Using less annotation workload to establish a pathological auxiliary diagnosis system for gastric cancer.

Pathological diagnosis of gastric cancer requires pathologists to have extensive clinical experience. To help pathologists improve diagnostic accuracy and efficiency, we collected 1,514 cases of stomach H&E-stained specimens with complete diagnostic information to establish a pathological auxiliary diagnosis system based on deep learning. At the slide level, our system achieves a specificity of 0.8878 while maintaining a high sensitivity close to 1.0 on 269 biopsy specimens (147 malignancies) and 163 surgical specimens (80 malignancies). The classified accuracy of our system is 0.9034 at the slide level for 352 biopsy specimens (201 malignancies) from 50 medical centers. With the help of our system, the pathologists' average false-negative rate and average false-positive rate on 100 biopsy specimens (50 malignancies) are reduced to 1/5 and 1/2 of the original rates, respectively. At the same time, the average uncertainty rate and the average diagnosis time are reduced by approximately 22% and 20%, respectively.

ATSE: a peptide toxicity predictor by exploiting structural and evolutionary information based on graph neural network and attention mechanism.

MOTIVATION: Peptides have recently emerged as promising therapeutic agents against various diseases. For both research and safety regulation purposes, it is of high importance to develop computational methods to accurately predict the potential toxicity of peptides within the vast number of candidate peptides. RESULTS: In this study, we proposed ATSE, a peptide toxicity predictor by exploiting structural and evolutionary information based on graph neural networks and attention mechanism. More specifically, it consists of four modules: (i) a sequence processing module for converting peptide sequences to molecular graphs and evolutionary profiles, (ii) a feature extraction module designed to learn discriminative features from graph structural information and evolutionary information, (iii) an attention module employed to optimize the features and (iv) an output module determining a peptide as toxic or non-toxic, using optimized features from the attention module. CONCLUSION: Comparative studies demonstrate that the proposed ATSE significantly outperforms all other competing methods. We found that structural information is complementary to the evolutionary information, effectively improving the predictive performance. Importantly, the data-driven features learned by ATSE can be interpreted and visualized, providing additional information for further analysis. Moreover, we present a user-friendly online computational platform that implements the proposed ATSE, which is now available at http://server.malab.cn/ATSE. We expect that it can be a powerful and useful tool for researchers of interest.

Downregulation of Frizzled-7 induces the apoptosis of hepatocellular carcinoma cells through inhibition of NF-κB.

The aim of the present study was to investigate the functional role of Frizzled-7 (FZD7) in the apoptosis of hepatoma cells. HepG2 and Huh-7 hepatocellular carcinoma (HCC) cell lines with FZD7 expression were selected for use in the present study. The small hairpin RNA (shRNA) eukaryotic expression vector specific to FZD7 was constructed using gene recombination, and was then transfected into HepG2 and Huh-7 hepatoma cell lines using Lipofectamine 2000 to assess whether the downregulation of FZD7 could affect the proliferative ability of these cells. The results demonstrated that the downregulation of FZD7 expression significantly inhibited the proliferative ability of both cell types through the induction of cell apoptosis, as evidenced using Cell Counting kit-8 assays and flow cytometry. Furthermore, the western blotting results demonstrated that silencing of FZD7 increased the activities of caspase-3 and caspase-9. These increases were also associated with the downregulation of the inhibitor of the apoptosis protein family. Additionally, it was revealed that silencing of FZD7 expression caused the downregulation of apoptosis regulator Bcl-2 and Bcl-XL in HepG2, and Huh-7 cells, as determined through western blot analysis and reverse transcription-quantitative polymerase chain reaction. In the following work, ELISA and western blot analysis revealed that the knockdown of FZD7 inhibited the expression and activities of nuclear factor-κB (NF-κB) p65. Furthermore, it was demonstrated that the expression levels of phosphylated-Smad2/3 were markedly upregulated in sh-FZD7-transfected HepG2 and Huh-7 cells. Then, shRNA eukaryotic expression vector specific to transforming growth factor (TGF)-ß receptor II was transfected into both cell lines to investigate the association between the TGF-ß/Smad signaling pathway and NF-κB p65. Notably, when the TGF-ß/Smad signaling pathway was inhibited, no significant differences in the cell apoptosis rate and NF-κB expression levels were identified in HCC cells. Overall, the results of the present study suggest that the shRNA-mediated knockdown of FZD7 induces apoptosis of hepatoma cell lines through the inhibition of NF-κB. In addition, the TGF-ß/Smad signaling pathway appeared to partially participate in the underlying molecular mechanism of FZD7 in HCC.

Short hairpin RNA silencing of TGF-ßRII and FZD-7 synergistically suppresses proliferation and metastasis of hepatocellular carcinoma cells.

Transforming growth factor-ß (TGF-ß) is a multifunctional regulator of cell growth, apoptosis, differentiation and migration. The Wnt/ß-catenin signaling pathway has been implicated in a wide spectrum of diseases, including numerous cancers and degenerative disease. The aim of the present study was to investigate if simultaneous blocking of TGF-ß and Wnt/ß-catenin signaling pathways exerts synergistic anti-tumor effects on hepatocellular carcinoma (HCC) cells. Short hairpin (sh) RNA eukaryotic expression vectors, specific to TGF-ß receptor II (RII) and Frizzled receptor (FZD)-7, were constructed by gene recombination. The expression vectors were transfected into human HCC HepG2 and Huh-7 cells using Lipofectamine 2000 to investigate the synergistic effects between TGF-ß and Wnt/ß-catenin signaling pathways on HCC cell proliferation, invasion and migration and the cell-cycle distribution. Western blot analysis was used to identify the expression of ß-catenin, c-Myc and cyclin D1 in transfected cells to investigate the underlying mechanisms that cause TGF-ß and Wnt/ß-catenin signaling in HCC cells. shTGF-ßRII-c and shFZD-7-2 were selected as the most efficient plasmids. A cell growth assay and colony-forming assay consistently demonstrated that the proliferative activity of the co-transfected group was significantly decreased compared to the single-transfected group. A wound healing invasion and migration assay demonstrated that co-transfection of shTGF-ßRII-c and shFZD-7-2 decreased the invasion and migration abilities of the cells compared with either single-transfected group. In addition, the present study demonstrated that the observed reduction in cell proliferation was due to the cells arresting at the G1 phase of the cell cycle, and the downregulation of ß-catenin, c-Myc and cyclin D1 impaired the proliferative and invasive abilities of the HCC cells. The present results demonstrate that simultaneous blocking of TGF-ß and Wnt/ß-catenin signaling by targeting TGF-ßRII and FZD-7 may inhibit the proliferation and metastasis of HCC cells more effectively compared with blocking either the TGF-ß or Wnt/ß-catenin pathway.

[Regulatory effect of Yangjing Capsule on the expressions of phosphor-Erk1 and phosphor-Akt1 in the corpus cavernosum of aged rats].

OBJECTIVE: To observe the effect of Yangjing Capsule on the expressions of P-Erk1 and P-Akt1 in the corpus cavernosum of aged rats and to explore its action mechanism. METHODS: Forty 24-month-old SD rats were equally randomized into an experimental and a control group, 10 selected from each group for detection of the eNOS expression before medication. The rats in the experimental group (n = 10) were treated intragastrically with Yangjing Capsule, while those in the control with physiological saline, both at 0.5 g per kg body weight per day for 4 weeks. Then all the rats were killed, and the corpus cavernosum tissues harvested for determination of the expressions of eNOS, P-Erk1 and P-Akt1 by HE staining, RT-PCR and immunohistochemistry. RESULTS: Obvious distension was observed in the experimental group, but not in the control. The expression of eNOS in the rat corpus cavernosum was significantly higher after treatment than before treatment in the experimental group (24.10 +/- 2.40 vs 18.80 +/- 2.04, P < 0.05), but presented no obvious difference in the control (18.15 +/- 1.98 vs 19.35 +/- 1.50, P > 0.05), and it was remarkably higher in the former than in the latter (P < 0.05). The expression of P-Erk1 was markedly lower in the experimental than in the control rats (0.71 +/- 0.13 vs 0.83 +/- 0.17, P < 0.01), but that of P-Akt1 exhibited no remarkable difference in the same condition of GAPDH between the two groups (0.58 +/- 0.17 vs 0.48 + 0.13, P > 0.01). CONCLUSION: Both P-Erk1 and P-Akt were expressed in the corpus cavernosum of the aged rats. Yangjing Capsule could improve the sexual function of aged rats, which might be associated with the lowered expression of P-Erk1.