGC803, and SGC7901 Cells

To select the benefiting concentration in the following assays, the effects on cell viability of the candidate concentrations of BBR (10, 20, 40, 80, 160, and 320μM) in HepG2, MGC803, and SGC7901 cells were detected by MTT [3-(4,5-dimethythiazol-2-yl)-2,5-diphenyl tetrazoliumbromide] experiment. Treated with BBR for 24 hours, the IC50 (μM) values were 94.08±0.06, 154.4±0.05, and 102.9±0.04 in HepG2, MGC803, and SGC7901 cells, respectively. Treated with BBR for 48 hours, the IC50 (μM) values were 25.01±0.03, 34.47±0.02, and 33.84±0.03, respectively. BBR inhibited the cancer cell activity in a dose- and time-dependent manner (Figure 1). However, the ability of BBR inhibiting cancer cells was not significant compared with many reported compounds and clinical medication.Figure 1
BBR has a low cytotoxicity effect on HepG2, SGC7901, and MGC803 cells. HepG2, MGC803, and SGC7901 cells were treated with different concentrations of BBR (10, 20, 40, 80, 160, and 320μM). The cell viability was measured by MTT assay and showed at 24 h and 48 h (Figure 1), respectively. Data are presented as means standard deviation (SD) (∗p<0.05, ∗∗p<0.01 vs. ctrl group).


## 3.2. BBR Inhibited Invasion and Migration of HepG2, MGC803, and SGC7901 Cells

Wound healing assays and Transwell assays were conducted to determine whether BBR restrained metastasis and invasion of HepG2, MGC803, and SGC7901 cells. The consequence showed that the invasion and migration of BBR (10, 20, and 40μM for 24 h) groups were significantly inferior to control groups, decreased in a dose-dependent manner (Figures 2(a) and 2(b), p<0.05). Treated with BBR (40 μM) for 24 h, the relative migration inhibition rate (%) was 89.4±2.3, 93.3±2.5, and 78.0±3.0 in HepG2, MGC803, and SGC7901 cells, respectively (Figure 2(a), p<0.01), while the growth inhibition rate (%) was 36.0±2.7, 36.3±7.5, and 28.4±7.8, respectively (Figure 2(b), p<0.01). The relative migration and invasion inhibition rate was much higher than the growth inhibition rate. It indicated that BBR had higher inhibitory capacity of migration and invasion, which was not caused by growth inhibition.Figure 2
BBR inhibited migration and invasion of HepG2, MGC803 cells, and SGC7901. We used migration and transwell assays to evaluate the ability of migration and invasion in HepG2, SGC7901, and MGC803 cells. In the experiment, HepG2, SGC7901, and MGC803 cells were treated with different berberine concentrations for 24 h, followed by a taken picture for migration and transwell assays. Data were presented as means SD (∗p<0.05 vs. ctrl group).
(a)(b)


## 3.3. Transcriptome Sequencing Assays and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway and GO Enrichment Analysis

HepG2 cells were treated with BBR (40μM) in 12 and 24 hours, respectively, collected cells of each group, and extracted total RNA. Gene transcription levels of 12 samples (3 groups, n=4) were analyzed, subsequently, GO analysis of RNA-seq data (Figure 3(a)). A total of 10,000 transcripts were sequenced and detected 659 RNA fragments with significant differences in transcription levels. The genes were reported significant differences in transcription level by the ratio greater than 1.5 or less than 0.67, and p<0.05 in T-Test. The difference-expression genes that have been reported to be involved in EMT were shown in (Table 1(a)). TAB2, binding protein 2 of TGF-β activated Kinase1 (MAP3K7), Smad2, and Smad6 were significantly upregulated, while MMP28 and VIM were significantly downregulated in the 12 h group compared with 0 h group. Smad2, TJAP1(ZO-1), claudin 7, and Smad6 were significantly upregulated, while MMP28, VIM, and Smad3 were significantly downregulated in the 24 h group compared with the 0 h group. Claudin 7 was significantly upregulated, while VIM was significantly downregulated in the 24 h group compared with the 12 h group (Table 1(b)). The two transcripts of VIM-204 and VIM-209 were the same results. Remarkably, Smad2 and Vimentin had a significant difference degree. Mostly, fold change (different multiple) of Smad2 was greater than 6.7, when treated with BBR for both 12 h and 24 h. KEGG pathway enrichment analysis showed a significant difference in TGF-β signaling pathway among 0 h,12 h, and 24 h group (Figures 3(b) and 3(c)). There was a significant difference in the p53 pathway, IL-17 pathway, PI3K/Akt, Wnt/β-catenin, and JAK/Stat pathway only between 0 h and 24 h group (Figure 3(c)). In addition, some amino acid metabolism pathways showed a significant difference (Figure 3(b)). So, we supposed that berberine inhibited EMT via TGF-β/Smad, PI3K/Akt, and Wnt/β-catenin pathway, and TGF-β/Smad was a crucial procedure.Figure 3
Transcriptome sequencing assay in HepG2 cells with BBR treatment. HepG2 cells were treated with berberine. Furthermore, the transcriptome sequencing technology was performed by Shanghai Yasunari biotechnology company (a). The pathway analysis showed a significant difference in the TGF-β signaling pathway in 12 h and 24 h (b) and (c). The genes were reported closely related to EMT and have significant differences in transcription level (Tables 1 and 2). The top 20 with a lower p value was shown.
(a)(b)(c)Table 1
Analyze BBR treatment by transcriptome sequencing assay.
(a)
The target genes of BBR related to EMT were significantly upregulated
Gene_nameTrans_nameDescriptionFold_changep_value12 h/0 hSMAD2SMAD2-205SMAD family member 26.72230.03633SMAD2SMAD2-207SMAD family member 21.89560.0060TAB2TAB2-209TGF-beta activated kinase 1 (MAP3K7) binding protein 21.58110.0015SMAD6SMAD6SMAD family member 61.50900.000024 h/0 hSMAD2SMAD2-205SMAD family member 26.96330.0215TJAP1(ZO1)TJAP1-201Tight junction associated protein 12.20250.03990CLDN7CLDN7-201Claudin 71.88720.00161SMAD6SMAD6SMAD family member 61.55295.1607E-06JMYJMY-201Junction mediating and regulatory protein, p53 cofactor1.88397.4150E-09SMAD2SMAD2-207SMAD family member 21.53020.010024 h/12 hCLDN7CLDN7-207Claudin 71.81333.4290E-06CLDN7CLDN7-201Claudin 71.62260.0201CLDN7CLDN7-202Claudin 71.62040.0221(b)
EMT-related genes were significantly downregulated by berberine
Gene_nameTrans_nameDescriptionFold_changep_value12 h/0 hMMP28MMP28-201Matrix metallopeptidase 280.58870.0398VIMVIM-204Vimentin0.64860.0102TMEM42TMEM42-201Transmembrane protein 420.64860.010324 h/0 hSMAD3SMAD3-203SMAD family member 30.36960.0338VIMVIM-204Vimentin0.38770.0003EMP3EMP3-202Epithelial membrane protein 30.47370.0120VIMVIM-209Vimentin0.54470.0011MMP28MMP28-201Matrix metallopeptidase 280.55900.010124 h/12 hVIMVIM-204Vimentin0.59790.0115VIMVIM-209Vimentin0.63980.0036(a) and (b) The level of transcriptional was significantly upregulated and downregulated BBR treatment related to EMT genes (difference from large to small).


## 3.4. BBR Reversed EMT in HCC and Gastric Carcinoma Cells

Western blot method and immunofluorescence assays analyze the biomarker protein expression related to EMT in tumor cells. The results showed that the expression of N-cadherin, Vimentin, MMP-9, Snail, and Slug (mesenchymal marker) was obviously restrained with BBR (10, 20, and 40μM for 24 h) treatment (Figure 4(a)). On the contrary, E-cadherin and ZO-1 expression increased observably. Additionally, the BBR (40 μM) group markedly declined the fluorescence expression of vimentin compared to the control group (Figure 4(b)). The assay results indicated that BBR could effectively restrain EMT in HepG2, MGC803, and SGC7901 cells.Figure 4
Effects of BBR on epithelial-mesenchymal transition (EMT) in HCC cells and gastric carcinoma cells. (a) HepG2, SGC7901, and MGC803 cells were treated with BBR (10, 20, and 40μM) for 24 h. The level of EMT markers, including E-cadherin, ZO-1, N-cadherin, vimentin, Snail, and Slug, was assessed by Western blotting assays. (b) When treated with BBR (10, 20, and 40 μM), vimentin was determined by confocal microscopy in HepG2, SGC7901, and MGC803 cells, Vimentin-positive expression was indicated by green fluorescence, and blue fluorescence indicates 4′,6-diamidino-2-phenylindole- (DAPI-) labeled nuclei. Scale bars: 20 μm. Representative images and typical graphs (mean±SD) are shown, (n=3. ∗p<0.05, ∗∗p<0.01 versus the control group).
(a)(b)


## 3.5. The Inhibitory Effect of BBR on EMT in HepG2, MGC803, and SGC7901 Cells through TGF-β/Smad and PI3K/Akt

According to the previous result of 2.3, it was possible that BBR affects EMT related to TGF-β/Smad, PI3K/Akt, and Wnt/β-catenin pathways. So, we tested the conjecture by the Western Blot method. The band proteins intensities displayed that the proteins of p-Akt, p-Smad3, and β-catenin were remarkably downregulated but p-Smad2 was upregulated when added BBR (10, 20, and 40 μM for 24 h) in HepG2 and gastric cancer cells. Whereas total protein levels of Akt, PI3K, Smad2, and Smad3 were essentially unchanged (Figure 5(a)). The result showed that BBR downregulated PI3K/Akt and Wnt/β-catenin pathways and adjusted the TGF-β/Smad pathway by upregulated p-Smad2 and downregulated p-Smad3.Figure 5
Effects of BBR on the TGF-β/Smad, PI3K/Akt, and Wnt/β-catenin pathways in HepG2, MGC803, and SGC7901 cells by Western Blot. (a) HepG2, MGC803, and SGC7901 cells were treated with BBR (10, 20, and 40 μM) for 24 h. The pathway proteins of TGF-β/Smad, PI3K/Akt, and Wnt/β-catenin, including Smad2, p-Smad2, Smad3, p-Smad3, Akt, p-Akt, PI3K, and β-catenin, were measured. (b) HepG2 and MGC803 cells were treated alone or cotreated berberine (40 μM) and LY. Measured the proteins of E-cadherin, ZO-1, N-cadherin, vimentin, Snail, Slug, Akt, p-Akt, PI3K, and β-catenin. (c) Treated alone or cotreated BBR (40 μM) and SB (10 μM), the proteins of E-cadherin, ZO-1, N-cadherin, vimentin, Snail, Slug Smad2, p-Smad2, Smad3, and p-Smad3. (d) and (e) Treated alone or cotreated BBR (40 μM) and IGF-1 (100 ng/ml) or TGF-β (10 ng/ml) the proteins of relating to EMT, Smad2, Smad3, p-Smad2, and p-Smad3 and were measured. (f) To compare the effect of BBR (20 μM) and SB (20 μM) in TGF-β pathway, Smad2, Smad3, p-Smad2, and p-Smad3 protein expression level was detected. β-Actin was used as a loading control. Representative images and typical graphs (mean±SD) are shown, (n=3. ∗p<0.05, ∗∗p<0.01 versus the control group, #p<0.05, ##p<0.01 versus the inhibitors group).
(a)(b)(c)(d)(e)(f)We further detected the effect of BBR when function weaken or function intensify of TGF-β/Smad and PI3K/Akt by the corresponding inhibitor or agonist. TGF-β, a ligand of TGFβR, can regard as a specific activator of TGFβR and the initiating factor of the entire TGF-β/Smad pathway. Cells were preincubated with LY (PI3K/Akt inhibitor), or SB (TGFβR inhibitor), or IGF-1(PI3K/Akt agonist), or TGF β (TGFβR agonist) for 12 h, and treated alone or cotreated with BBR (40 μM) for 24 h, the proteins of EMT was similar to the result of 2.4 when treated with BBR alone. Similar and even more effective inhibition of EMT was obtained with the LY and SB treatment. The effect of BBR on Smad2/3 was extremely similar to SB, which brought a high level of p-Smad2 but decreased p-Smad3, whereas total protein of Akt, PI3K, Smad2, and Smad3 was essentially unchanged. Combination berberine with SB/LY was significantly better than BBR or SB/LY alone (Figures 5(b) and 5(c), ∗p<0.05, ∗∗p<0.01, vs. the ctrl group; #p<0.05, ##p<0.01, vs. the combined group). To compare BBR with SB on Smad2/3, we detected the proteins of Smad2/3, p-Smad2/3 with the same drug concentration (20 μM) treatment in MGC803 cells. The effect of BBR was slightly weaker than SB (Figure 5(d)).IGF-1 could enhance EMT andβ-catenin and reverse the effect of BBR on EMT and β-catenin. It did not affect either p-Smad2/Smad2 or p-Smad3/Smad3. IGF-1 did not reverse the regulation of BBR on p-Smad2 or p-Smad3 (Figure 5(e)). TGF-β could enhance the process of EMT and reversed the effect of BBR on EMT, p-Smad2, and p-Smad3 (Figure 5(f)). These results showed that BBR reduced EMT through TGF-β/Smad and PI3K/Akt, regulating TGF-β/Smad could influence PI3K/Akt, whereas activator IGF-1 of PI3K/Akt had little effects on the TGF-β/Smad pathway.


## 3.6. Target Prediction of BBR Based on Molecular Docking Method

The TGF-β/Smad pathway is probably the crucial pathway for BBR. To certify this assumption, we analyzed the interactions between the TGF-β receptor and BBR. The TGF-β receptor information were shown in Table 2. The ligand cocrystallized in TGFβR1 (4-amino -8-(4-aminophenyl) pyrido [2, 3-D] pyrimidin-5 (8H)-one) or TGFβR2 (N-{4-[3-(6-methoxypyridin-3-yl)-1H-pyrrolo [3,2-b]pyridin-2-yl]pyridin-2-yl}acetamide) was used as the control. The interaction diagrams between BBR and TGFβR were shown in Figures 6(a) and 6(b). BBR formed two conventional hydrogen bonds with TYR249 and SER287 of TGFβR1. It also had a Pi-Cation interaction with Lys232. BBR formed three conventional hydrogen bonds with ASN332 and THR325. The binding energy between TGFβR1 and BBR was -7.5 kcal/mol, compared with −6.62 kcal/mol between TGFβR1 and its ligand. The binding energy of TGFβR2 and BBR was −8.54 kcal/mol, compared with −10.16 kcal/mol between TGFβR2 and its ligand (Table 2). BBR had a high affinity with TGFβR1, which was higher than that of the original ligand. The binding energy between TGFβR2 and BBR was not as good as that between TGFβR2 and its ligand. However, the affinity between TGFβR2 and BBR was considerably high (The IC50 was 40 nM). Thus, it indicated that BBR would have a certain capacity of binding with TGFβR2.Table 2
Details experiment results showed in the molecular docking complex of the TGFβ R1 and TGFβR2 with BBR.
TGFβRUniProt IDPDBReferenceThe binding energy between TGFβR and berberineTGFβR1P368974X2FPubMed: 25437144-7.50 kcal/molTGFβR2P371735QINPubMed: 30429955-8.54 kcal/molFigure 6
Between TGF-β receptor proteins and BBR ligands. (a) TGF-βI receptors bound to BBR; (b) TGF-βII receptors bound to BBR.
(a)(b)


## 3.7. Relation of TGF-β and Smad2 on EMT, Proliferation in MGC803 Cells

Unfortunately, we have not found specific agonists and inhibitors that can directly target p-Smad2/3. So we used an inhibitor and agonist of TGFβR instead of overexpression or siRNA interference with Smad2/3, as p-Smad2/3 was more important than Smad2/3 in the pathway. Treated with TGF-β and SB to analyze the interrelationship of TGFβ and Smad2 and Smad3 on tumor proliferation and metastasis. TGF-β downregulated p-Smad2, upregulated p-Smad3, and promoted EMT and proliferation, and SB was on the opposite of TGF-β. The influence of SB was similar to BBR above (Figure 7(a)).Figure 7
Relation of TGF-β and Smad on EMT and proliferation in MGC803 cells. (a) Treated alone or cotreated SB (10 μM) and TGF-β (10 ng/ml) in 24 h; (10 μM) for 36 h in MGC803 cells by WB methods. (b) and (c) Treated alone or cotreated BBR (40 μM) and SB (10 μM) for 12 h and 36 h to detect relating proteins by WB method. (d) Treated with TGF-β (5, 10, 20, 40, 80, 160, and 320 ng/ml) in MGC803 cells to detect cell viability by MTT assays. (e) Treated with TGF-β (5, 10, 20, 40, and 80 ng/ml) in MGC803 cells to detect p-Smad2 by WB assay. (n=3. ∗p<0.05, ∗∗p<0.01 versus the control group, #p<0.05, ##p<0.01 versus the inhibitors group).
(a)(b)(c)(d)(e)Figure 8
A schematic representation showed the effect of BBR on EMT in tumor cells. BBR restrained the TGF-β/Smad, PI3K/Akt, and Wnt-/β-catenin pathways, and in the end, restrained the ability of migration and invasion in liver carcinoma and gastric tumor cells. “↓” indicates promotion; “⊥” indicates inhibition.As the relation of TGF-β and p-Smad2 was so different from the reported, we further analyzed whether the effect was changed due to different times treated with drugs. Treated with SB for 12 h, treated alone, or cotreated with BBR (40 μM) for 12 h and 36 h, respectively. The results were similar to drug treatment for 24 h above, both 12 h and 36 h (Figures 7(b) and 7(c)). These results indicated that BBR and SB upregulating p-Smad2 did not change with shortened or prolonged the action time. With the concentration of TGF-β (5, 10, 20, 40, 80, 160, and 320 ng/ml) in MGC803cells, TGF-β promoted the cell proliferation and downregulated p-Smad2 at 5 ~ 10 ng/mL, but TGF-β upregulated p-Smad2 at 20~ 40 ng/mL (Figures 7(d) and 7(e)). The results showed that the concentration of TGF-β affected the increase or decrease of p-Smad2.


## 4. Discussion

HCC and GC were extremely malignant tumor [36, 37]. Malignant tumor metastasis is one of the main causes of death of cancer patients worldwide [38–41]. Therefore, cancer metastasis is a significant target in clinical treatment. EMT plays a significant role in metastasis. When EMT occurs, the connection between cells was broken, the cytoskeleton was rearranged, and the ability of migration, invasion, and antiapoptosis can be enhanced [42]. Therefore, it is of great significance for tumor invasion and metastasis via inhibition of EMT.BBR is low toxicity natural compound in various medicinal plants such as Coptis, which has been proved to have a specific antitumor effect and validity for clinical application [20, 21]. The studies showed that BBR can effectively resist the invasion of cancer cells and has no toxic effect on normal cells and inhibits the invasion and migration of melanoma, colon, and lung cancer cells via inhibiting EMT [26, 31, 43]. BBR inhibited EMT through ERK, PI3K, and other pathways [31, 44, 45]. Among them, some studies (5 papers) have reported that BBR inhibits EMT through the TGF-β/Smad pathway, 3 of which (1 for intestinal cancer, 2 for lung cancer) considered that the TGF-β pathway promoted cancer metastasis and EMT, and BBR including its derivatives reduced p-Smad2, p-Smad3 and inhibited EMT. One article identified that BBR significantly increased Smad2, Smad3, Smad4, and p-Smad3, but p-Smad2 remained unchanged in colon cells [31]. One paper reported only medium and high concentrations could reduce p-Smad2 and p-Smad3, and low concentrations of BBR (50 μM) could even increase p-Smad2 and p-Smad3 in colon epithelial cells. The ratio of p-Smad2/p-Smad3 increased significantly or remained unchanged treated with low concentration of BBR, and medium-high BBR decreased the ratio significantly [32]. Our study supported that the TGF-β/smad pathway promoted proliferation and EMT, and BBR suppressed EMT mainly through the TGF-β/smad pathway by adjusting Smad2, Smad3, and Smad6 but it was inconsistent with the traditional view about the effect of Smad2, relationship of Smad2 and TGFβ. We speculated Smad2 may be a tumor suppressor, as reported clinical literature [33, 35, 46]. In our study, we evaluated the impact of BBR on the level of transcription by transcriptome sequencing first and found that target genes of BBR related to cancer focused on apoptosis and EMT. BBR had a relatively weak inhibitory effect compared with other apoptosis-inducing drugs. In vivo experiment, the effect of BBR was not very well reducing the size and weight of the planted tumor (the results were shown in supplement materials). We considered it was of little clinical significance that BBR inhibited proliferation and induced apoptosis. Therefore, its anticancer action was mainly aimed at EMT. Then, the expression of the genes related to EMT was evaluated by immunofluorescence staining and Western Blot method. The results showed that gastric cancer MGC803 and SGC7901 cells were exactly similar to liver cancer HepG2. Our results and published articles indicated that BBR could reverse EMT, broad-spectrum, and less tissue specificity. The effective concentration of BBR was 20~40 μM.EMT is activated through oncogenic signaling pathways such as PI3K/Akt, Akt-mTOR, NF-κB, Wnt/β-catenin, Ras/MAPK, and Notch.43 [47–49]. TGF-β1 can eliminate intercellular adhesion and promote the mesenchymal phenotype switch and the ability of migration and invasion in many kinds of tumor cells. Therefore, the TGF-β/Smad pathway is closely related to EMT [28, 29]. PI3K/Akt, TGF-β/Smad, and Wnt-β/catenin signaling pathways were so important that we did not ignore the mechanisms related to EMT in cancer cells [30]. We found a total of five pathways were altered treated with BBR through Transcriptometric Sequencing and KEGG pathways analysis. Three of them, TGF-β/Smad, PI3K/Akt, and Wnt/β-catenin, are related to EMT. Transcriptome sequencing is a powerful technique that allows the identification of large-scale gene transcription analysis. It provided a comprehensive investigation of drug target genes. Furthermore, it helps find out the starting genes/signaling pathway of drug-driven. At 12 h, transcriptome sequencing analysis showed 6.7-fold increasing Smad2 transcription, upregulating TAB2, the binding protein 2 of TGF-beta activated Kinase1 (MAP3K7), and Smad6 (negative regulator of TGF-β/Smad), which indicated TGF-/Smad was the earlier, driving pathway of BBR. At 24 h, significant transcription changes are related to proteins of 5 pathways, including TGF-/Smad, p53 pathway, PI3K/Akt, Wnt/β-catenin, and JAK/Stat pathway (Table 1 and Figure 3(c)). The level of Smad2 significantly increased about 7.0-fold, which indicated that TGF-β/Smad may be the initiating, crucial signaling pathway of BBR. We used Western Blot to verify most of the results of transcriptome sequencing. There was a significant change in the level of E-cadherin, N-cadherin, and Snail Slug in WB, but it was no significant variation in transcriptome sequencing. The probable reason is that the transcript difference up to 50% was considered as significant in transcriptome sequencing. It was unexpected that BBR had no effect on total proteins of Smad2 and Smad3, but it significantly increased p-Smad2 and decreased p-Smad3, which was inconsistent with the transcription level results. It may be due to the specificity of Smad2 and Smad3 antibody. Probably Smad2 and Smad3 proteins were not the total protein since the antibody, which means the Smad2 and Smad3 proteins were only the nonphosphorylated part. In this case, the detection of Western Blot was consistent with the results of transcriptome sequencing. In other words, BBR treatment maybe affects the expression of phosphorylation and total Smad2 and Smad3, but there was not much change in nonphosphorylation Smad2 and Smad3.Molecular docking analysis showed that BBR had a higher affinity for both TGFβR1 and TGFβR2. BBR probably regulated the TGF-β/Smad pathway through binding with TGFβR1 and TGFβR2. Therefore, we speculated that the TGF-β receptor is the significant and sensitive receptor of BBR on the cell surface. BBR first mediated the TGF-β/Smad and then PI3K/Akt and Wnt/β-catenin pathways. Consequently, EMT progression was restrained. BBR can enhance the effect of the TGFβR inhibitor SB on EMT, which indicated that there is no competitiveness between BBR and SB when binding with TGFβR. We speculated that the amino acid sites of the combination are different.The effect of Smad2 was contrary to previous reports, not only BBR but also the TGF-β. Our results suggested that the role of Smad2 is more complicated than previously known in the TGF-β/Smad pathway.As mentioned above, 5 papers have reported that BBR inhibits EMT through TGF-β/Smad pathway, 3 of which had the similar conclusions as the mainstream view, and BBR reduced p-Smad2 and p-Smad3. One paper reported that low concentrations of BBR (50 μM) could even increase p-Smad2 and p-Smad2/p-Smad3, but BBR of 100 or 200 μM decreased p-Smad2 and p-Smad3. The concentration (100 or 200 μM) was so high that gene expression reduction may be the effect of apoptosis. Our study displayed that the TGF-β/smad pathway was inconsistent with the traditional view, and BBR promotes p-Smad2. TGF-β of low concentration downregulated p-Smad2, TGFβ of high concentration was on the contrary. TGF-β accelerates the cancer cell proliferation and EMT. Smad2 may be a tumor suppressor under certain conditions. One paper reported that miR-27a upregulated in lung cancer cell lines and patients and impaired TGF-β signaling by inhibiting Smad2 and Smad4, and its overexpression decreased Smad2 and Smad4 mRNA and protein levels. TGF-β enhanced the proliferation in lung cancer cell with miR-27a, but the effect was reversed by Smad2 or Smad4 overexpression [35]. A study showed that Snail, Slug increased, and E-cadherin decreased with Smad2 siRNA or deletion of Smad2, but the results were opposite when interferenced Smad3 with Smad3 siRNA [46]. Some clinical research literature demonstrated Smad2 may be a tumor suppressor indeed, and patients with Smad2 deletion had a worse prognosis [50–53]. Further clarifying function of Smad2 is necessary.



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