Cell culture
The HCC cell lines SNU-739 and LM3 were cultured in DMEM supplemented with 10% fetal bovine serum (Invitrogen, CA, USA) and 1% penicillin-streptomycin in an incubator at 37°C with 5% CO2.
Western blotting analysis
The harvested cells were lysed with RIPA on ice for 30 min. Then, the proteins were harvested by low-temperature high-speed centrifugation for 10 min. The primary antibodies used in our study include Integrin Beta 1 polyclonal antibody (1:1000; Proteintech, 12594-1-AP, China), β-Actin monoclonal antibody (1:2000; Sigma-Aldrich, A5316, USA). Goat anti-rabbit HRP-conjugated antibody (1:5000; Beyotime, A0181, China) and goat anti-mouse HRP-conjugated antibody (1:5000; Beyotime, A0216, China) were used as secondary antibodies. Then, the ultra-high sensitivity ECL kit (Mishushengwu, MI00607A, China) was used for chromogenic development for 1 to 30 seconds. The bands were detected using a chemiluminescence system Tanon 5500 (Tanon Science & Technology, China). The ImageJ program was used to quantify the detected protein bands.
Wound healing assay
Cells were seeded into 6-well plates. When cells reached confluence, a wound was made with a 100-µL sterile pipette tip and photographed (0 h). The rate of wound closure was measured at different time points. Each experiment was performed in triplicate.
Plate colony formation assay
The trypsinized cells were suspended and seeded into 6-well plates peer well. two weeks later, the cells were washed with PBS and fixed with 4% paraformaldehyde for 15 minutes and stained with 0.5% (w/v) crystal violet (Sigma-Aldrich) for 15 minutes. Colons in the plate were scanned using Odyssey Scanner (LI-COR, Lincoln, NE, USA) and the number of colons was quantified by Image J software.
The soft agar colony formation assay
cells were resuspended in PRMI 1640 containing 10% fetal bovine serum along with 0.3% low-melting agarose and plated onto a layer of 0.5% agrarose-containing medium in 6-wells plate (5 000 to 10 000 cells per well). Colonies were counted after 2–3 weeks, a phase-contrast microscopic pictures were taken for each sample using a digital camera coupled to a microscope.
TIMER (Tumor Immune Estimation Resource)
TIMER (https://cistrome.shinyapps.io/timer/) is a web server that provides immune infiltrates’ abundances estimated by multiple immune deconvolution methods, and allows users to generate high-quality figures dynamically to explore tumor immunological, clinical and genomic features. In this study, we analyzed the correlation of ITGB1-YAP1, ITGB1-TEAD1 and ITGB1-TEAD3 in HCC by gene modules. The correlation analysis is the Spearman’s correlation, statistical significance with p < 0.05 was indicated with ∗; p < 0.01 was indicated with ∗∗; p < 0.001 were indicated with ∗∗∗; and p < 0.0001 were indicated with ∗∗∗∗.
GEPIA (Gene Expression Profiling Analysis) 2 Database
GEPIA2 (http://gepia2.cancer-pku.cn/#index) is an enhanced web server for large-scale expression profiling and interactive analysis. It has extended gene expression quantification from the gene level to the transcript level, and supports analysis of a specific cancer subtype, and comparison between subtypes. It features 198 619 isoforms and 84 cancer subtypes. In this paper, for the expression of ITGB1/YAP1/TEAD1/3 in figure, the threshold of |log2FC| was 1, p-value cutoff was 0.05. Statistical significance with p < 0.05 was indicated with ∗, p < 0.01 was indicated with ∗∗, p < 0.001 were indicated with ∗∗∗, and p < 0.0001 were indicated with ∗∗∗∗. Besides, in this study, we also generated the survival map of ITGB1/YAP1/TEAD1/3 in the “survival analysis” module, and the significance level was 0.05.
cBioPortal
The cBio Cancer Genomics Portal (www.cbioportal.org/) is an open-access platform for interactive study of multidimensional cancer genomics data sets, with data from over 5,000 tumor samples from 20 cancer studies now available. This study looked at copy number variation (CNV) of ITGB1 and YAP1 in HCC.
ODE (Ordinary differential equation) modeling
In this work, we have created a mathematical model of a positive feedback loop between integrin and YAP (or TEAD1/3). In particular, we have built a rudimentary dynamical model consisting of two molecules: YAP/TEAD (for the ability of cell proliferation) and ITGB1 (for the ability of cell adhesion). According to our experimental results, there are two main regulatory pathways: (1) YAP1 expression is enhanced by integrin, and (2) integrin expression is enhanced by YAP/TEAD. Michaelis-Menten kinetics can be used to characterize the dynamics of various chemical processes. To further mimic the dynamics of positive feedback loops, we used a coupled ordinary differential equation. The mathematical equations are as follows:
$$\frac{d\left[{C}_{ITGB1}\right]}{dt}=\left[{k}_{1f}+\delta \left(t\right)\frac{{{C}_{YAP-TEAD}}^{n}}{1+{{C}_{YAP-TEAD}}^{n}}\right]\left(1-\left[{C}_{ITGB1}\right]\right)-{k}_{1r}\left[{C}_{ITGB1}\right]$$
$$\frac{d\left[{C}_{YAP-TEAD}\right]}{dt}={k}_{2f}\left(1-\left[{C}_{YAP-TEAD}\right]\right)-{k}_{2r}\left[{C}_{YAP-TEAD}\right]$$
where \({k}_{1f}\) (1 s− 1) and \({k}_{2f}\) (1 s− 1) represent the basal values of protein production; and \({k}_{1r}\) (0.1 s− 1) and \({k}_{2r}\) (0.1 s− 1). Here, we assumed that \(\delta \left(t\right)\) is the positive feedback strength (from 0 and finally to 20); n (5) is Hill coefficient which represents the activation threshold. \(\left[{C}_{ITGB1}\right]\) and \(\left[{C}_{YAP-TEAD}\right]\) represent the concentrations of integrin, and YAP/TEAD molecules, respectively. All these concentrations are normalized to 1. Above all equations are solved numerically by Matlab.
Cellular Potts Model
The Cellular Potts Model (CPM) is a computational model of cells and tissues used to simulate individual and collective cell behavior, tissue morphogenesis and cancer development1. It is a spatial lattice-based formalism for the study of spatiotemporal behavior of biological cell populations. The details of intercellular interaction are essentially determined by the shape and the size of the individual cells as well as the length of the contact area between neighboring cells. Here is a general outline of how to build a Cellular Potts Model (CPM) for tumor cells entering the matrix microchannel from the left to the right: (1) Define the geometry of the microchannel and the initial position of the tumor cells. (2) Define the parameters of the CPM such as cell-cell adhesion energy, cell-substrate adhesion energy, and cell-cell surface tension. (3) Initialize the CPM lattice with cells and their properties. (4) Simulate the movement of cells using Monte Carlo methods. (5) Implement boundary conditions that reflect the geometry of the microchannel. (6) Analyze simulation results.
For each configuration of cells, the CPM utilizes a function known as the Hamiltonian H to characterize the energy (favorable behaviors). By selecting a random lattice site x, a section of a cell-cell interface, or a cell-media interface, cell motility evolved by trying to duplicate that site to a random nearby lattice site x'. The Hamiltonian was described as the product of four constraints, each of which stands for one of the four physical characteristics of simulated stem cells: 1) conservation of cell area, 2) locally polarized cell migration, 3) cell-cell adhesion, 4) and cell membrane length, which is frequently used to represent cortical tension. In the CPM, the objective was to reduce the Hamiltonian or the number of times that the ideal cellular behaviors were violated.
The free energy for a configuration of cells was defined as the sum of four constraints: local cell-cell/cell-ECM adhesion and cell area conservation:
$$H={H}_{adhesion}+{H}_{area}$$
For a configuration of cells, the free energy due to cell adhesion was
$${H}_{adhesion}=J(1-\delta ({\sigma }_{x},{\sigma }_{{x}^{{\prime }}}\left)\right)$$
where J represented the cell adhesion strength between lattice sites \({\sigma }_{x}\) and \({\sigma }_{{x}^{{\prime }}}\) that was defined by their cell type. The energy due to cells resisting changes from theirresting area was defined as,
$${H}_{area}=\sum \lambda {(a-A)}^{2}$$
where A represented the target area of a cell, a represented the current area of a cell, and \(\lambda\) was the relative strength of area conservation term.
Statistical analysis
GraphPad Prism 8 (GraphPad Software, San Diego, CA, USA) was used for statistical analysis. Data were presented as mean ± standard deviation (SD). Two-tailed Student's t-test was used to compare the difference between two samples. One-way analysis of variance (ANOVA) with Tukey post hoc test and Kruskal-Wallis test was performed for comparisons between three or four samples (*P < 0.05, **P < 0.01, ***P < 0.001, and ****P < 0.0001).