Systematic Framework to Predict Early-Stage Liver Carcinoma Using Hybrid of Feature Selection Techniques and Regression Techniques

The liver is the human body’s mandatory organ, but detecting liver disease at an early stage is very difficult due to the hiddenness of symptoms. Liver diseases may cause loss of energy or weakness when some irregularities in the working of the liver get visible. Cancer is one of the most common diseases of the liver and also the most fatal of all. Uncontrolled growth of harmful cells is developed inside the liver. If diagnosed late, it may cause death. Treatment of liver diseases at an early stage is, therefore, an important issue as is designing a model to diagnose early disease. Firstly, an appropriate feature should be identified which plays a more significant part in the detection of liver cancer at an early stage. Therefore, it is essential to extract some essential features from thousands of unwanted features. So, these features will be mined using data mining and soft computing techniques. These techniques give optimized results that will be helpful in disease diagnosis at an early stage. In these techniques, we use feature selection methods to reduce the dataset’s feature, which include Filter, Wrapper, and Embedded methods. Different Regression algorithms are then applied to these methods individually to evaluate the result. Regression algorithms include Linear Regression, Ridge Regression, LASSO Regression, Support Vector Regression, Decision Tree Regression, Multilayer Perceptron Regression, and Random Forest Regression. Based on the accuracy and error rates generated by these Regression algorithms, we have evaluated our results. The result shows that Random Forest Regression with the Wrapper Method from all the deployed Regression techniques is the best and gives the highest R2-Score of 0.8923 and lowest MSE of 0.0618.

Investigations on Anticancer Potentials by DNA Binding and Cytotoxicity Studies for Newly Synthesized and Characterized Imidazolidine and Thiazolidine-Based Isatin Derivatives

Imidazolidine and thiazolidine-based isatin derivatives (IST-01–04) were synthesized, characterized, and tested for their interactions with ds-DNA. Theoretical and experimental findings showed good compatibility and indicated compound–DNA binding by mixed mode of interactions. The evaluated binding parameters, i.e., binding constant (Kb), free energy change (ΔG), and binding site sizes (n), inferred comparatively greater and more spontaneous binding interactions of IST-02 and then IST-04 with the DNA, among all compounds tested under physiological pH and temperature (7.4, 37 °C). The cytotoxic activity of all compounds was assessed against HeLa (cervical carcinoma), MCF-7 (breast carcinoma), and HuH-7 (liver carcinoma), as well as normal HEK-293 (human embryonic kidney) cell lines. Among all compounds, IST-02 and 04 were found to be cytotoxic against HuH-7 cell lines with percentage cell toxicity of 75% and 66%, respectively, at 500 ng/µL dosage. Moreover, HEK-293 cells exhibit tolerance to the increasing drug concentration, suggesting these two compounds are less cytotoxic against normal cell lines compared to cancer cell lines. Hence, both DNA binding and cytotoxicity studies proved imidazolidine (IST-02) and thiazolidine (IST-04)-based isatin derivatives as potent anticancer drug candidates among which imidazolidine (IST-02) is comparatively the more promising.

Reactive Oxygen Species-Mediated Cytotoxicity in Liver Carcinoma Cells Induced by Silver Nanoparticles Biosynthesized Using Schinus molle Extract

Hepatocellular carcinoma (HCC) is the most common primary liver malignancy and is ranked as the third most common cause of cancer-related mortality worldwide. Schinus molle (S. mole) L. is an important medicinal plant that contains many bioactive compounds with pharmacological properties. The role of S. molle leaf extract in the biosynthesis of silver nanoparticles (AgNPs) was determined. The biosynthesized AgNPs were thoroughly characterized by UV–vis spectrophotometry, transmission electron microscopy (TEM), X-ray diffraction (XRD), and dynamic light scattering (DLS) techniques. Furthermore, the cytotoxic effect of the biosynthesized AgNPs using S. molle (SMAgNPs) against HepG2 liver cancer cells was investigated. Reactive oxygen species generation, apoptosis induction, DNA damage, and autophagy activity were analyzed. The results clearly showed that the biosynthesized silver nanoparticles inhibited the proliferation of HepG2 by significantly (p < 0.05) inducing oxidative stress, cytotoxicity, DNA damage, apoptosis, and autophagy in a dose- and time-dependent manner. These findings may encourage integrating the potential of natural products and the efficiency of silver nanoparticles for the fabrication of safe, environmentally friendly, and effective anticancer agents.

In Vitro Antineoplastic and Antiviral Activity and In Vivo Toxicity of Geum urbanum L. Extracts

This study evaluated the in vitro antineoplastic and antiviral potential and in vivo toxicity of twelve extracts with different polarity obtained from the herbaceous perennial plant Geum urbanum L. (Rosaceae). In vitro cytotoxicity was determined by ISO 10993-5/2009 on bladder cancer, (T-24 and BC-3C), liver carcinoma (HEP-G2) and normal embryonic kidney (HEK-293) cell lines. The antineoplastic activity was elucidated through assays of cell clonogenicity, apoptosis induction, nuclear factor kappa B p65 (NFκB p65) activation and total glutathione levels. Neutral red uptake study was applied for antiviral activity. The most promising G. urbanum extract was analyzed by UHPLC–HRMS. The acute in vivo toxicity analysis was carried out following OEDC 423. The ethyl acetate extract of aerial parts (EtOAc-AP) exhibited the strongest antineoplastic activity on bladder cancer cell lines (IC50 = 21.33–25.28 µg/mL) by inducing apoptosis and inhibiting NFκB p65 and cell clonogenicity. EtOAc and n-butanol extracts showed moderate antiviral activity against human adenovirus type 5 and human simplex virus type I. Seventy four secondary metabolites (gallic and ellagic acid derivatives, phenolic acids, flavonoids, etc.) were identified in EtOAc-AP by UHPLC–HRMS. This extract induced no signs of acute toxicity in liver and kidney specimens of H-albino mice in doses up to 210 mg/kg. In conclusion, our study contributes substantially to the detailed pharmacological characterization of G. urbanum, thus helping the development of health-promoting phytopreparations.

Oral Bacterial Microbiota in Digestive Cancer Patients: A Systematic Review

The relation between the gut microbiota and human health is increasingly recognized. Recently, some evidence suggested that dysbiosis of the oral microbiota may be involved in the development of digestive cancers. A systematic review was conducted according to the PRISMA guidelines to investigate the association between the oral microbiota and digestive cancers. Several databases including Medline, Scopus, and Embase were searched by three independent reviewers, without date restriction. Over a total of 1654 records initially identified, 28 studies (2 prospective cohort studies and 26 case-controls) were selected. They investigated oral microbiota composition in patients with esophageal squamous cell carcinoma (n = 5), gastric cancer (n = 5), colorectal cancer (n = 9), liver carcinoma (n = 2), and pancreatic cancer (n = 7). In most of the studies, oral microbiota composition was found to be different between digestive cancer patients and controls. Particularly, oral microbiota dysbiosis and specific bacteria, such as Fusobacterium nucleatum and Porphyromonas gingivalis, appeared to be associated with colorectal cancers. Current evidence suggests that differences exist in oral microbiota composition between patients with and without digestive cancers. Further studies are required to investigate and validate oral–gut microbial transmission patterns and their role in digestive cancer carcinogenesis.

Prognostic value of the proportion of the sclerosing component in fibrolamellar liver carcinoma

Introduction. Fibrolamellar hepatocellular carcinoma (FLC), which develops most often in the younger population. In FLC, variable histoarchitectonics are noted, possibly the presence of a sclerosing component, foci of necrosis and dystrophy of tumor cells.Objective. Assessment of the influence of the proportion of the sclerosing component in fibrolamellar carcinoma (FLC) of the liver on the course and prognosis of the disease. Determination of the relationship between the proportion of the sclerosing component in the tumor and the frequency of microvascular invasion.Materials and methods. A retrospective study included 34 patients with a diagnosis of FLC, who underwent radical surgical treatment at the first stage. A histological assessment of the proportion (%) of the sclerosing component in FLC was made. The effect of the proportion of the sclerosing component on overall (OS) and relapse-free (DFS) survival was assessed. The analysis of the relationship between the proportion of the sclerosing component in the tumor and the frequency of microvascular invasion was carried out.Results. Significantly worse RFS was achieved in the groups of patients with a sclerosing component in FLC > 5% than in the group of patients with a sclerosing component in FLC ≤ 5% (p = 0.0010; p = 0.024; log – rank test). Median DDS in group 1 is 107 (95% CI, 22–192) months; at 2 – 11 (95% CI, 8–14) months; in 3 – 21 (95% CI, 8–33). The frequency of histologically confirmed microvascular invasion in the compared groups was 29, 74, 87.5%, respectively. OS was significantly worse in 2 groups (27 patients in total) with a sclerosing component in FLC > 5% than in the group of patients with a sclerosing component in FLC ≤ 5%. Median OS in group 1 120 (95% CI, 60–180) months; at 2 – 41 (95% CI, 15–92) months; in 3 – 69 (95% CI, 35–103). A direct relationship was found between an increase in the proportion of the sclerosing component in a tumor and an increase in the frequency of microvascular invasion.Conclusions. We can assume that the severity of the sclerosing component in the FLK tumor can serve as an effective morphological marker of a less favorable prognosis for this HCC subtype and correlate with the frequency of microvascular invasion.

Evaluation of Phytochemical Contents and In Vitro Antioxidant, Anti-Inflammatory, and Anticancer Activities of Black Rice Leaf (Oryza sativa L.) Extract and Its Fractions

Black rice leaves (Oryza sativa L.) are a major part of rice straw left in open fields after rice harvest as agricultural waste. In this study, crude ethanolic extract (CEE) and various solvent fractions (hexane (Hex), ethyl acetate (EtOAc), n-butanol (n-BuOH), and aqueous fractions) of black rice leaves were investigated for their bioactive compound contents as well as antioxidant, anti-inflammatory, and anticancer activities. The results demonstrated that among all the fractions, the n-BuOH fraction presented the greatest contents of total phenolics and flavonoids, while anthocyanins were found to be abundant in the n-BuOH and aqueous fractions, which also exhibited powerful antioxidant abilities according to DPPH and ABTS radical-scavenging assays and a reducing power assay. Regarding anti-inflammatory activity, CEE and EtOAc reduced the production of NO and cytokine secretion (PGE2, IL-6, and IL-1β) but displayed less effect on tumor necrosis factor α (TNF-α) release in lipopolysaccharide (LPS)-induced RAW 264.7 cells. They also significantly decreased iNOS and COX-2 protein expression. Additionally, the phenolics-rich ethyl acetate fraction showed the greatest activity against HepG2 liver carcinoma cells, inhibited cell growth, increased the Sub-G1 population, and induced apoptosis via mitochondrion-dependent mechanisms. In conclusion, black rice leaves, a byproduct of rice, exhibited strong antioxidant, anti-inflammatory, and anticancer capacities and might be useful for application in functional foods and the pharmaceutical industry.

Proteomics of lipid accumulation and DGAT inhibition in HepG2 liver carcinoma cells

<p>Non-alcoholic fatty liver disease (NAFLD) is a manifestation of the metabolic syndrome in the liver. It is marked by hepatocyte accumulation of triacylglycerol (TAG) rich lipid droplets. In some patients, the disease progresses to non-alcoholic steatohepatitis (NASH), characterized by cellular damage, inflammation and fibrosis. In some cases, cirrhosis and liver failure may occur. However, the pathogenesis of NAFLD is still unclear. The present project is based on the hypothesis that hepatocytes are equipped with mechanisms that allow them to manage lipid accumulation to a certain extent. Continued or increased lipid accumulation beyond this triggers molecular mechanisms such as oxidative stress, lipid peroxidation and cell death that aggravate the condition and cause disease progression. The aim of this project is to study the effects of lipid accumulation on the cells using proteomics approach to identify proteins involved in the disease progression. A cell culture model was used in the study. HepG2 cells, a human liver carcinoma cell line, were treated with a mixture of fatty acids (FA) to induce lipid accumulation. The lipid accumulation in HepG2 cells was measured with Oil red O assay and the effect of lipid accumulation on the proliferation of the cells was measured using an MTT cell proliferation assay. HepG2 cells treated with 1 mM FA mixture for 6 hours induced lipid accumulation 1.4 times of control with 90% of cell proliferation capacity of the control cells. The final and the only committed step in TAG biosynthesis is catalysed by acyl-CoA diacylglycerol acyltransferase (DGAT) enzymes. To investigate if limiting lipid accumulation in HepG2 cells would prevent molecular mechanisms of pathogenesis, inhibition of DGAT by small molecule inhibitors was performed. Among the three DGAT inhibitors (A922500, PF06424439 and PF04620110) tested, PF04620110 reduced the lipid accumulation to 1.2 fold of the control cells when they were treated with 100 μM of the inhibitor in the presence of 1 mM FA mixture for 6 h. Proteomic analyses were carried out for the control, FA-treated and inhibitor-treated cell groups to identify protein changes in the abundance. Functional analyses of the changed proteins identified suggest that lipid accumulation tends to adversely affect the functioning of the ER and the mitochondria. A complex interplay between the two organelles, possibly mediated by Ca2+ signalling may be vital in ensuring cell survival. PF04620110 was able to counter the FA induced changes in the abundance of some proteins involved in the metabolic processes but it had limited effect on the ER chaperones whose abundance in the inhibitor-treated sample was comparable to that of the FA-treated sample. These data provided important information for future discoveries of biomarkers and molecular mechanisms involved in the progression of NAFLD.</p>

Proteomics of lipid accumulation and DGAT inhibition in HepG2 liver carcinoma cells

<p>Non-alcoholic fatty liver disease (NAFLD) is a manifestation of the metabolic syndrome in the liver. It is marked by hepatocyte accumulation of triacylglycerol (TAG) rich lipid droplets. In some patients, the disease progresses to non-alcoholic steatohepatitis (NASH), characterized by cellular damage, inflammation and fibrosis. In some cases, cirrhosis and liver failure may occur. However, the pathogenesis of NAFLD is still unclear. The present project is based on the hypothesis that hepatocytes are equipped with mechanisms that allow them to manage lipid accumulation to a certain extent. Continued or increased lipid accumulation beyond this triggers molecular mechanisms such as oxidative stress, lipid peroxidation and cell death that aggravate the condition and cause disease progression. The aim of this project is to study the effects of lipid accumulation on the cells using proteomics approach to identify proteins involved in the disease progression. A cell culture model was used in the study. HepG2 cells, a human liver carcinoma cell line, were treated with a mixture of fatty acids (FA) to induce lipid accumulation. The lipid accumulation in HepG2 cells was measured with Oil red O assay and the effect of lipid accumulation on the proliferation of the cells was measured using an MTT cell proliferation assay. HepG2 cells treated with 1 mM FA mixture for 6 hours induced lipid accumulation 1.4 times of control with 90% of cell proliferation capacity of the control cells. The final and the only committed step in TAG biosynthesis is catalysed by acyl-CoA diacylglycerol acyltransferase (DGAT) enzymes. To investigate if limiting lipid accumulation in HepG2 cells would prevent molecular mechanisms of pathogenesis, inhibition of DGAT by small molecule inhibitors was performed. Among the three DGAT inhibitors (A922500, PF06424439 and PF04620110) tested, PF04620110 reduced the lipid accumulation to 1.2 fold of the control cells when they were treated with 100 μM of the inhibitor in the presence of 1 mM FA mixture for 6 h. Proteomic analyses were carried out for the control, FA-treated and inhibitor-treated cell groups to identify protein changes in the abundance. Functional analyses of the changed proteins identified suggest that lipid accumulation tends to adversely affect the functioning of the ER and the mitochondria. A complex interplay between the two organelles, possibly mediated by Ca2+ signalling may be vital in ensuring cell survival. PF04620110 was able to counter the FA induced changes in the abundance of some proteins involved in the metabolic processes but it had limited effect on the ER chaperones whose abundance in the inhibitor-treated sample was comparable to that of the FA-treated sample. These data provided important information for future discoveries of biomarkers and molecular mechanisms involved in the progression of NAFLD.</p>

Correlation of MKI67 with prognosis, immune infiltration, and T cell exhaustion in hepatocellular carcinoma

Background MKI67 plays a vital role in the tumour microenvironment (TME) and congenital immunity. The present work focuses on exploring the prognosis prediction performance of MKI67 and its associations with T cell activity and immune infiltration within numerous cancers, especially hepatocellular liver carcinoma (LIHC). Methods Oncomine, GEPIA2, and HPA were adopted to analyse MKI67 levels in different types of cancers. The prognostic prediction performance of MKI67 was evaluated through the TCGA portal, GEPIA2, LOGpc, and Kaplan–Meier Plotter databases. The associations of MKI67 with related gene marker sets and immune infiltration were inspected through TISIDB, GEPIA2, and TIMER. We chose MKI67 to analyse biological processes (BPs) and KEGG pathways related to the coexpressed genes. Furthermore, the gene–miRNA interaction network for MKI67 in liver cancer was also examined based on the miRWalk database. Results MKI67 expression decreased in many cancers related to the dismal prognostic outcome of LIHC. We found that MKI67 significantly affected the prognosis of LIHC in terms of histology and grade. Increased MKI67 levels were directly proportional to the increased immune infiltration degrees of numerous immune cells and functional T cells, such as exhausted T cells. In addition, several critical genes related to exhausted T cells, including TIM-3, TIGIT, PD-1, LAG3, and CXCL13, were strongly related to MKI67. Further analyses showed that MKI67 was associated with adaptive immunity, cell adhesion molecules (CAMs), and chemokine/immune response signal transduction pathways. Conclusion MKI67 acts as a prognostic prediction biomarker in several cancers, particularly LIHC. Upregulation of MKI67 elevates the degree of immune infiltration of many immune cell subtypes, including functional T cells, CD4+ T cells, and CD8+ T cells. Furthermore, MKI67 shows a close correlation with T cell exhaustion, which plays a vital role in promoting T cell exhaustion within LIHC. Detection of the MKI67 level contributes to prognosis prediction and MKI67 modulation within exhausted T cells, thus providing a new method to optimize the efficacy of anti-LIHC immunotherapy.