G6PD facilitates clear cell renal cell carcinoma invasion by enhancing MMP2 expression through ROS‑MAPK axis pathway

Glucose-6-phosphate dehydrogenase (G6PD) is crucial rate-limiting enzyme of the pentose phosphate pathway (PPP). G6PD dysregulation has been reported in various types of human cancer, and the role of G6PD in cancer progression was demonstrated in numerous studies. A previous study from our laboratory described the prognostic significance of G6PD in clear cell renal cell carcinoma (ccRCC), and demonstrated its proliferative role through positive feedback regulation of the phosphorylated form of signal transducer and activator of transcription 3. However, the role of G6PD in ccRCC invasion remains unclear. In the present study, reverse transcription-quantitative (RT-q) PCR, western blotting, enzyme activity assay, transwell assay and immunohistochemistry analysis in cell model, xenograft mice model and human specimen studies were performed to evaluate the role of G6PD in ccRCC invasion. The results from the present study demonstrated that G6PD may promote ccRCC cell invasive ability by increasing matrix metalloproteinase 2 (MMP2) mRNA and protein expression both in vitro and in vivo. In addition, a positive correlation between G6PD and MMP2 expression was demonstrated by RT-qPCR and western blotting in twenty pairs of ccRCC tumor specimens and matched adjacent normal tissues. Furthermore, G6PD promoted reactive oxygen species (ROS) generation and activated the MAPK signaling pathway in ccRCC cells. In addition, ROS significantly promoted the MAPK signaling pathway activation, which in turn contributed to MMP2 overexpression in ccRCC cells. In conclusion, the present study demonstrated that G6PD may facilitate ccRCC cell invasive ability by enhancing MMP2 expression through ROS-MAPK axis pathway.

Compositional characterization of Pyrus ussuriensis Maxim and their antioxidant activities and induction of apoptosis in Bel-7402 cell

In this work, a comparison study on active sites (the total phenolic, total flavonoids, and total triterpenes contents) and antioxidant activities (DPPH, ABTS, and FRAP assays) of different fractions from Pyrus ussuriensis Maxim was evaluated. Moreover, the inhibition capability on human hepatocarcinoma cells Bel-7402 cells and the mechanism was also discussed. Results showed that the ethyl acetate fraction significantly scavenged DPPH and ABTS⁺ radicals, exhibited ferric ion reducing antioxidant, and inhibited Bel-7402 cells proliferation. In addition, oleanolic acid was the dominant compound act on the Bel-7402 cells in the extract and it induced apoptosis by the caspase pathway and induced cell cycle arrest at the G0/G1 phase by inhibiting the cyclin D1/CDK4 pathway. The extracts of P. ussuriensis Maxim were confirmed to have anti-oxidative and antiproliferative effects against Bel-7402 cell in vitro. PRACTICAL APPLICATIONS: Fruits and vegetables which contain high levels of antioxidants can help to reduce the risk of chronic diseases such as cancer. Pyrus ussuriensis Maxim is a kind of edible and medical fruit with multiple bioactivities, whereas the capability to anti-lung cancer activity has not been investigated. The extracts of P. ussuriensis Maxim were revealed to have anti-oxidative and antiproliferative effects against Bel-7402 cell in vitro. Accordingly, it is the first time to verify that oleanolic acid was the main chemical components of P. ussuriensis with antitumor potential.

Rab22a is a novel prognostic marker for cell progression in breast cancer

Breast cancer (BC) is the most common female malignant tumor worldwide. The mechanism of tumorigenesis is still unclear. Ras‑related proteins in brain (Rab)22a belongs to the Ras superfamily, which may act as an oncogene and participate in carcinogenesis. The present study aims to identify whether Rab22a could be a novel biomarker of prognosis and determine the effects of Rab22a on BC cell progression. A total 258 BC and 56 para‑tumor or non‑tumor formalin fixed paraffin embedded tissues were stained through immunohistochemistry. The association between Rab22a expression and clinicopathological features, as well as overall survival status were analyzed. The expression level of Rab22a in breast cell lines were detected using reverse transcription‑quantitative PCR and western blotting. SK‑BR‑3 cells were infected with Rab22a short hairpin RNA lenti‑virus and the ability of cell proliferation, migration and invasion were measured. Gene Set Enrichment Analysis (GSEA) was employed to analyze the pathways involved in the Rab22a mRNA high level group. Rab22a was found to be overexpressed in BC tissues and upregulated in BC cells. High expression of Rab22a was related to a poor prognosis of patients with BC. Knockdown of Rab22a decreased the proliferation, migration and invasion ability of BC cells. GSEA indicated that certain pathways, including mammalian target of rapamycin complex 1 and protein secretion were upregulated, while pathways, such as hypoxia and KRas were downregulated in the Rab22a high level group. Rab22a is of prognostic value for BC and necessary for BC cell proliferation.

Ubiquitin-like modifier-activating enzyme 7 as a marker for the diagnosis and prognosis of breast cancer

Ubiquitin-like modifier-activating enzyme 7 (UBA7) is a specific E1-like ubiquitin-activating enzyme involved in interferon-stimulated gene 15 (ISG15) conjugation. UBA7 expression has been reported to be notably decreased in lung cancer. The present study aimed to investigate the changes in UBA7 expression in breast cancer and the association between UBA7 expression and clinical characteristics, and to elucidate the diagnostic and prognostic significance of UBA7 in breast cancer. The clinical data and RNA-sequencing expression values of 1,104 patients with breast cancer were downloaded from The Cancer Genome Atlas database. The associations between UBA7 expression and clinical characteristics were determined using χ2 and Fisher's exact tests. UBA7 expression values were divided into low and high groups using the optimal cut-off value, as determined by the overall survival (OS) value identified via a receiver operating characteristic (ROC) curve analysis, to further study the association between UBA7 expression and clinical characteristics. The diagnostic capability of UBA7 was assessed via ROC analysis, and Kaplan-Meier curve and Cox regression analyses were performed to determine the prognostic value of UBA7. The results demonstrated that UBA7 expression was decreased in breast cancer, and significant differences were observed between groups with regards to vital status, tumor classification, metastasis classification, histological type, sex, molecular subtype, and expression levels of progesterone receptor, estrogen receptor (ER) and human epidermal growth factor receptor 2. Low and high UBA7 expression levels were associated with age, ER expression, menopause status, Tumor-Node-Metastasis classification stage, margin status, vital status, radiation therapy use, OS and relapse-free survival. Furthermore, patients with low UBA7 expression levels had a poor prognosis. UBA7 expression also demonstrated an ability to diagnose patients at all clinical stages. Taken together, the results indicated that UBA7 expression was significantly decreased in breast cancer, and was associated with clinical characteristics and prognosis. Thus, UBA7 can be deemed as a potential biomarker in breast cancer, and may serve as a target in treatment.

Integrated analysis of miRNA and mRNA expression profiles in p53-edited PFF cells

p53 is the most frequently mutated gene in human cancers, with over half of all tumors harboring mutation at this locus. R248 and R249 (corresponding to porcine R241 and R242), are among the hotspot mutations frequently mutated in liver, lung, breast, and some other cancers. In this study, p53 gene was knocked out or point-edited (R241 and R242 were converted to 241W and 242S) in porcine fetal fibroblast (PFF) cells via CRISPR-Cas9 technique. High throughput sequencing of miRNA and mRNA uncovered a total of 225 differentially expressed miRNAs (DEMs) and 738 differentially expressed genes (DEGs) in the p53 knockout (p53-KO) cells, and a total of 211 DEMs and 722 DEGs in the point-modified (p53-241W242S) cells. Totally 28 annotated DEMs were found to overlap between p53-KO/p53-WT and p53-241W242S/p53-WT miRNAs datasets, of which miR-34 c, miR-218, miR-205, miR-105-1, miR-105-2, miR-206, miR-224 and miR-429 play important roles in p53 regulatory network. Among the top 10 DEGs in p53-KO and p53-241W242S cells, most genes were reported to be involved in tumors, cell proliferation or cell migration. p53-KO and p53-241W242S cells showed a significantly higher (P < 0.01) proliferation rate compared with p53-WT cells. In conclusion, genetic modifications of p53 gene significantly affect the expression levels of a large number of genes and miRNAs in the PFF cells. The p53-edited PFF cells could be used as non-tumor cell models for investigating the p53 signaling network, and as donor cells for somatic nuclear transfer, with the aim to develop porcine models with the corresponding p53 mutations.Abbreviations: CRISPR-Cas9: Clustered regularly interspaced short palindromic repeats-associated protein 9; PFF: porcine fetal fibroblasts; SCNT: somatic cell nuclear transfer; RNA sequencing: small RNA sequencing and mRNA sequencing; DEGs: differentially expressed mRNAs; DEMs: differentially expressed miRNAs.

Abnormal expression of ABCD3 is an independent prognostic factor for colorectal cancer

ATP binding cassette subfamily D member 3 (ABCD3) is a member of the superfamily of ATP-binding cassette (ABC) transporters, which serve crucial roles in the process of tumor cell resistance to chemotherapy. The present study investigated the diagnostic and prognostic capabilities of ABCD3 in colorectal cancer (CRC) by bioinformatics analysis. Gene expression data and corresponding clinical information of patients with CRC were collected from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. The results demonstrated that ABCD3 mRNA level was decreased in CRC tissues compared with normal tissues following Wilcoxon test analysis. Furthermore, ABCD3 protein expression was significantly higher in normal colon tissues compared with colon adenocarcinoma tissues according to the Human Protein Atlas. In addition, the area under the Receiver Operating Characteristic curve based on comparison between the tumor and normal groups derived from TCGA and GEO databases demonstrated that the use of ABCD3 mRNA level may be used for the diagnosis of CRC. ABCD3 expression was significantly associated with clinical stage, T stage, and lymph node status following Kruskal-Wallis test or Wilcoxon rank sum test, logistic regression and χ² test. Furthermore, the results from Kaplan-Meier survival analysis indicated that low ABCD3 mRNA expression had a poorer prognosis value compared with ABCD3 high expression in patients with CRC. In addition, results from univariate Cox regression analysis indicated that ABCD3 mRNA expression was associated with overall survival (OS), and results from multivariate Cox analysis indicated that ABCD3 mRNA expression may be considered an independent prognostic factor from other clinical factors, such as clinical stage, sex and age. The results from Gene Set Enrichment Analysis demonstrated that the ABCD3 high-expression phenotype was differentially enriched in five biological processes, including apoptosis, cell cycle, renal cell carcinoma, thyroid cancer and colorectal cancer. The findings from this study demonstrated that ABCD3 mRNA expression may be considered as a potential diagnostic and prognostic biomarker in patients with CRC. ABCD3 expression levels may participate in the regulation of cell apoptosis and cell cycle. In addition, GSEA analysis identified Kyoto Encyclopaedia of Genes and Genomes pathways for renal cell carcinoma, thyroid cancer and CRC involving ABCD3.

Expression-based, consistent biomarkers for prognosis and diagnosis in lung cancer

OVERVIEW

Lung cancer is one of the deadliest cancers in the world. Its histological classification depends on early diagnosis and successful treatment. Therefore, having specific biomarkers for a quick sorting widens the successful output of lung cancer treatment.

MATERIAL AND METHODS

High-throughput sequencing (RNA-seq) was performed of small cohorts of BioBanco samples from healthy and tumour cells from lung adenocarcinoma (LUAD) and squamous cell carcinoma of the lung (lSCC). RNA-seq samples from small cell lung cancer (SCLC) were downloaded from databases. A bioinformatic workflow has been programmed for the identification of differentially expressed genes (DEGs).

RESULTS

A total of 4777 DEGs were differentially expressed in SCLC, 3676 DEGs were in lSCC, while the lowest number of DEGs, 2819, appeared in LUAD. Among them, 945 DEGs were common to the three histological types. Once validated their expression profile and their survival predictive capacity in large, public cohorts, three DEGs can be exclusively considered as diagnostic biomarkers, three as prognosis biomarkers, and other three exhibit both diagnosis and prognosis capabilities.

CONCLUSIONS

This prospective study presents evidences for the diagnostic and prognostic capabilities of expression changes in CAPN8-2, TMC5 and MUC1 in LUAD, while they are non-significant in SCLC and lSCC. Their translation to clinical practice is proposed.

MicroRNA hsa-mir-3923 serves as a diagnostic and prognostic biomarker for gastric carcinoma

Gastric carcinoma (GC) refers to a common digestive system disease that exhibits a very high incidence. MicroRNA hsa-mir-3923 belongs to a type of miRNA, of which the function has been merely investigated in breast, pancreatic cancers and pre-neoplasic stages of gastric cancer. It has not been studied or reported in gastric carcinoma, so the relationship between gastric hsa-mir-3923 expression and the clinics feature and pathology of GC cases was examined. This study employed data mining for analyzing gastric carcinoma data in The Cancer Genome Atlas database. A Chi squared test was performed for assessing the relations of hsa-mir-3923 expression with clinics-related and pathology-regulated variables. This study conducted the assessment of the role of hsa-mir-3923 in prognostic process using Kaplan-Meier curves, Receiver operating characteristic (ROC) analysis and proportional hazards model (Cox) study. With the use of Gene Expression Omnibus, this study carried out gene set enrichment analysis (GSEA). In the meantime, the common miRNA database was compared to predict potential target genes; as revealed by co-expression analysis, a regulatory network probably existed, containing hsa-mir-3923. For the analysis of the most tightly associated cytological behavior and pathway in GC, this study adopted the databases for Annotation, Visualization and Integrated Discovery (David) and KO-Based Annotation System (KOBAS). Cytoscape, R and STRING were employed for mapping probable regulatory networks displaying relations to hsa-mir-3923. Lastly, we obtained 69 genes most tightly associated with hsa-mir-3923 and described their relationship with Circos plot. As revealed from the results, hsa-mir-3923 displayed up-regulation in gastric carcinoma, and it displayed associations with vital status, N stage and histologic grade when being expressed. The predicted results of miRNA target genes suggested that there may be a close relationship between 66 genes and hsa-mir-3923 in gastric cancer. As indicated from co-expression data, a small regulating network of 4 genes probably existed. Our results elucidated that hsa-mir-3923 high-expression reveals poor prognosis of GC patients.

Identification and integrated analysis of hepatocellular carcinoma-related circular RNA signature

Background

Circular RNAs (circRNAs), a novel type of non-coding RNA, play a vital role in the pathogenesis and development of cancer. CircRNAs signatures may be useful as prognostic and predictive factors as well as clinical tools for evaluating disease status and prognosis. This study was carried out to explore novel circRNA signatures in hepatocellular carcinoma (HCC).

Methods

The expression profiles of circRNAs were retrieved from the Gene Expression Omnibus (GEO). The expression profiles of miRNAs and mRNAs were obtained from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) database. The results of the microarray were validated by quantitative real-time RCR (qPCR). Based on circRNA-miRNA pairs and miRNA-mRNA pairs, a competitive endogenous RNA (ceRNA) network was constructed. Functional analysis was performed via Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), gene set enrichment analysis (GSEA), and gene set variation analysis (GSVA). Furthermore, survival analysis was carried out using the Kaplan-Meier curve and the log-rank test.

Results

Differentially expressed circRNAs in HCC from GEO databases (GSE94508 and GSE97332) were screened and analyzed using the bioinformatics method. We detected a total of 26 differentially expressed circRNAs by qPCR and then selected 6 circRNAs to construct the circRNA-miRNA-mRNA networks. Through prognostic analysis, 3 target hub genes (AURKA, KIF5B, and RHOA) of circRNAs were discovered. Moreover, GSEA and GSVA were used to reveal the functions of AURKA, KIF5B, and RHOA in HCC.

Conclusions

We identified three hub genes, and our results suggest that the circHMGCS1/miR-581/AURKA, circHMGCS1/miR-892a/KIF5B, and circTMCO3/miR-577/RHOA axes may play a vital role in HCC progression.

Optimizing deep belief network parameters using grasshopper algorithm for liver disease classification

Image processing plays a vital role in many areas such as healthcare, military, scientific and business due to its wide variety of advantages and applications. Detection of computed tomography (CT) liver disease is one of the difficult tasks in the medical field. Hand crafted features and classifications are the two types of methods used in the previous approaches, to classify liver disease. But these classification results are not optimal. In this article, we propose a novel method utilizing deep belief network (DBN) with grasshopper optimization algorithm (GOA) for liver disease classification. Initially, the image quality is enhanced by preprocessing techniques and then features like texture, color and shape are extracted. The extracted features are reduced by utilizing the dimensionality reduction method like principal component analysis (PCA). Here, the DBN parameters are optimized using GOA for recognizing liver disease. The experiments are performed on the real time and open source CT image datasets which embraces normal, cyst, hepatoma, and cavernous hemangiomas, fatty liver, metastasis, cirrhosis, and tumor samples. The proposed method yields 98% accuracy, 95.82% sensitivity, 97.52% specificity, 98.53% precision, and 96.8% F‐1 score in simulation process when compared with other existing techniques.

UHPLC-ESI-HRMS/MS analysis on phenolic compositions of different E Se tea extracts and their antioxidant and cytoprotective activities

E Se tea, prepared from the leaves of Malus toringoides (Rehd.) Hughes, is a traditional beverage, but there is little known about its chemical substances. This paper is aimed to investigate the chemical composition, antioxidant, and cytoprotective activities of the extract and fractions from E Se tea. Sixteen compounds were characterized by UHPLC-ESI-HRMS/MS. Phloridzin was the main compound, especially in ethyl acetate fraction (EAF). Moreover, EAF had the highest total phenolic and flavonoid contents with 197.54 ± 7.52 mg gallic acid equivalents/g extract and 85.94 ± 5.39 mg rutin equivalents/g extract, respectively, and exhibited the strongest antioxidant capacity (DPPH: IC₅₀ = 54.91 ± 3.38 μg/mL; ABTS: IC₅₀ = 98.08 ± 6.92 μg/mL). Different fractions of E Se tea, especially EAF, significantly inhibited intracellular ROS generation, reduced cell apoptosis, and decreased oxidative stress damage in H₂O₂-induced HepG-2 cells. Therefore, the obtained results highlight that E Se tea is a promising source for functional beverage or nutritional foods.

Upregulation of exosomal microRNA‑21 in pancreatic stellate cells promotes pancreatic cancer cell migration and enhances Ras/ERK pathway activity

Pancreatic stellate cells (PSCs) are typically activated in pancreatic ductal adenocarcinoma (PDAC) and release exosomes containing high levels of microRNA‑21 (miR‑21). However, the specific roles of exosomal miR‑21 in regulating the PDAC malignant phenotype remain unknown. The present study aimed to determine the effects of exosomal miR‑21 on the migratory ability of PDAC cells and explore the potential underlying molecular mechanism. Weighted gene correlation network and The Cancer Genome Atlas database analysis revealed that high miR‑21 levels were associated with a poor prognosis in patients with pancreatic adenocarcinoma, and that the Ras/ERK signaling pathway may be a potential target of miR‑21. In vitro, PDAC cells were demonstrated to internalize the PSC-derived exosome, resulting in high miR‑21 levels, which subsequently promoted cell migration, induced epithelial‑to‑mesenchymal transition (EMT) and increased matrix metalloproteinase‑2/9 activity. In addition, exosomal miR‑21 increased the levels of ERK1/2 and Akt phosphorylation in PDAC cells. Collectively, these results suggested that PSC‑derived exosomal miR‑21 may promote PDAC cell migration and EMT and enhance Ras/ERK signaling activity. Thus, miR‑21 may be a potential cause of poor prognosis in patients with pancreatic cancer and a new treatment target.

Small Nucleolar RNA Host Gene 1 (SNHG1) and Chromosome 2 Open Reading Frame 48 (C2orf48) as Potential Prognostic Signatures for Liver Cancer by Constructing Regulatory Networks

Background

Liver cancer is a common malignant tumor with poor prognosis. The present study sought to identify potential signatures that can predict the prognosis of patients with liver cancer.

Material/Methods

The RNA sequencing (RNA-seq) and clinical information of liver cancer patients were obtained from the Cancer Genome Atlas (TCGA) database. Differentially expressed long noncoding RNAs (lncRNAs), microRNAs (miRNAs), and messenger RNAs (mRNAs) were identified between liver cancer and adjacent normal tissues. After predicting lncRNA–miRNA and miRNA–mRNA pairs using online databases, the competing endogenous RNA (ceRNA) networks were constructed. Furthermore, the prognostic value of these differentially expressed genes was evaluated using univariate and multivariate Cox regression analyses.

Results

After constructing the ceRNA network, 2 lncRNAs small nucleolar RNA host gene 1 (SNHG1) and chromosome 2 open reading frame 48 (C2orf48) with the most nodes were identified. Correlation analysis revealed that SNHG1 was correlated with miR-195 and C2orf48 was correlated with miR-195 and miR-93. High expression of SNHG1, C2orf48, and miR-93 can contribute to poorer clinical outcomes compared to low expression. Furthermore, low miR-195 expression was correlated with shorter survival time than was high expression. SNHG1 and C2orf48 were closely associated with histology grade. Univariate and multivariate Cox regression analyses confirmed that SNHG1 and C2orf48 are risk factors for liver cancer.

Conclusions

Our findings revealed that SNHG1 and C2orf48 possess potential prognostic value and should be considered as possible biomarkers for predicting clinical outcomes for patients with liver cancer.

Comprehensive evaluation of SPATS2 expression and its prognostic potential in liver cancer

Spermatogenesis associated serine rich 2 (SPATS2) has been reported to be dysregulated in few types of cancer; however, no reports have investigated SPATS2 in liver cancer. The aim of the present study was to investigate SPATS2 expression in liver cancer and to analyze its association with the prognosis of liver cancer patients.We examined the differential expression of SPATS2 in liver cancer by exploring The Cancer Genome Atlas (TCGA) database. The diagnostic efficiency of SPATS2 was obtained by Receiver Operating Characteristic (ROC) curve. The Chi-Squared test was used to assess clinical relevance. Survival analysis and Cox regression model were used to detect the effect of SPATS2 on the survival of liver cancer patients. Gene Set Enrichment Analysis (GSEA) was used to identify signaling pathways related to SPATS2 expression.SPATS2 is highly expressed in liver cancer (P < 2.2e-16) and has the high diagnostic ability (AUC = 0.964). Survival analysis showed that patients with high SPATS2 expression have an apparently shorter overall survival (OS, P < .0001) and relapse-free survival (RFS, P < .0001). Cox regression analysis showed that high SPATS2 expression might be an independent risk factor for liver cancer (OS, HR = 2.41, P = .000; RFS, HR = 1.90, P < .001). GSEA analysis identified 3 signaling pathways (Mitotic spindle, G2 M checkpoint, E2F targets) that were enriched in the presence of high SPATS2 expression.SPATS2 expression could be a novel diagnostic and prognostic biomarker in liver cancer.

The prognostic value of lncRNA SNHG4 and its potential mechanism in liver cancer

BACKGROUND AND OBJECT

Emerging evidence shows that non-coding RNA functions as new gene regulators and prognostic markers in several cancers, including liver cancer. Here, we focused on the small nucleolar RNA host gene 4 (SNHG4) in liver cancer prognosis based on The Cancer Genome Atlas (TCGA) data.

METHODS

The expression data and clinical information were downloaded from TCGA. Chi-square tests evaluated the correlation between SNHG4 expression and clinical parameters. Differences in survival between high and low expression groups (optic cutoff value determined by ROC) from Cox regression analysis were compared, and P-value was calculated by a log-rank test. Kaplan-Meier curves were compared with the log-rank test. GSEA and ceRNA network were conducted to explore the potential mechanism.

RESULTS

Data mining of lncRNA expression data for 371 patients with primary tumor revealed overexpression of SNHG4 in liver cancer. High SNHG4 expression was correlated with histological type (P = 0.01), histologic grade (P = 0.001), stage (P = 0.01), T classification (P = 0.004) and survival status (P = 0.013). Patients with high SNHG4 expression had poor overall survival and relapse-free survival compared with those with low SNHG4 expression. Multivariate analysis identified SNHG4 as an independent prognostic factor of poor survival in liver cancer. GSEA revealed related signaling pathway and ceRNA network explored the further mechanism.

CONCLUSION

High SNHG4 expression is an independent predictor of poor prognosis in liver cancer.

Clinical characteristics and prognostic value of MEX3A mRNA in liver cancer

BACKGROUND

MEX3A is an RNA-binding proteins (RBPs) that promotes the proliferation, invasion, migration and viability of cancer cells. The aim of this study was to explore the clinicopathological characteristics and prognostic significance of MEX3A mRNA expression in liver cancer.

METHODS

RNA-Seq and clinical data were collected from The Cancer Genome Atlas (TCGA). Boxplots were used to represent discrete variables of MEX3A. Chi-square tests were used to analyze the correlation between clinical features and MEX3A expression. Receiver operating characteristic (ROC) curves were used to confirm diagnostic ability. Independent prognostic ability and values were assessed using Kaplan-Meier curves and Cox analysis.

RESULTS

We acquired MEX3A RNA-Seq from 50 normal liver tissues and 373 liver cancer patients along with clinical data. We found that MEX3A was up-regulated in liver cancer which increased according to histological grade (p < 0.001). MEX3A showed moderate diagnostic ability for liver cancer (AUC = 0.837). Kaplan-Meier curves and Cox analysis revealed that the high expression of MEX3A was significantly associated with poor survival (OS and RFS) (p < 0.001). Moreover, MEX3A was identified as an independent prognostic factor of liver cancer (p < 0.001).

CONCLUSIONS

MEX3A expression shows promise as an independent predictor of liver cancer prognosis.

Development and application of two novel monoclonal antibodies against overexpressed CD26 and integrin α3 in human pancreatic cancer

Monoclonal antibody (mAb) technology is an excellent tool for the discovery of overexpressed cell surface tumour antigens and the development of targeting agents. Here, we report the development of two novel mAbs against CFPAC-1 human pancreatic cancer cells. Using ELISA, flow cytometry, immunoprecipitation, mass spectrometry, Western blot and immunohistochemistry, we found that the target antigens recognised by the two novel mAbs KU44.22B and KU44.13A, are integrin α3 and CD26 respectively, with high levels of expression in human pancreatic and other cancer cell lines and human pancreatic cancer tissue microarrays. Treatment with naked anti-CD26 mAb KU44.13A did not have any effect on the growth and migration of cancer cells nor did it induce receptor downregulation. In contrast, treatment with anti-integrin α3 mAb KU44.22B inhibited growth in vitro of Capan-2 cells, increased migration of BxPC-3 and CFPAC-1 cells and induced antibody internalisation. Both novel mAbs are capable of detecting their target antigens by immunohistochemistry but not by Western blot. These antibodies are excellent tools for studying the role of integrin α3 and CD26 in the complex biology of pancreatic cancer, their prognostic and predictive values and the therapeutic potential of their humanised and/or conjugated versions in patients whose tumours overexpress integrin α3 or CD26.

The Emerging Role of Adhesion GPCRs in Cancer

Aberrant expression, function, and mutation of G protein-coupled receptors (GPCRs) and their signaling partners, G proteins, have been well documented in many forms of cancer. These cell surface receptors and their endogenous ligands are implicated in all aspects of cancer including proliferation, angiogenesis, invasion, and metastasis. Adhesion GPCRs (aGPCRs) form the second largest family of GPCRs, most of which are orphan receptors with unknown physiological functions. This is mainly due to our limited insight into their structure, natural ligands, signaling pathways, and tissue expression profiles. Nevertheless, recent studies show that aGPCRs play important roles in cell adhesion to the extracellular matrix and cell-cell communication, processes that are dysregulated in cancer. Emerging evidence suggests that aGPCRs are implicated in migration, proliferation, and survival of tumor cells. We here review the role of aGPCRs in the five most common types of cancer (lung, breast, colorectal, prostate, and gastric) and emphasize the importance of further translational studies in this field.

Identification of Platform-Independent Diagnostic Biomarker Panel for Hepatocellular Carcinoma Using Large-Scale Transcriptomics Data

The high mortality rate of hepatocellular carcinoma (HCC) is primarily due to its late diagnosis. In the past, numerous attempts have been made to design genetic biomarkers for the identification of HCC; unfortunately, most of the studies are based on small datasets obtained from a specific platform or lack reasonable validation performance on the external datasets. In order to identify a universal expression-based diagnostic biomarker panel for HCC that can be applicable across multiple platforms, we have employed large-scale transcriptomic profiling datasets containing a total of 2,316 HCC and 1,665 non-tumorous tissue samples. These samples were obtained from 30 studies generated by mainly four types of profiling techniques (Affymetrix, Illumina, Agilent, and High-throughput sequencing), which are implemented in a wide range of platforms. Firstly, we scrutinized overlapping 26 genes that are differentially expressed in numerous datasets. Subsequently, we identified a panel of three genes (FCN3, CLEC1B, and PRC1) as HCC biomarker using different feature selection techniques. Three-genes-based HCC biomarker identified HCC samples in training/validation datasets with an accuracy between 93 and 98%, Area Under Receiver Operating Characteristic curve (AUROC) in a range of 0.97 to 1.0. A reasonable performance, i.e., AUROC 0.91–0.96 achieved on validation dataset containing peripheral blood mononuclear cells, concurred their non-invasive utility. Furthermore, the prognostic potential of these genes was evaluated on TCGA-LIHC and GSE14520 cohorts using univariate survival analysis. This analysis revealed that these genes are prognostic indicators for various types of the survivals of HCC patients (e.g., Overall Survival, Progression-Free Survival, Disease-Free Survival). These genes significantly stratified high-risk and low-risk HCC patients (p-value <0.05). In conclusion, we identified a universal platform-independent three-genes-based biomarker that can predict HCC patients with high precision and also possess significant prognostic potential. Eventually, we developed a web server HCCpred based on the above study to facilitate scientific community (http://webs.iiitd.edu.in/raghava/hccpred/).

Screening and Discovery of New Potential Biomarkers and Small Molecule Drugs for Cervical Cancer: A Bioinformatics Analysis

BACKGROUND

Cervical cancer (CC) is the second most common type of malignant tumor survival rate is low in advanced stage, metastatic, and recurrent CC patients. This study aimed at identifying potential genes and drugs for CC diagnosis and targeting therapies.

METHODS

Three GEO mRNA microarray datasets of CC tissues and non-cancerous tissues were analyzed for differentially expressed genes (DEGs) by limma package. GO (Gene Ontologies) and KEGG (Kyoto Encyclopedia of Genes and Genomes) were used to explore the relationships between the DEGs. Protein-protein interaction (PPI) of these genes was established by the STRING database. MCODE was used for screening significant modules in the PPI networks to select hub genes. Biochemical mechanisms of the hub genes were investigated with Metascape. GEPIA database was used for validating the core genes. According to these DEGs, molecular candidates for CC were recognized from the CMAP database.

RESULTS

We identified 309 overlapping DEGs in the 2 tissue-types. Pathway analysis revealed that the DEGs were involved in cell cycle, DNA replication, and p53 signaling. PPI networks between overlapping DEGs showed 68 high-connectivity DEGs that were chosen as hub genes. The GEPIA database showed that the expression levels of RRM2, CDC45, GINS2, HELLS, KNTC1, MCM2, MYBL2, PCNA, RAD54 L, RFC4, RFC5, TK1, TOP2A, and TYMS in CC tissues were significantly different from those in the healthy tissues and were significantly relevant to the OS of CC. We found 10 small molecules from the CMAP database that could change the trend of gene expression in CC tissues, including piperlongumine and chrysin.

CONCLUSIONS

The 14 DEGs identified in this study could serve as novel prognosis biomarkers for the detection and forecasting of CC. Small molecule drugs like piperlongumine and chrysin could be potential therapeutic drugs for CC treatment.

Elevated high mobility group A2 expression in liver cancer predicts poor patient survival

BACKGROUND

liver cancer is a malignant tumor with a high morbidity and mortality that endangers human health. High mobility group A2 (HMGA2) is a chromosome associated protein that participates in embryogenesis, tissue development, tumorigenesis and development.

OBJECTIVE

to explore the relationship between HMGA2 expression and the clinicopathological parameters and survival of liver cancer patients using The Cancer Genome Atlas Liver Hepatocellular Carcinoma (HCC) data.

METHODS

RNA-sequencing data and the corresponding clinical characteristics of the patients were downloaded from the Atlas database. The Chi-squared test was used to assess the relationship between HMGA2 expression and clinical variables. Cox regression analysis was used to compare survival rates between the high- and low-expressing groups; the p-values and Kaplan-Meier survival curves were compared using the log-rank test.

RESULTS

RNA-seq data from 373 cases of liver cancer cases were analyzed. HMGA2 was overexpressed in liver cancer and significantly associated with gender (p = 0.0357), T classification (p = 0.0063), clinical classification (p = 0.0026) and overall survival (p = 0.0386). According to the multivariate analysis, HMGA2 could independently predict overall survival in liver cancer.

CONCLUSIONS

HMGA2 independently predicts poor prognosis in liver cancer and serves as a molecular marker to determine disease prognosis.

LncRNA ROR1‑AS1 high expression and its prognostic significance in liver cancer

Hepatocellular carcinoma (HCC) is a common disease of the digestive system with no curative treatments. Long noncoding RNA tyrosine protein kinase transmembrane receptor 1 antisense RNA 1 (lncRNA ROR1‑AS1) is an lncRNA whose functions have been predicted in human diseases; however, its important role in cancer has been probed only in mantle cell lymphoma, not in HCC. Therefore, the present study aimed to elucidate the prognostic significance of lncRNA ROR1‑AS1 in HCC. The Cancer Genome Atlas Liver Hepatocellular Carcinoma was used to analyze the expression of ROR1‑AS1 in liver cancer. χ2 tests were performed to evaluate associations between clinical characteristics and ROR1‑AS1 expression. The role of ROR1‑AS1 in HCC prognosis was assessed using Kaplan‑Meier curves and proportional hazards model (Cox) analysis. Gene set enrichment analysis was performed by using a Gene Expression Omnibus dataset. At the same time, Multi Experiment Matrix was used to predict genes that may be co‑expressed with ROR1‑AS1. The Database for Annotation, Visualization and Integrated Discovery and KO‑Based Annotation System were used to analyze the most closely associated cytological behaviors and pathways in HCC. Then, the genes in the three databases were integrated to screen mRNAs, microRNAs and lncRNAs that had co‑expression relationships with ROR1‑AS1. Cytoscape, Search Tool for the Retrieval of Interacting Genes/Proteins and Molecular Evolutionary Genetics Analysis were used to map potential regulatory networks and developmental relationships associated with ROR1‑AS1. Finally, 12 genes most closely associated with ROR1‑AS1 were identified, and their relationship was described using a Circos plot. The results showed that ROR1‑AS1 was upregulated in HCC, and its expression was related to clinical stage, T stage and N stage. Furthermore, Kaplan‑Meier curves and Cox analysis indicated that high expression of ROR1‑AS1 was associated with poor prognosis, and that ROR1‑AS1 was an independent risk factor for HCC. Co‑expression data suggested that there may be a large regulatory network of 45 genes with indirect associations with ROR1‑AS1, a small regulatory network of 15 genes with direct or indirect regulatory relationships, and a special regulatory network containing 12 genes directly associated with ROR1‑AS1. The present findings indicated that high expression of ROR1‑AS1 suggests poor prognosis in patients with HCC.

GPSM2 Serves as an Independent Prognostic Biomarker for Liver Cancer Survival

BACKGROUND AND OBJECTIVE

Liver cancer is a malignancy with a poor prognosis. G protein signaling modulator 2 is mainly related to cell division and cell cycle regulation. In this review, the relationship between G protein signaling modulator 2 and clinical characteristics of patients with liver cancer has been explored, especially with respect to its prognostic value.

METHODS

G protein signaling modulator 2 messenger RNA expression and clinicopathological characteristics of patients with liver cancer were obtained from The Cancer Genome Atlas. The expression level of G protein signaling modulator 2 RNA-Seq was validated by using Gene Expression Omnibus. Chi-square test was performed to evaluate the relationship between G protein signaling modulator 2 expression and clinical characteristics. The threshold value of G protein signaling modulator 2 in the diagnosis of liver cancer was evaluated by a receiver-operating characteristic curve. Cox regression analysis and Kaplan-Meier curves were performed to evaluate the relationship between G protein signaling modulator 2 and liver cancer prognosis, which included overall and residual-free survival, and explored the prognostic value of G protein signaling modulator 2. Liver cancer survival analyses were validated by using the data of G protein signaling modulator 2 RNA-Seq from the International Cancer Genome Consortium.

RESULTS

The expression level of G protein signaling modulator 2 messenger RNA was remarkably higher in liver cancer than that in healthy tissues (P < 2.2 × e-16), which was also validated by data from the GSE14520 database. In addition, high G protein signaling modulator 2 expression significantly correlated with histological grade (P = .020), vital status (P < .001), clinical (P = .001), and T stage (P = .001). The receiver-operating characteristic curves showed G protein signaling modulator 2 to be an advantageous diagnostic molecule for liver cancer (area under curve = 0.893). Furthermore, the results of Cox analysis and Kaplan-Meier curves suggested that the upregulation of G protein signaling modulator 2 expression is linked to poor prognosis and G protein signaling modulator 2 messenger RNA could be an independent predictor for liver cancer, which was validated by data from the International Cancer Genome Consortium database.

CONCLUSIONS

G protein signaling modulator 2 messenger RNA was overexpressed in liver cancer, and G protein signaling modulator 2 is an independent prognostic factor. G protein signaling modulator 2 is expected to be a treatment target for cancer.

Low EIF2B5 expression predicts poor prognosis in ovarian cancer

Ovarian cancer has the highest mortality among gynecological cancers. Although ovarian cancer usually responds well to chemotherapy, most patients still have a poor prognosis. EIF2B5 is a crucial molecule in posttranscriptional modifications involved in tumor progression, and here we investigated the prognostic role of EIF2B5 in ovarian cancer. We examined the differential expression of EIF2B5 mRNA in ovarian cancer by exploring The Cancer Genome Atlas (TCGA) database. The chi square test was used to identify a clinical correlation. Survival analysis and Cox regression model were performed to determine the association between EIF2B5 expression and overall survival (OS) in ovarian cancer patients. As a result, Low EIF2B5 expression was found in ovarian cancer tissues and correlated with survival status. Survival analysis showed that ovarian cancer patients with low EIF2B5 expression had a short OS. Moreover, Cox regression analysis indicated that low EIF2B5 expression was an independent risk factor for a poor prognosis in ovarian cancer. Additionally, according to gene set enrichment analysis, mesenchymal transition, angiogenesis, coagulation, and bile acid metabolism were differentially enriched in ovarian cancer with high EIF2B5 expression. In conclusion, Low EIF2B5 expression is an independent risk factor for a poor prognosis in ovarian cancer patients.

PIMREG, a Marker of Proliferation, Facilitates Aggressive Development of Cholangiocarcinoma Cells Partly Through Regulating Cell Cycle-Related Markers

BACKGROUND

Phosphatidylinositol binding clathrin assembly protein interacting mitotic regulator (PIMREG) is a protein associated with cell proliferation. Its aberrant expression was reported to be correlated with the development in multiple tumors. However, its role in cholangiocarcinoma (CAA) has not yet been evaluated in detail.

METHODS

Data were acquired from the public TCGA database for evaluating the expression pattern of PIMREG and assessing its clinical relevance as well as its correlation with overall survival. RBE and HUH28 cell lines were selected to perform loss- and gain-of-function of PIMREG assays respectively. Quantitative real-time PCR (RT-qPCR) and western blot analyses were used to measure the mRNA and protein levels of PIMREG. Cell Counting Kit-8, colony formation tests, and Transwell assays served to measure the effect of PIMREG on the proliferative, invasive and migratory capacities of CAA cells, appropriately. Gene set enrichment analysis (GSEA) was conducted to identify PIMREG associated gene set, which was further confirmed by western blot.

RESULTS

PIMREG was found to be highly expressed in CAA tissues and cell lines according to the public dataset and RT-qPCR analysis, and negatively related to the prognosis of patients with CAA. Moreover, knockdown of PIMREG suppressed and overexpression of PIMREG promoted the proliferation, invasion and migration of CAA cells. Furthermore, GSEA revealed that high PIMREG expression was positively associated with cell cycle signaling. And the next western blot analysis demonstrated that silencing PIMREG resulted in a reduction on the levels of p-CDK1, CCNE1, and CCNB1, whereas PIMREG overexpression led to an opposite result.

CONCLUSION

The results suggested that PIMREG facilitates the growth, invasion and migration of CAA cells partly by regulating the cell cycle relative biomarkers, revealing that PIMREG may be a crucial molecule in the progression of CAA.

Comprehensive multi-omics analysis identified core molecular processes in esophageal cancer and revealed GNGT2 as a potential prognostic marker

BACKGROUND

Esophageal cancer is one of the most poorly diagnosed and fatal cancers in the world. Although a series of studies on esophageal cancer have been reported, the molecular pathogenesis of the disease remains elusive.

AIM

To investigate comprehensively the molecular process of esophageal cancer.

METHODS

Differential expression analysis was performed to identify differentially expressed genes (DEGs) in different stages of esophageal cancer from The Cancer Genome Atlas data. Exacting gene interaction modules were generated, and hub genes in the module interaction network were found. Further, through survival analysis, methylation analysis, pivot analysis, and enrichment analysis, some important molecules and related functions/pathways were identified to elucidate potential mechanisms in esophageal cancer.

RESULTS

A total of 7457 DEGs and 14 gene interaction modules were identified. These module genes were significantly involved in the positive regulation of protein transport, gastric acid secretion, insulin-like growth factor receptor binding, and other biological processes as well as p53 signaling pathway, epidermal growth factor signaling pathway, and epidermal growth factor receptor signaling pathway. Transcription factors (including hypoxia inducible factor 1A) and non-coding RNAs (including colorectal differentially expressed and hsa-miR-330-3p) that significantly regulate dysfunction modules were identified. Survival analysis showed that G protein subunit gamma transducin 2 (GNGT2) was closely related to survival of esophageal cancer. DEGs with strong methylation regulation ability were identified, including SST and SH3GL2. Furthermore, the expression of GNGT2 was evaluated by quantitative real time polymerase chain reaction, and the results showed that GNGT2 expression was significantly upregulated in esophageal cancer patient samples and cell lines. Moreover, cell counting kit-8 assay revealed that GNGT2 could promote the proliferation of esophageal cancer cell lines.

CONCLUSION

This study not only revealed the potential regulatory factors involved in the development of esophageal cancer but also deepens our understanding of its underlying mechanism.

High MAST2 mRNA expression and its role in diagnosis and prognosis of liver cancer

Liver cancer is a high morbidity and low survival disease all over the world. Chromosomal instability is hallmark of liver cancer. Microtubule-associated serine and threonine kinase 2 (MAST2), as a microtubule associated protein, may involve in tumorous chromosomal instability and plays important roles in cell proliferation and survival. The role of MAST2 in liver cancer has not been well elucidated, which is the aim of our study. In this study, The Cancer Genome Atlas database was used to study the MAST2 mRNA expression in liver cancer, and Chi-squared tests were performed to test the correlation between clinical features and MAST2 expression. ROC curve was performed to examined the diagnostic capacity. The prognostic value of MAST2 in liver cancer was assessed through Kaplan-Meier curves as well as Cox analysis. Our results showed MAST2 was upregulated in liver cancer, and the area under the curve (AUC) was 0.925 and indicated powerful diagnostic capability. High MAST2 expression was associated with advanced clinical status such as histological type (p = 0.0059), histologic grade (p = 0.0142), stage (p = 0.0008), T classification (p = 0.0028), N classification (p = 0.0107), survival status (p = 0.0062), and poor prognosis of patients. Importantly, MAST2 was an independent risk factor for patients' prognosis after adjusting for other risk factors including stage, T classification, and residual tumor. In total, MAST2 is a potential diagnostic and prognostic biomarker of liver cancer.

TYMS presents a novel biomarker for diagnosis and prognosis in patients with pancreatic cancer

Pancreatic cancer is one of the most malignant tumors worldwide. DNA replication plays a critical role in the occurrence and development of pancreatic cancer. TYMS encodes thymidylate synthase, which is important for DNA synthesis. The TYMS gene has been assessed in some tumors. However, the specific role of TYMS in pancreatic cancer has not been identified. This study was designed to clarify the diagnostic and prognostic significance of TYMS in pancreatic cancer.The Cancer Genome Atlas (TCGA) database was used to compare TYMS expression in pancreatic cancer, and ROC curve analysis was used to investigate its diagnostic value. The correlation between clinical characteristics and TYMS expression was analyzed, and the prognostic value of TYMS expression in the patients with pancreatic cancer was assessed by Kaplan-Meier curves and Cox analysis.TYMS was upregulated in pancreatic cancer and associated with poor overall survival (OS) and recurrence-free survival (RFS). Univariate and multivariate survival analysis demonstrated that TYMS is an independent risk factor for OS and RFS in patients with pancreatic cancer.The upregulation of TYMS in pancreatic cancer leads to unfavorable OS and RFS in patients, and represents a diagnostic and prognostic biomarker for patients with pancreatic cancer.

STIP1 Regulates Proliferation and Migration of Lung Adenocarcinoma Through JAK2/STAT3 Signaling Pathway

Purpose

Recent studies have shown that STIP1 is associated with proliferation and migration in numerous types of tumors; however, the role of STIP1 in lung adenocarcinoma is still poorly understood. Therefore, the aim of this study was to evaluate the role of STIP1 in lung adenocarcinoma, in vitro and in vivo.

Methods

The expression of STIP1 in lung adenocarcinoma was assessed by immunohistochemistry, RT-qPCR, and Western blot. The effects of STIP1 on the proliferation of lung adenocarcinoma cells were detected by the cell counting kit-8 assay; the effect of STIP1 on adhesion of lung adenocarcinoma cells was detected by Giemsa staining, while the cell scratch and Transwell assays were employed to examine the effect of STIP1 on the migratory ability of lung adenocarcinoma cells. Finally, apoptosis was evaluated by Hoechst staining and flow cytometry.

Results

The expression level of STIP1 in lung adenocarcinoma tissue was significantly higher than that in adjacent normal tissue (P<0.05). Compared with that in nontransfected controls, cell proliferation, adhesion, and migration, as well as vimentin protein expression and levels of phosphorylated JAK2/STAT3, were significantly decreased (P<0.05) in A549 lung adenocarcinoma cells transfected with STIP1 shRNA, whereas E-cadherin protein expression and rates of apoptosis were significantly increased in these cells (P< 0.05).

Conclusion

Elevated expression of STIP1 in lung adenocarcinoma may enhance the proliferative, adhesive, and migratory ability, and reduce the apoptosis of lung adenocarcinoma cells through the JAK2/STAT3 signaling pathway and epithelial-mesenchymal transition (EMT), thereby promoting the recurrence and metastatic potential of this cancer. The results indicate that STIP1 may be an effective therapeutic target for the treatment of lung adenocarcinoma.

Betulinic Acid Attenuates T-2-Toxin-Induced Testis Oxidative Damage Through Regulation of the JAK2/STAT3 Signaling Pathway in Mice

T-2 toxin is one of the most toxic type A trichothecene mycotoxins in nature, and it exhibits reproductive toxicity. Betulinic acid (BA) is a natural pentacyclic triterpene compound found in species of Betula, and it has been reported to have antioxidant activity. The aim of the present study was to investigate the protective effect of BA on T-2-toxin-induced testicular injury in mice and explore its molecular mechanism. Sixty adult male mice were randomly divided into groups. The mice were pretreated orally with BA (0.25, 0.5, and 1.0 mg/kg) daily for 14 days, and the T-2 toxin (4 mg/kg body weight) was administered via intraperitoneal injection to induce oxidative stress after the last administration of BA. BA pretreatment significantly increased the secreted levels of testosterone and sperm motility. Moreover, BA pretreatment significantly increased the total antioxidant capacity (T-AOC), the activity of SOD and CAT, and the content of GSH, and it reduced the content of MDA. Furthermore, BA relieved testicular injury and reduced the number of apoptotic cells, and it significantly decreased the protein expression of Janus kinase 2 (JAK2), signal transducers and activators of transcription 3 (STAT3), caspsae-3, and Bcl-2-associated X protein (Bax). BA also increased the expression of B-cell lymphoma-2 (Bcl-2). We suggest that BA reduced the oxidative damage induced by T-2 toxin, and that these protective effects may be partially mediated by the JAK2/STAT3 signaling pathway.

MiR-942-3p Promotes the Proliferation and Invasion of Hepatocellular Carcinoma Cells by Targeting MBL2

MicroRNAs (miRNAs), a subgroup of small noncoding RNAs, play critical roles in tumor growth and metastasis. Accumulating evidence shows that the dysregulation of miRNAs is associated with the progression of hepatocellular carcinoma (HCC). However, the molecular mechanism by which miR-942-3p contributes to HCC remains undocumented. The association between miR-942-3p expression and the clinicopathological characteristics in HCC patients was analyzed by The Cancer Genome Atlas data set. The targets of miR-942-3p were identified by bioinformatic analysis and dual luciferase report assay. 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) and Transwell assays were performed to assess the functional role of miR-942-3p in HCC cells. Consequently, we found that miR-942-3p expression level was elevated in HCC tissues and cell lines as compared with the normal tissues and was associated with the pathological stage and tumor node metastasis (TNM) stage, acting as an independent prognostic factor of poor survival in patients with HCC. Ectopic expression of miR-942-3p enhanced the proliferation and invasive potential of HCC cells, but inhibition of miR-942-3p expression had the opposite effects. Mannose-binding lectin 2 (MBL2) was further identified as a direct target of miR-942-3p and possessed a negative correlation with miR-942-3p expression and unfavorable survival in patients with HCC. Restoration of MBL2 inhibited the progression of HCC cells and attenuated the tumor-promoting effects induced by miR-942-3p. In conclusion, miR-942-3p may act as an oncogenic factor in HCC cells by targeting MBL2 and provide a potential marker for patients with HCC.

High peroxidasin-like expression is a potential and independent prognostic biomarker in breast cancer

Breast cancer is a frequent female malignant tumor with high mortality and poor prognosis. Peroxidasin like (PXDNL) has many biological functions, including characteristic activity of hormone biosynthesis, host defense, and cell motility. In addition, PXDNL is closely connected with the progression of breast cancer. In this study, we found that PXDNL may be an independent prognostic biomarker of breast cancer.We tested the mRNA expression of PXDNL in breast cancer by detecting The Cancer Genome Atlas (TCGA) database. The chi-squared test was used to evaluate clinical correlation. The receiver operating characteristic (ROC) curves were drawn to evaluate diagnosis potential in breast cancer. Subsequently, survival analyses were performed to identify the relevance between the expression of PXDNL and the overall survival/relapse-free survival of patients with breast cancer. Univariate/multivariate Cox regression model was executed to detect risk factors affecting the prognosis of patients with breast cancer.PXDNL is highly expressed in breast cancer tissues and is related to survival status of patients. The ROC curve showed that PXDNL had beneficial diagnostic ability in breast cancer. Survival analysis indicated that patients with breast cancer with high PXDNL expression generally had decreased overall survival/relapse-free survival. Univariate/multivariate Cox model analyses further suggested an association between PXDNL expression and prognosis of patients with breast cancer.High PXDNL expression is a potential and independent prognostic biomarker in breast cancer.

A new prognostic factor of breast cancer: High carboxyl ester lipase expression related to poor survival

OBJECTIVE

The enzyme carboxyl ester lipase (CEL), known as bile salt-dependent lipase (BSDL) or bile salt-stimulated lipase (BSSL), is mainly expressed in pancreatic acinar cells and lactating mammary glands. To investigate the link between CEL expression of breast cancer (BC) tissues and the survival of BC patients by analyzing The Cancer Genome Atlas Breast Carcinoma (TCGA-BRCA) level 3 data.

METHODS

The clinical information and RNA-sequencing (RNA-Seq) expression data were downloaded from TCGA. Patients were divided into a high CEL expression group and a low CEL expression group using the optimal cutoff value (5.611) identified from the ROC curve. Chi-square test and Fisher exact test were used to find the correlation between the expression of CEL and clinicopathologic features. To assess the diagnostic capability, the receiver operating characteristic (ROC) curve of CEL was drawn. The survival differences between high and low CEL expression groups were compared by Cox regression analysis. Log-rank test was applied to the calculation of p values and the comparison of the Kaplan-Meier curves. Furthermore, Gene Expression Omnibus (GEO) datasets were used for external data validation.

RESULTS

Analysis of 1104 cases of tumor data showed that CEL was over-expressed in breast cancer. There were relationships between high CEL expression and clinicopathologic features. The high CEL expression group had a lower survival. By analyzing the area under the ROC curve (AUC) of CEL, it was found to have a limited diagnostic capability. CEL expression may be an independent prognostic factor for breast cancer survival through the multivariate analysis. The validation in GEO datasets also showed that CEL expression was higher in breast tumor tissues than in normal breast tissues. High CEL expression was associated with the poor overall survival of breast cancer.

CONCLUSIONS

High CEL expression may be an independent prognostic factor for the poor survival of breast cancer.

Investigation of the Clinical Significance and Prognostic Value of the lncRNA ACVR2B-As1 in Liver Cancer

A refined liver cancer staging system and effective prognostic prediction can help clinicians make optimized treatment decisions, which is essential in our fight against cancer and for improving the unsatisfying survival rate of liver cancer globally. The prognosis of liver cancer is not only related to tumor status, it is also affected by the patients' liver functions and the chosen treatment. Currently, several staging systems are being tested. Herein, we analyzed RNA-seq data from the TCGA database and identified a newly annotated lncRNA, ACVR2B-AS1, whose expression is upregulated in liver cancer. Higher ACVR2B-AS1 expression is an independent adverse prognostic factor for overall survival (OS) and relapse-free survival (RFS) in liver cancer patients. Our work suggests that the lncRNA ACVR2B-AS1 could be a candidate biomarker for liver cancer prognosis. Furthermore, ACVR2B-AS1 might serve as a potential therapeutic target, which is a possibility that is worthy of further study.

Expression of La Ribonucleoprotein Domain Family Member 4B (LARP4B) in Liver Cancer and Their Clinical and Prognostic Significance

BACKGROUND AND OBJECTIVE

Liver cancer is a common malignant tumor with few poor diagnostic and prognostic markers, which greatly shortens the potential life span of patients. The RNA-binding protein la ribonucleoprotein 4B (LARP4B) has a la motif (lam) that is important in the process of cancer. We aimed to explore the role of LARP4B in the diagnosis and prognosis of liver cancer.

METHODS

The Cancer Genome Atlas (TCGA) database was searched to detect LARP4B gene expression in liver cancer. The clinical relevance and diagnostic ability of LARP4B were evaluated by a chi-squared test and a receiver operating characteristic (ROC) curve, respectively. Survival and risk factors of patients with liver cancer were assessed by survival analysis and univariate/multivariate Cox regression model. Additionally, we carried out gene set enrichment analysis (GSEA) to identify LARP4B-related signaling pathways in liver cancer.

RESULTS

LARP4B mRNA was highly expressed in liver cancer tissues and was correlated with survival status. The chi-squared test showed that LARP4B had clinical relevance, while ROC curves showed that LARP4B had good diagnostic ability. Survival analysis showed that liver cancer patients with high LARP4B expression had shorter overall/relapse-free survival. The univariate/multivariate Cox regression model indicated that high LARP4B expression may be an independent risk factor for the prognosis of liver cancer patients. Finally, we found that genes involved in the G2M checkpoint, E2F targets, and mitotic spindle were differentially enriched in the high LARP4B-expression phenotype.

CONCLUSIONS

LARP4B is a potential independent biomarker for diagnosis and prognosis in liver cancer patients.

OGDHL Expression as a Prognostic Biomarker for Liver Cancer Patients

BACKGROUND AND OBJECTIVE

Liver cancer is a highly malignant tumor, and patients typically have poor prognoses. Metabolic reprogramming is a hallmark of cancer, and downregulation of oxoglutarate dehydrogenase-like (OGDHL) contributes to the onset and progression of several cancers. We examined the role of altered OGDHL expression in liver cancer and determined its value as a diagnostic and prognostic indicator for patients.

MATERIAL AND METHODS

R (version 3.5.1) and several R extensions were used for data mining of The Cancer Genome Atlas (TCGA) dataset (including RNAseq and clinical information) and statistical analysis. Receiver operating characteristic analysis was used to determine the diagnostic value of OGDHL. The chi-squared test was used to identify the clinical correlates of OGDHL downregulation. Survival analysis (with the log-rank test) and univariate and multivariate Cox analysis were used to evaluate the effect of OGDHL expression on overall survival (OS) and relapse-free survival. TCGA was used for analysis of gene set enrichment.

RESULTS

OGDHL had lower expression in cancerous liver tissues than noncancerous adjacent tissues, and low expression correlated with more advanced patient age, histologic grade, stage, T classification, and poor survival. Patients with lower OGDHL expression had shorter OS and relapse-free survival. Multivariate Cox regression indicated that low OGDHL expression was an independent risk factor for poor prognosis. Gene set enrichment analysis indicated enrichment of the mitotic spindle, G2M checkpoint, and E2F targets in the OGDHL low expression phenotype.

CONCLUSION

OGDHL has potential as a diagnostic and prognostic biomarker for liver cancer.

Low CYP24A1 mRNA expression and its role in prognosis of breast cancer

Breast cancer is the most common malignant cancer in women. CYP24A1 expression regulates cellular response to vitamin D, which has antitumor effects against breast cancer. This study aimed to identify the correlation between CYP24A1 mRNA expression and prognosis of breast cancer. This study enrolled 1102 patients, including 1090 females and 12 males, from TCGA-BRCA cohort. The Cancer Genome Atlas database was used to study CYP24A1 mRNA expression in breast cancer, and Chi-squared tests were performed to test the correlation between clinical features and CYP24A1 expression. The prognostic value of CYP24A1 in breast cancer was assessed using Kaplan-Meier curves and Cox analysis. Low CYP24A1 expression was associated with age, molecular subtype, ER, PR, HER2, menopause status, N classification, vital status, overall survial and relapse-free survival. CYP24A1 presented a moderate diagnostic ability in breast cancer. Furthermore, low CYP24A1 expression was correlated with poor prognosis. CYP24A1 was an independent risk factor for breast cancer. CYP24A1 plays an important role in prognosis of breast cancer. CYP24A1 has the potential to be a biomarker, especially in predicting prognosis.

Overexpression of HOXC6 promotes cell proliferation and migration via MAPK signaling and predicts a poor prognosis in glioblastoma

Background

Homeobox (HOX) genes encode transcription factors that are critical to morphogenesis and cell differentiation. Although the dysregulation of several HOX genes in glioblastoma (GBM) has been reported, little is known about HOXC6 expression in GBM. Therefore, in this study, we investigated the expression levels of the HOXC6 in GBM and explored the regulatory mechanism underlying the role of HOXC6 in GBM progression.

Methods

The ONCOMINE and Oncolnc databases were used to predict the expression level of HOXC6 mRNA and its prognostic value in GBM. The expressions of HOXC6 mRNA in GBM tissues and adjacent brain tissues were detected using qRT-PCR and Western blot. Immunohistochemistry was performed to verify the HOXC6 protein expression in 107 GBM tissues. Kaplan–Meier and Cox analyses were performed to validate the correlation between HOXC6 expression and GBM prognosis. Lentivirus-mediated HOXC6 mRNA overexpression and interference system were established and transfected into U251 and U87 cell lines. CCK-8, colony formation, wound healing and transwell assay were utilized to evaluate the effects of HOXC6 on proliferation and migration of human GBM cells.

Results

High expression of HOXC6 was observed in GBM tissues and GBM cells lines, and it correlated with a decreased overall survival and disease-free survival. Overexpression of HOXC6 promoted the GBM cell proliferation and migration, whereas depletion of HOXC6 reduced GBM cell proliferation and migration. Mechanistic study showed that upregulation of HOXC6 significantly increased the phosphorylation of Jun amino-terminal kinase, ERK and P38, as well as the expression of mitogen-activated protein kinase (MAPK) signaling–related genes, including c-myc, c-jun and p53. Inversely, silencing HOXC6 showed the opposite results.

Conclusion

HOXC6 promoted proliferation and migration of GBM cells via the activation of MAPK pathway.

Low lncRNA ZNF385D‑AS2 expression and its prognostic significance in liver cancer

Hepatocellular carcinoma (HCC) is a common digestive system disease with no curative treatment. Zinc finger protein 385D antisense RNA 2 (ZNF385D‑AS2) is a long non‑coding RNA (lncRNA) that has been predicted to function in human diseases, including several types of cancer. Yet, it has not been investigated in relation to liver cancer. Thus, the present study was designed with an aim to elucidate the prognostic significance of lncRNA ZNF385D‑AS2 in HCC. The Cancer Genome Atlas‑Liver Hepatocellular Carcinoma (TCGA‑LIHC) collection of data was utilized to analyze the expression of lncRNA ZNF385D‑AS2 in liver cancer. Then Chi‑square tests were used to evaluate the correlation between clinical characteristics and lncRNA ZNF385D‑AS2 expression. The significance of lncRNA ZNF385D‑AS2 in patient prognosis was evaluated using Kaplan‑Meier curves and Cox analysis. Concomitantly, Gene Set Enrichment Analysis (GSEA) was performed to analyze the most closely related cytological behavior. Finally, we used the Database for Annotation, Visualization and Integrated Discovery (DAVID) and KOBAS software and data from the Gene Expression Omnibus (GEO) database to analyze the possible competing endogenous RNA (ceRNA) network pattern as well as the co‑expression network in liver cancer. Based on the results, analysis of RNA‑Seq gene expression data for 303 patients with primary tumors revealed low expression of ZNF385D‑AS2 in liver cancer. Low expression of ZNF385D‑AS2 was found to be significantly associated with sex (P=0.050), T stage (P=0.049), M stage (P=0.040), N stage (P<0.001) and clinical stage (P=0.037). Patients with ZNF385D‑AS2 low‑expression liver cancers had a shorter median overall survival compared with the patients with ZNF385D‑AS2 high‑expression liver cancers (P=0.0079). Cox analysis identified ZNF385D‑AS2 low‑expression as an independent prognostic variable (AUC=0.594) for overall survival in liver cancer patients. Co‑expression and ceRNA predictive analysis data suggested that there may be a regulatory signaling axis between ZNF385D‑AS2 and miR‑96 and miR‑182. In conclusion, our results suggests that low expression of ZNF385D‑AS2 is predictive of a poor prognosis of liver cancer patients.

Sevoflurane Protects Hepatocytes From Ischemic Injury by Reducing Reactive Oxygen Species Signaling of Hepatic Stellate Cells: Translational Findings Based on a Clinical Trial

BACKGROUND

Randomized controlled trials (RCTs) data demonstrate that sevoflurane postconditioning improves clinical outcomes of liver resection with inflow occlusion, presumably due to hepatocyte protection from ischemic injury. However, mechanisms remain unclear. This study examines liver biopsy samples obtained in an RCT of sevoflurane postconditioning to test the hypothesis that sevoflurane attenuates hepatocyte apoptosis.

METHODS

Messenger ribonucleic acid (mRNA) of pro- and antiapoptotic regulators Bax and B-cell lymphoma 2 (Bcl2) was examined in hepatic biopsies obtained during the RCT. Hepatic stellate cells (HSCs) and hepatocytes were exposed to hypoxia/reoxygenation (H/R) in vitro to evaluate the effect of sevoflurane postconditioning on apoptosis. The role of HSC as a potential apoptosis trigger in hepatocytes through the production of reactive oxygen species induced by H/R was explored by transferring supernatants from H/R-exposed HSC to hepatocytes as target cells.

RESULTS

In patients of the RCT, the Bax/Bcl2 mRNA ratio in liver tissue was markedly decreased in the sevoflurane arm (25% ± 21% reduction; P = .001). In vitro, H/R increased reactive oxygen species production in HSC by 33% ± 16% (P = .025), while it was abolished in the presence of sevoflurane (P < .001). In hepatocytes, caspase was minimally activated by H/R. However, incubation of hepatocytes with supernatants of HSC, previously exposed to H/R, increased caspase activity by 28% ± 13% (P < .001). When exposed to supernatants from HSC undergoing sevoflurane postconditioning, caspase activation in hepatocytes was reduced by 20% ± 9% (P < .001), similarly to the sevoflurane effect on the BAX/Bcl2 mRNA ratio in the liver samples.

CONCLUSIONS

The study shows that sevoflurane postconditioning affects apoptosis of hepatocytes after ischemia-reperfusion injury in patients. It also demonstrates that HSC may be the effector cells of sevoflurane protection.

PGM5: a novel diagnostic and prognostic biomarker for liver cancer

BACKGROUND

Liver cancer is a common malignancy and a significant public health problem worldwide, but diagnosis and prognostic evaluation remain challenging for clinicians. Metabolic reprogramming is a hallmark of cancer, and we therefore examined the diagnostic and prognostic value of a metabolic enzyme, phosphoglucomutase-like protein 5 (PGM5), in liver cancer.

METHODS

All data were from The Cancer Genome Atlas database. R and related statistical packages were used for data analysis. Hepatic PGM5 expression was determined in different groups, and the chi-squared test and Fisher's exact test were used to determine the significance of differences. The pROC package was used to determine receiver operating characteristic (ROC) curves, the survival package was used to for survival analysis and development of a Cox multivariable model, and the ggplot2 package was used for data visualization.

RESULTS

PGM5 expression was significantly lower in cancerous than adjacent normal liver tissues, and had modest diagnostic value based on ROC analysis and calculations of area under the curve (AUC). Hepatic PGM5 expression had positive associations with male sex and survival, but negative associations with advanced histologic type, advanced histologic grade, advanced stage, and advanced T classification. Patents with low PGM5 levels had poorer overall survival and relapse-free survival. PGM5 was independently associated with patient prognosis.

CONCLUSION

PGM5 has potential use as a diagnostic and prognostic biomarker for liver cancer.

Kinetic and computational molecular docking simulation study of novel kojic acid derivatives as anti-tyrosinase and antioxidant agents

The novel kojic acid derivatives KAD1 and KAD2 have been demonstrated that they exhibited potent anti-melanogenesis activity in our previous report. In this study, we further study the inhibitory mechanism on mushroom tyrosinase. The inhibitory types of both KADs on diphenolase were classified as mixed type based on the results of the kinetic model. The interaction between KADs and tyrosinase was illustrated by fluorescence quenching, molecular docking and copper chelate activity. The KADs were also evaluated with respect to their antioxidant activities by DPPH and ABTS⁺ assays. The results showed that KADs have more potent antioxidant activities than kojic acid. Our study could provide new ideas for the development of new anti-tyrosinase and antioxidant agents.

Somatic Mutations in miRNA Genes in Lung Cancer-Potential Functional Consequences of Non-Coding Sequence Variants

A growing body of evidence indicates that miRNAs may either drive or suppress oncogenesis. However, little is known about somatic mutations in miRNA genes. To determine the frequency and potential consequences of miRNA gene mutations, we analyzed whole exome sequencing datasets of 569 lung adenocarcinoma (LUAD) and 597 lung squamous cell carcinoma (LUSC) samples generated in The Cancer Genome Atlas (TCGA) project. Altogether, we identified 1091 somatic sequence variants affecting 522 different miRNA genes and showed that half of all cancers had at least one such somatic variant/mutation. These sequence variants occurred in most crucial parts of miRNA precursors, including mature miRNA and seed sequences. Due to our findings, we hypothesize that seed mutations may affect miRNA:target interactions, drastically changing the pool of predicted targets. Mutations may also affect miRNA biogenesis by changing the structure of miRNA precursors, DROSHA and DICER cleavage sites, and regulatory sequence/structure motifs. We identified 10 significantly overmutated hotspot miRNA genes, including the miR-379 gene in LUAD enriched in mutations in the mature miRNA and regulatory sequences. The occurrence of mutations in the hotspot miRNA genes was also shown experimentally. We present a comprehensive analysis of somatic variants in miRNA genes and show that some of these genes are mutational hotspots, suggesting their potential role in cancer.

ITGA3 serves as a diagnostic and prognostic biomarker for pancreatic cancer

Background and objective: ITGA3 is a cell surface adhesion protein that interacts with extracellular matrix proteins which function in cancer metastasis. We examined the relationship of pancreatic ITGA3 expression with the clinical and pathological characteristics of patients with pancreatic cancer. Methods: Data mining was used to analyze pancreatic cancer data from The Cancer Genome Atlas database. A Chi squared test was used to evaluate correlations of ITGA3 expression with clinical and pathological parameters. Receiver operating characteristic (ROC) analysis was used to evaluate the diagnostic performance of ITGA3 expression. Survival analysis and Cox regression analysis were used to examine the prognostic value of ITGA3 expression. Gene Set Enrichment Analysis (GSEA) was used to identify signaling pathways related to ITGA3 expression. Results: Pancreatic expression of ITGA3 was greater in patients with pancreatic cancer than those without cancer, and was also associated with histological type, histological grade, stage, T classification, vital status, and relapse. ROC analysis indicated that ITGA3 had significant diagnostic value, in that high expression correlated with poor overall survival and relapse-free survival, especially in patients with early-stage cancer. Cox analysis indicated that high ITGA3 expression was an independent prognostic factor for pancreatic cancer. GSEA analysis identified 9 signaling pathways that were enriched in the presence of high ITGA3 expression. Conclusion: Expression of ITGA3 can be used as a diagnostic and prognostic biomarker in pancreatic cancer.

TROAP Promotes Breast Cancer Proliferation and Metastasis

Trophinin-associated protein (TROAP) is a cytoplasmic protein required for microtubular cytoskeleton regulation and spindle assembly, and its expression plays a critical role in the initiation and progression of various types of cancer. However, little is known about the role of TROAP in breast cancer (BC). TROAP mRNA expression levels and clinical data from Gene Expression Omnibus (GEO) datasets (GSE42568, 104 BC patients; GSE1456, 159 BC patients; and GSE21653, 266 BC patients) were analyzed by the R2: Genomics Analysis and Visualization Platform to estimate overall survival (OS). We also analyzed the genes correlated with TROAP by gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis to predict potential relationships between TROAP and other genes in BC. Our study verified that both TROAP mRNA and protein expression levels were upregulated in human BC samples and cell lines. In vitro experiments demonstrated that TROAP knockdown significantly inhibited cell proliferation, the G1 to S phase transition, and the migration and invasion abilities of BC cells. The present study suggests that TROAP plays an important role in promoting the proliferation, invasion, and metastasis of BC.

ATP binding cassette subfamily B member 9 (ABCB9) is a prognostic indicator of overall survival in ovarian cancer

Ovarian cancer (OC) is one of the most common gynecological malignancies and owns the highest mortality rate among all gynecological malignant tumors. ATP binding cassette subfamily B member 9 (ABCB9) is an antigen processing-like (TAPL) transporter that has been found to be involved in the development and progression of various malignant tumors in accumulating reports. However, the potential role of ABCB9 in OC has never been reported.In this study, ABCB9 expression was evaluated in normal ovarian tissues and ovarian cancer tissues using The Cancer Genome Atlas (TCGA) database. And the associations between ABCB9 expression and clinical parameters of patients of OC were evaluated by Chi-square tests. Kaplan-Meier analysis and Cox regression analysis were performed to evaluate the prognostic significance of ABCB9. GSEA was performed to explore related signaling pathway.ABCB9 expression levels were significantly decreased in OC compared with normal ovarian tissues (P < .001). Low ABCB9 expression was associated with survival status (P = .0148) in OC. Kaplan-Meier analysis showed that low ABCB9 expression was associated with poor overall survival in OC (P = .0032). Multivariable Cox regression analysis indicated that low ABCB9 expression was an independent prognostic factor (HR 0.64; P = .01) in OC patients. Besides, epithelial mesenchymal transition, UV response, and TGF-β signaling were enriched in low ABCB9 expression phenotype, respectively, examined by gene set enrichment analysis.These results suggest that ABCB9 is an independent prognostic indicator in OC with certain clinical significance.

Trophinin-associated protein expression is an independent prognostic biomarker in lung adenocarcinoma

Background

Lung cancer is the leading cause of cancer-related deaths worldwide, with lung adenocarcinoma (LAC) representing the most common subtype. Trophinin-associated protein (TROAP) is a cytoplasmic protein first identified to mediate the process of embryo transplantation, which has been recently found to be involved in microtubule regulation. However, limited information about the role of TROAP in LAC is available.

Methods

We evaluated the relationship of TROAP expression in LAC tissues with clinical pathologic parameters and the survival time in LAC patients based on a statistical analysis of The Cancer Genome Atlas (TCGA) lung cancer data (N=528). Differences in survival between high and low expression groups (median expression cutoff) from the Cox univariate/multivariate regression analysis were then compared.

Results

According to the Chi-square tests, we found high TROAP expression correlated with younger age (≤60) (P=0.047), male sex (P<0.005), an earlier T-stage (P=0.011), N-stage (P=0.017), M-stage (P=0.022), TNM (P=0.007), and a longer smoking history (>30 pack-year) (P<0.001). A Kaplan-Meier analysis demonstrated that high TROAP expression may correspond with poor overall survival of LAC patients in T3 stage (P=0.0013), N0 stage (P=0.014), and M0 stage (P=0.0023). Multivariate analysis confirmed that TROAP expression was related to overall survival in LAC patients independently [hazard ratio (HR): 1.784, 95% confidence interval (CI): 1.072-2.968, P=0.026].

Conclusions

Our results suggested that TROAP is an independent prognostic biomarker of poor survival in LAC.

Natural antioxidants of plant origin

Interest in the content of natural antioxidants in plant-based foods can be from the human health perspective, in terms of how these compounds might help promote one's health and wellness, or from the storage point-of-view, as the endogenous antioxidant constituents aid to extend a foodstuff's shelf-life. This chapter reports essential information about the mechanism of antioxidant action and methods employed for determination of their activity, classes of phenolic compounds (phenolic acids, flavonoids, lignans, stilbenes, tannins), sources of plant antioxidants (oil seeds, cereals, legumes, plants of the Lamiaceae family, tea and coffee, tree nuts, fruits, and berries), extraction strategies of phenolic compounds from plant material, and the influence of processing and storage on the content of natural antioxidants in foods and their antioxidant activity. Thermal processing, if not releasing bound phenolics from the structural matrices of the food, tends to decrease the antioxidant potential or, in the best case scenario, has no significant negative impact. Gentler sterilization processes such as high-pressure processing tend to better retain the antioxidant potential of a foodstuff than thermal treatments such as steaming, boiling, or frying. The impact of processing can be assessed by determining the antioxidant potential of foodstuffs either at the point of formulation or after different periods of storage under specified conditions.