Comprehensive Bioinformatics Analysis and Machine Learning of TTK as a Transhepatic Arterial Chemoembolization Resistance Target in Hepatocellular Carcinoma.

Transhepatic arterial chemoembolization (TACE) is the standard treatment for intermediate-stage hepatocellular carcinoma (HCC). However, a significant proportion of patients are non-responders or poor responders to TACE. Therefore, our aim is to identify the targets of TACE responders or non-responders. GSE104580 was utilized to identify differentially expressed genes (DEGs) in TACE responders and non-responders. Following the protein-protein interaction (PPI) analysis, hub genes were identified using the MCC and MCODE plugins in Cytoscape software, as well as LASSO regression analysis. Gene set enrichment analysis (GSEA) was performed to investigate potential mechanisms. Subsequently, the hub genes were validated using data from The Cancer Genome Atlas (TCGA), the Cancer Cell Line Encyclopedia (CCLE), and The Human Protein Atlas (HPA) database. To evaluate the clinical significance of the hub genes, Kaplan-Meier (KM) survival and Cox regression analysis were employed. A total of 375 DEGs were identified, with 126 remaining following PPI analysis, and TTK, a dual-specificity protein kinase associated with cell proliferation, was ultimately identified as the hub gene through multiple screening methods. Data analysis from TCGA, CCLE, and HPA databases revealed elevated TTK expression in HCC tissues. GSEA indicated that the cell cycle, farnesoid X receptor pathway, PPAR pathway, FOXM1 pathway, E2F pathway, and ferroptosis could be potential mechanisms for TACE non-responders. Analysis of immune cell infiltration showed a significant correlation between TTK and Th2 cells. KM and Cox analysis suggested that HCC patients with high TTK expression had a worse prognosis. TTK may play a pivotal role in HCC patients' response to TACE therapy and could be linked to the prognosis of these patients.

Desmocollin-2 inhibits cell proliferation and promotes apoptosis in hepatocellular carcinoma via the ERK/c-MYC signaling pathway.

Hepatocellular carcinoma (HCC) is one of the most common cancers around the world with a poor prognosis. The main reason for poor prognosis is early stage HCC is inconspicuous so it is difficult to detect and effective treatment strategies are lacking for advanced HCC. In this context, novel molecular targets are urgently needed for the diagnosis and therapy of HCC. In this study, we investigated the expression level, biological function, and relative mechanism of Desmocollin-2(DSC2) in HCC. DSC2 expression levels were decreased significantly in HCC cell lines SMMC-7721(7721), Huh7, HCC-LM3(LM3), and MHCC-97H(97H), especially in LM3 cells, compared with human liver cell line L02(L02). DSC2 overexpression in LM3 cells could inhibit the proliferation (in vitro and in vivo), colony formation, migration, and invasion abilities of HCC cells, and promote cell apoptosis, while DSC2 inhibition in 7721 cells performed the opposite effect. Consistent with these results, regulating DSC2 expression in 7721 and LM3 cells could affect the expression levels of apoptosis-related proteins (Bax, Bcl-2, c-Caspase-3, Caspase-3, Caspase-8, and Survivin) and cell cycle-related proteins (Cyclin D1, Cyclin B1, CDK1, and CDK2). Furthermore, DSC2 expression was significantly negatively correlated with the levels of p-ERK and c-MYC in both LM3 and 7721 cell lines. These findings confirmed that DSC2 overexpression could inhibit the proliferation, migration, and invasion abilities while promoting apoptosis of HCC cells via the ERK/c-MYC signaling pathway. In a conclusion, DSC2 was a tumor suppressor with low expression in liver cancer.

Bioinformatic Deconstruction of Differentially Expressed Sequence Tags in Hepatocellular Carcinoma Based on Artificial Neural Network.

Traditional medical imaging methods for diagnosing hepatocellular carcinoma can only provide information for differential diagnosis in terms of morphology and blood supply of the lesion, and the determination of the nature of the lesion still relies on tissue biopsy. Although ultrasound or CT-guided biopsy has become an effective method for the diagnosis of liver cancer in recent years, the puncture has the possibility of tumor irritation, liver tumor rupture, or needle tract metastasis. In this paper, the use of bioinformatics method is to gradually screen potentially high-risk genes associated with HCC recurrence on a genome-wide scale would help to discover the key target molecules. The ANN method was used to establish a gene prediction model that can predict the recurrence and survival of HCC, so as to construct a tool to identify patients at risk of HCC recurrence. It provided a certain therapeutic basis for future clinical work, thereby improving the prognosis of patients with HCC. Using the "survfit" function of the "survival" package in the R language, the log-rank test (the log-rank test was a common method for comparing two survival curves) was performed on all genes with posthoc recurrence of hepatocellular carcinoma as the outcome event. Then, the BLAST tool (Basic Local Alignment Search Tool) was used to search the similarity of each hepatocellular carcinoma database to find out the genes with similar sequences to each hepatocellular carcinoma, so as to determine the function of each differentially expressed sequence tag. This paper found that the AUC of the ANN model was greater than that of the discriminant analysis model (P < 0.05). This paper promoted the development of new therapeutic measures for hepatocellular carcinoma and provided important theoretical guidance for human beings to fight cancer.

Serum N-glycan profiling as a diagnostic biomarker for the identification of hepatitis B virus-associated hepatocellular carcinoma.

Background: Changes in N-glycosylation of proteins are thought to play a key role in cancer. This study aims to investigate the changes in the serum N-glycan profiles of patients with hepatitis B virus (HBV)-related liver disease, and to evaluate the role of N-glycan markers in the noninvasive diagnosis of hepatocellular carcinoma (HCC). Methods: Serum samples were available for 21 patients with HCC, 20 patients with liver cirrhosis (LC), 20 patients with chronic hepatitis B (CHB), and 20 healthy subjects. Serum N-glycans were released and analyzed using DNA sequencer-assisted fluorophore-assisted carbohydrate electrophoresis (DSA-FACE). Serum AFP was determined by electrochemiluminescence (ECL) (AFP reference value range: <10 ng/mL). Results: There were characteristic changes in the serum N-glycan profiles of patients with HBV-related liver disease, including NA2FB, NA3, and NA3Fb. NA2FB was the most abundant in LC patients, while NA3Fb abundance was the highest in HCC patients. For HCC screening in patients, especially in patients with LC, the sensitive of Log peak 9 (94.4%) and Log (peak 9/peak 7) (88.9%) were better than alpha-fetoprotein (AFP) (33.3-61.1%), and their specificity was similar to that of AFP. The receiver operating characteristic (ROC) curve showed that the accuracy of Log peak 9 (AUC: 0.81±0.07) and Log (peak 9/peak 7) (AUC: 0.87±0.06) was better than that of AFP (AUC: 0.72±0.09), while the accuracy of AFP combined with the above 2 indexes was better than that of a single index. Moreover, Log (peak 9/peak 7) combined with AFP (AUC: 0.89±0.06) had the best accuracy in the diagnosis of HCC. Conclusions: Our research indicates that N-glycan may serve a new, valuable, and noninvasive alternative method for diagnosing HCC, and it may be a supplement to AFP in the diagnosis of HCC in patients with HBV-related liver disease.

Integrated bioinformatics analyses of key genes involved in hepatocellular carcinoma immunosuppression.

Hepatocellular carcinoma (HCC) is a typical inflammation-driven cancer. Chronically unresolved inflammation may remodel the immunosuppressive tumor microenvironment, which is rich in innate immune cells. The mechanisms via which HCC progresses through the evasion of the innate immune surveillance remain unclear. The present study thus aimed to identify key genes involved in HCC immunosuppression and to establish an innate immune risk signature, with the ultimate goal of obtaining new insight into effective immunotherapies. HCC and normal liver tissue mRNA expression and clinicopathological data were obtained from the Cancer Genome Atlas database. The immunosuppressive innate immune-related genes (IIRGs) in HCC were screened using integrated bioinformatics analyses. Gene expression was then validated using the Gene Expression Omnibus database and the Human Protein Atlas database, and tissues were obtained from patients with HCC who underwent surgery. In total, 3,676 genes were identified as differentially expressed mRNAs after comparing the HCC tissues with the normal liver tissues in TCGA. Gene Set Enrichment Analyses revealed 21 highly expressed IIRGs in HCC tissues. A survival analysis and Cox regression model were used to construct an innate immune risk signature, including three IIRGs: Collectin-12 (COLEC12), matrix metalloproteinase-12 (MMP12) and mucin-12 (MUC12) genes. Univariate and multivariate Cox analyses revealed that the signature of the three IIRGs was a robust independent risk factor in relation to the overall survival (OS) of patients with HCC. The expression of the three aforementioned IIRGs was confirmed through external validation. Moreover, COLEC12 and MMP12 expression significantly correlated with that of immune checkpoint molecules or immunosuppressive cytokines. The tumor immune dysfunction and exclusion tool predicted that the increased expression of the three IIRGs in patients with HCC was significantly associated with the efficacy of relatively poor immune checkpoint blockade therapy. Conclusively, a novel innate immune-related risk signature for patients with HCC was constructed and validated. This signature may be involved in immunosuppression, and may be used to predict a poor prognosis, functioning as a potential immunotherapeutic target for patients with HCC.

Validation and comparison of non-invasive prediction models based on liver stiffness measurement to identify patients who could avoid gastroscopy.

Several non-invasive tests (NITs) based on liver stiffness measurement (LSM) have been developed to rule out varices needing treatment (VNT), including the Baveno VI criteria (B6C), the expanded Baveno VI criteria (EB6C), the LSM-spleen diameter to platelet ratio score (LSPS), and the VariScreen algorithm. We aimed to validate and compare those NITs in patients with compensated advanced chronic liver disease (cACLD). This retrospective study enrolled 354 patients with cACLD; LSM, platelet count (PLT), international normalized ratio (INR), gastroscopy and spleen diameter (SD) were collected. VNT prevalence was 28.5%. In comparison, patients with VNT included higher LSM, INR, and SD and lower PLT. Gastroscopies were spared for 27.7% of patients using the B6C with 1.0% VNT missed rate, 47.2% of patients using the EB6C with 5.9% VNT missed rate, 57.6% of patients using the LSPS with 9.9% VNT missed rate, and 45.5% of patients using the VariScreen algorithm with 3.0% VNT missed rate. Only the B6C and the VariScreen algorithm could safely avoid gastroscopies, and the VariScreen algorithm spared more gastroscopies than the B6C. The results were consistent with the previous when performed subgroup analysis. In conclusion, the VariScreen algorithm performed the best and can be used in clinical.

Multiwalled carbon nanotubes co-delivering sorafenib and epidermal growth factor receptor siRNA enhanced tumor-suppressing effect on liver cancer.

OBJECTIVE: This study aimed to investigate the effects of multiwalled carbon nanotubes (MWNTs) co-delivering sorafenib (Sor) and epidermal growth factor receptor (EGFR) siRNA (MWNT/Sor/siRNA) on tumor growth in liver cancer (LC). RESULTS: MWNT/Sor/siRNA was proved to possess increased Sor release, high siRNA stability, and enhanced cellular uptake. In addition, MWNT treatment has few effects on cell proliferation and apoptosis in HepG2 cells; however, MWNT/Sor/siRNA treatment significantly inhibited clone number and induced cell apoptosis, which shows a more favorable antitumor effect than MWNT/Sor and free Sor and free siRNA in HepG2 cells. Moreover MWNT/Sor/siRNA treatment has the most significant antitumor effect in vivo. CONCLUSIONS: MWNT/Sor/siRNA exhibited a superior antitumor effect in vitro and in vivo. METHODS: The MWNT/Sor and MWNT/Sor/siRNA were prepared, and then the morphologies of MWNT/Sor/siRNA were analyzed. In vitro Sor release assay, siRNA stability and cellular uptake of MWNT/Sor/siRNA were performed as well. Next, the effects of MWNT, free Sor, free siRNA, MWNT/Sor and MWNT/Sor/siRNA were evaluated by colony-forming assay, and cell apoptosis assay in HepG2 cells. Meanwhile, the level of EGFR and proteins associated with apoptosis was tested. Furthermore, the anti-tumor effects of MWNT/Sor/siRNA on LC xenograft mice were also unraveled.

Comparing the diagnostic value of serum oligosaccharide chain (G-test) and alpha-fetoprotein for hepatitis B virus-related liver cancer.

OBJECTIVES: The study compared the diagnostic efficiency of serum oligosaccharide chain (G-test) and alpha-fetoprotein (AFP) for hepatitis B-related hepatocellular carcinoma (HCC). METHODS: Serum samples from 100 patients (divided into five groups of 20 each, namely the hepatitis, liver cirrhosis, liver cancer, health, and interference groups) who were admitted to the Second Affiliated Hospital of Nanchang University from October 2019 to January 2020 were collected, and the levels of G-test and AFP were determined. The sensitivity and specificity of the two indicators were compared, and the receiver operating characteristic curve of the subjects was drawn to evaluate the diagnostic values of G-test and AFP for HCC. RESULTS: The diagnostic ability of G-test (area under the curve [AUC]: 0.88 ± 0.05) was better than that of AFP (AUC: 0.76 ± 0.05). When G-test and AFP were combined for detection, the AUC was larger than that of either indicator. The G-test was superior to AFP in the differential diagnosis of early HCC and cirrhosis. A combination of the two indicators (AUC: 0.769 ± 0.05) significantly improved the diagnostic rate for early HCC, indicating that G-test and AFP complemented each other. CONCLUSION: G-test was better than AFP for screening HCC in patients with chronic hepatitis B and cirrhosis. The combination of the two further improved the diagnostic rate of hepatitis B-related liver cancer. The G-test improves the screening rate of early HCC in patients with cirrhosis. Therefore, these markers are of great clinical significance and can improve the sensitivity of HCC detection and reduce missed diagnosis rates.

Recombinant expression and biochemical characterization of a novel keratinase BsKER71 from feather degrading bacterium Bacillus subtilis S1-4.

Bacillus subtilis S1-4, isolated from chicken feather could efficiently degrade feathers by secreting several extracellular proteases. In order to get insight into the individual protease involved in keratin hydrolysis, a keratinase designed as BsKER71 was cloned and expressed in Bacillus subtilis WB600. In silico analysis revealed that BsKER71 protein contained a mature protein of 36.1 kDa. Further, purified BsKER71 could hydrolyze a variety of natural proteins, such as fibrous protein, collagen protein, casein, keratin and bovine serum albumin. In addition, this keratinase exhibited high enzyme activity in a wide range of pH and optimal pH of 10.0 and 9.0 in the hydrolysis of casein and keratin, respectively. Similarly, the optimal temperature was 55 °C and 50 °C for the hydrolysis of above two substrates, respectively. The hydrolytic activity was significantly inhibited by phenylmethanesulfonyl fluoride (PMSF), indicating the presence of serine residue in the active site. Moreover, ethylenediaminetetraacetic acid (EDTA) and phenanthroline moderately inhibited the hydrolytic activity. The catalytic activity was stimulated by Mg2+ and Ca2+, but greatly inhibited by Cu2+. Furthermore, several chemicals exhibited different effects on the hydrolysis of casein and keratin by BsKER71. These results provided a better understanding of BsKER71 from feather degrading bacterium B. subtilis S1-4.

LncRNA ANCR promotes hepatocellular carcinoma metastasis through upregulating HNRNPA1 expression.

LncRNA ANCR plays important roles in the modulation of epithelial mesenchymal transition (EMT) and tumour metastasis in many tumours. However, the role of ANCR in regulating hepatocellular carcinoma (HCC) metastasis is still not known. The current study aims to investigate the underlying mechanism for tumour oncogenesis of ANCR in HCC metastasis. HCC cell proliferation and migration/invasion were measured by MTT and Transwell assays. Xenograft model was established to determine the effect of ANCR on HCC growth and metastasis. ChIP assay was used to detect the H3 and H4 histone acetylation levels at the ANCR promoter region. RNA pull-down and RIP assay was performed to analyse the relationship between ANCR and heterogeneous nuclear ribonucleoprotein A1 (HNRNPA1). Dual-luciferase reporter gene assay was conducted to determine the interaction between ANCR and miR-140-3p. The results indicated that ANCR was highly expressed in HCC tissues and cells, which promoted the proliferation and migration/invasion of HCC cells. In vivo experiments showed interfering ANCR suppressed the growth and metastasis of HCC. H3/H4 histone acetylation levels at the ANCR promoter region were elevated in HCC tissues and cells, and interfering histone deacetylases 3 (HDAC3) significantly up-regulated ANCR expression. ANCR could bind to HNRNPA1, and promoted the expression of HNRNPA1 through regulating its degradation. In addition, ANCR upregulated the expression of HNRNPA1 through sponging miR-140-3p. Finally, we found that ANCR promoted the EMT and invasion/migration of HCC cells through regulating HNRNPA1. In conclusion, ANCR promoted HCC metastasis by upregulating HNRNPA1, inhibiting HNRNPA1 degradation and sponging miR-140-3p.

Research on a Visual Electronic Nose System Based on Spatial Heterodyne Spectrometer.

Light absorption gas sensing technology has the characteristics of massive parallelism, cross-sensitivity and extensive responsiveness, which make it suitable for the sensing task of an electronic nose (e-nose). With the performance of hyperspectral resolution, spatial heterodyne spectrometer (SHS) can present absorption spectra of the gas in the form of a two dimensional (2D) interferogram which facilitates the analysis of gases with mature image processing techniques. Therefore, a visual e-nose system based on SHS was proposed. Firstly, a theoretical model of the visual e-nose system was constructed and its visual maps were obtained by an experiment. Then the local binary pattern (LBP) and Gray-Level Co-occurrence Matrix (GLCM) were used for feature extraction. Finally, classification algorithms based on distance similarity (Correlation coefficient (CC); Euclidean distance to centroids (EDC)) were chosen to carry on pattern recognition analysis to verify the feasibility of the visual e-nose system.