Upregulation of LGALS1 is associated with oral cancer metastasis

Effects of hyperglycemia on the TGF-β pathway in trabecular meshwork cells

BACKGROUND

Hyperglycemia, which can lead to apoptosis, hypertrophy, fibrosis, and induces hyperinflammation in diabetic vascular complications due to oxidative stress. In order to elucidate the potential dual roles and regulatory signal transduction of TGF-β1 and TGF-β2 in human trabecular meshwork cells (HTMCs), we established an oxidative cell model in HTMCs using 5.5, 25, 50, and 100 mM d-glucose-supplemented media and characterized the TGF-β-related oxidative stress pathway.

METHODS

Further analysis was conducted to investigate oxidative damage and protein alterations in the HTMC caused by the signal transduction. This was done through a series of qualitative cell function studies, such as cell viability/apoptosis analysis, intracellular reactive oxygen species (ROS) detection, analysis of calcium release concentration, immunoblot analysis to detect the related protein expression alteration, and analysis of cell fibrosis to study the effect of different severities of hyperglycemia. Also, we illustrated the role of TGF-β1/2 in oxidative stress-induced injury by shRNA-mediated knockdown or stimulation with recombinant human TGF-β1 protein (rhTGF-β1).

RESULTS

Results from the protein expression analysis showed that p-JNK, p-p38, p-AKT, and related SMAD family members were upregulated in HTMCs under hyperglycemia. In the cell functional assays, HTMCs treated with rhTGFβ-1 (1 ng/mL) under hyperglycemic conditions showed higher proliferation rates and lower ROS and calcium levels.

CONCLUSIONS

To summarize, mechanistic analyses in HTMCs showed that hyperglycemia-induced oxidative stress activated TGF-β1 along with its associated pathway.

GENERAL SIGNIFICANCE

While at low concentrations, TGF-β1 protects cells from antioxidation, whereas at high concentrations, it accumulates in the extracellular matrix, causing further HTMC dysfunction.

ZNF643/ZFP69B Exerts Oncogenic Properties and Associates with Cell Adhesion and Immune Processes

The global cancer burden remains high; thus, a better understanding of the molecular mechanisms driving carcinogenesis is needed to improve current prevention and treatment options. We previously detected the ZNF643/ZFP69B gene upregulated in multiple tumors, and we speculated it may play a role in tumor biology. To test this hypothesis, we employed TCGA-centered databases to correlate ZNF643 status with various clinicopathological parameters. We also performed RNA-seq analysis and in vitro studies assessing cancer cell phenotypes, and we searched for ZNF643-bound genomic loci. Our data indicated higher levels of ZNF643 in most analyzed tumors compared to normal samples, possibly due to copy number variations. ZNF643 mRNA correlated with diverse molecular and immune subtypes and clinicopathological features (tumor stage, grade, patient survival). RNA-seq analysis revealed that ZNF643 silencing triggers the deregulation of the genes implicated in various cancer-related processes, such as growth, adhesion, and immune system. Moreover, we observed that ZNF643 positively influences cell cycle, migration, and invasion. Finally, our ChIP-seq analysis indicated that the genes associated with ZNF643 binding are linked to adhesion and immune signaling. In conclusion, our data confirm the oncogenic properties of ZNF643 and pinpoint its impact on cell adhesion and immune processes.

A novel long noncoding RNA located on the antisense strand of MAL promotes the invasion and metastasis of oral squamous cell carcinoma

OBJECTIVES

This study aims to investigate the role of the long non-coding RNA-AC103563.8 (lncRNA) in promoting oral squamous cell carcinoma (OSCC) development and to conduct preliminary research on its mechanism.

DESIGN

Microarray technology were used to screen out a lncRNA significantly upregulated in OSCC. Fluorescence in situ hybridization was used to analyze the position of lncRNA-AC103563.8 in cells. A Cal-27 cell line with knockout of the lncRNA-AC103563.8 gene was constructed. Transwell assay and tumor xenograft experiment was used to determine the metastasis and invasion of the cell. Detection of mutations in genes encoding myelin and lymphocyte proteins (MAL) by pyrosequencing. Identification of RNA-Binding Proteins by Mass Spectrometry (ChIRP-MS) experiments were carried out to enrich the proteins that directly bind to lncRNA-AC103563.8. Bioinformatics was used to analyze the target proteins. Some of the selected proteins were verified by parallel reaction monitoring (PRM) to confirm their binding to lncRNA-AC103563.8.

RESULTS

lncRNA-AC103563.8 is upregulated in OSCC tissue and the presence of lncRNA-AC103563.8 in both the nucleus and the cytoplasm. lncRNA-AC103563.8 promoted OSCC cell invasion and metastasis. Methylation occurs in MAL gene promoter. ChIRP-MS identified 330 proteins binding to lncRNA-AC103563.8, and bioinformatics analysis showed that they were involved in a variety of biological processes. PRM experiments confirmed some protein directly bound to lncRNA-AC103563.8.

CONCLUSION

lncRNA-AC103563.8 is a functional lncRNA that promotes OSCC development by acting on MAL or interacting with other tumor-related proteins. This study also indicates that this lncRNA may exert regulatory functions in OSCC and is a potential target for OSCC therapy.

Galectin-1-mediated MET/AXL signaling enhances sorafenib resistance in hepatocellular carcinoma by escaping ferroptosis

Sorafenib, a small-molecule inhibitor targeting several tyrosine kinase pathways, is the standard treatment for advanced hepatocellular carcinoma (HCC). However, not all patients with HCC respond well to sorafenib, and 30% of patients develop resistance to sorafenib after short-term treatment. Galectin-1 modulates cell-cell and cell-matrix interactions and plays a crucial role in HCC progression. However, whether Galectin-1 regulates receptor tyrosine kinases by sensitizing HCC to sorafenib remains unclear. Herein, we established a sorafenib-resistant HCC cell line (Huh-7/SR) and determined that Galectin-1 expression was significantly higher in Huh-7/SR cells than in parent cells. Galectin-1 knockdown reduced sorafenib resistance in Huh-7/SR cells, whereas Galectin-1 overexpression in Huh-7 cells increased sorafenib resistance. Galectin-1 regulated ferroptosis by inhibiting excessive lipid peroxidation, protecting sorafenib-resistant HCC cells from sorafenib-mediated ferroptosis. Galectin-1 expression was positively correlated with poor prognostic outcomes for HCC patients. Galectin-1 overexpression promoted the phosphorylation of AXL receptor tyrosine kinase (AXL) and MET proto-oncogene, receptor tyrosine kinase (MET) signaling, which increased sorafenib resistance. MET and AXL were highly expressed in patients with HCC, and AXL expression was positively correlated with Galectin-1 expression. These findings indicate that Galectin-1 regulates sorafenib resistance in HCC cells through AXL and MET signaling. Consequently, Galectin-1 is a promising therapeutic target for reducing sorafenib resistance and sorafenib-mediated ferroptosis in patients with HCC.

The interrelation of galectins and autophagy

Autophagy is a vital physiological process that maintains intracellular homeostasis by removing damaged organelles and senescent or misfolded molecules. However, excessive autophagy results in cell death and apoptosis, which will lead to a variety of diseases. Galectins are a type of animal lectin that binds to β-galactosides and can bind to the cell surface or extracellular matrix glycans, affecting a variety of immune processes in vivo and being linked to the development of many diseases. In many cases, galectins and autophagy both play important regulatory roles in the cellular life course, yet our understanding of the relationship between them is still incomplete. Galectins and autophagy may share common etiological cofactors for some diseases. Hence, we summarize the relationship between galectins and autophagy, aiming to draw attention to the existence of multiple associations between galectins and autophagy in a variety of physiological and pathological processes, which provide new ideas for etiological diagnosis, drug development, and therapeutic targets for related diseases.

Narciclasine suppresses oral cancer metastasis by modulating cathepsin B and extracellular signal-related kinase pathways

Oral cancer is a malignancy with unfavorable prognosis due to its high rates of recurrence and lymph node metastasis. Narciclasine is extracted from Narcissus species (Amaryllidaceae), which have antitumor and anti-inflammatory properties. However, the antitumor properties of narciclasine toward oral cancer remain unclear. The present study explored the antimetastatic effects of narciclasine in oral cancer as well as the underlying molecular mechanisms. We treated three oral cancer cell lines with noncytotoxic concentrations of narciclasine and discovered a dose-dependent antimetastatic effect. Mitogen-activated protein kinase (MAPK) pathways, including extracellular signal-related kinase (ERK), p38, and c-Jun N-terminal kinase (JNK), were regulated by narciclasine. We further discovered the ERK pathway to directly affect narciclasine-induced metastasis inhibition by combining treatment with narciclasine and ERK inhibitor. Furthermore, downregulation of cathepsin B (CTSB) in the SAS and SCC-47 cell lines revealed the critical role of CTSB in the antimetastatic effect of narciclasine. Our findings indicate that narciclasine inhibits oral cancer metastasis by regulating the ERK pathway and CTSB. This study provides evidence of the mechanism of narciclasine-induced inhibition oral cancer metastasis and suggests potential targets for use in oral cancer treatment.

Identification of Potential mRNA Biomarkers in Milk Small Extracellular Vesicles of Enzootic Bovine Leukosis Cattle

Enzootic bovine leukosis (EBL) is a disease caused by bovine leukemia virus (BLV); only a small percentage of BLV-infected cattle develop EBL and present with B-cell lymphosarcoma. There is no vaccine against BLV, treatment for EBL, or method for predicting the possibility of EBL onset, thus making EBL control difficult. Herein, to explore biomarkers for EBL in milk, we examined the mRNA profiles of small extracellular vesicles (sEVs) in milk from four BLV-uninfected and four EBL cattle by microarray analysis. It was revealed that 14 mRNAs were encapsulated in significantly higher quantities, and these mRNAs were therefore selected as biomarker candidates. Primers for these mRNAs were designed, and nine primer sets were available for quantitative real-time PCR. Nine mRNAs were evaluated for their availability as biomarkers for EBL using sEVs from newly-collected milk of 7 uninfected and 10 EBL cattle. The quantities of eight mRNAs (TMEM156, SRGN, CXCL8, DEFB4A, FABP5, LAPTM5, LGALS1, and VIM) were significantly higher in milk sEVs of EBL cattle than in those of uninfected cattle. Therefore, our findings indicate that these eight mRNAs in milk sEVs can be used as potential EBL biomarkers with combination use, although single mRNA use is not enough. Consequently, cattle at risk of EBL onset can be identified by monitoring the fluctuation in quantities of these mRNAs in milk before they develop EBL.

P-element Induced WImpy protein-like RNA-mediated gene silencing 2 regulates tumor cell progression, apoptosis, and metastasis in oral squamous cell carcinoma

Objective

P-element Induced WImpy protein-like RNA-mediated gene silencing 2 (PIWIL2) is a reported oncogene strongly associated with tumorigenesis and cancer progression. However, the potential function of PIWIL2 in oral cancer is still largely unclear.

Methods

In this study, we investigated the clinical significance of PIWIL2 expression in human oral squamous cell carcinoma (OSCC) cell lines and tissues. We also examined its function in OSCC pathogenesis by knocking down PIWIL2 expression with short hairpin RNAs, followed by phenotypic experiments focused on cell migration, invasion, proliferation, and apoptosis rates.

Results

We found that PIWIL2 was overexpressed in OSCC cell lines and tissues and significantly correlated with the malignancy stage. Furthermore, knockdown of PIWIL2 in a human OSCC cell line Tca8113 induced cell cycle arrest and apoptosis. Silencing PIWIL2 expression also significantly suppressed the migration and invasion abilities of Tca8113 cells.

Conclusions

Collectively, our results suggest a functional role of PIWIL2 in regulating OSCC pathogenesis. Our data imply that PIWIL2 could serve as a potential therapeutic target for OSCC treatment.

Expression of matrix metalloproteinase-9 in histological grades of oral squamous cell carcinoma: An immunohistochemical study

Context

Oral squamous cell carcinoma (OSCC) is characterized by a high degree of local invasiveness and metastasis to cervical lymph nodes and distant sites. Degradation of extracellular matrix (ECM) requires the concerted action of several extracellular enzymes, the most prominent of which are matrix metalloproteinases (MMPs). Proteolytic degradation of ECM components by (MMP-9) facilitates carcinoma cell invasion, enhances angiogenesis and tumor progression.

Objective

To assess and correlate the immunohistochemical expression of MMP-9 with clinicopathological parameters and histological grades of OSCC.

Settings and Design

Thirty histopathologically diagnosed cases of OSCC including 12 cases of well-differentiated squamous cell carcinoma, 12 cases of moderately differentiated squamous cell carcinoma and 6 cases of poorly differentiated squamous cell carcinoma were included in the study group.

Materials and Methods

The samples were subjected to staining using monoclonal antibodies against MMP-9 and visualized using the polymer-HRP detection system. Expression of MMP-9 was assessed in tumor epithelium/parenchyma and connective tissue stroma separately, and the mean of both was considered as average MMP-9 expression.

Statistical Analysis

The parametric independent samples "t" test, one-way ANOVA test and Pearson's correlation test were used for the statistical analysis.

Results

Immunoexpression of MMP-9 increased with advancing stage and histological grade of OSCC with statistically significant results.

Conclusion

MMP-9 plays an important role in invasion and metastasis and can serve as an independent prognostic marker.

Risk characteristics with seven epithelial-mesenchymal transition-related genes are used to predict the prognosis of patients with hepatocellular carcinoma

Background

Epithelial-mesenchymal transition (EMT)-related genes (ERGs) have been shown to play an important role in cancer invasion, tumor resistance, and tumor metastasis of hepatocellular carcinoma. This study sought to examine the prognostic value of ERGs and other pre-hepatoma genes.

Methods

Relevant data from The Cancer Genome Atlas (TCGA) were analyzed and synthesized. Specifically, 1,014 ERGs were downloaded and subject to a gene set enrichment analysis; 318 different EAG expressions were found, and the possible molecular mechanism of EAG was predicted by GO analysis and KEGG analysis. To determine the prediction of ERGS, a Cox regression model was used to establish a risk hypothesis. Based on risk patterns, patients were divided into high- or low-risk groups. Kaplan-Meier and receiver operating characteristic (ROC) curves confirmed the predictive value of the model.

Results

Seven prognostically relevant ERGs (i.e., ECT2, EZH2, MYCN, ROR2, SPP1, SQSTM1, and STC2) were identified. Using Cox's regression analysis method, appropriate cases were selected to establish a new risk prediction model. Under the risk model, the overall survival rate of the low-risk group samples was higher than that of the high-risk group samples (P<0.00001).

Conclusions

In short, we developed a risk model for liver cancer based on ERGs terminology. This model improve the postpartum treatment of patients with liver cancer.

RNA sequencing and functional studies of patient-derived cells reveal that neurexin-1 and regulators of this pathway are associated with poor outcomes in Ewing sarcoma

Purpose

The development of biomarkers and molecularly targeted therapies for patients with Ewing sarcoma (ES) in order to minimise morbidity and improve outcome is urgently needed. Here, we set out to isolate and characterise patient-derived ES primary cell cultures and daughter cancer stem-like cells (CSCs) to identify biomarkers of high-risk disease and candidate therapeutic targets.

Methods

Thirty-two patient-derived primary cultures were established from treatment-naïve tumours and primary ES-CSCs isolated from these cultures using functional methods. By RNA-sequencing we analysed the transcriptome of ES patient-derived cells (n = 24) and ES-CSCs (n = 11) to identify the most abundant and differentially expressed genes (DEGs). Expression of the top DEG(s) in ES-CSCs compared to ES cells was validated at both RNA and protein levels. The functional and prognostic potential of the most significant gene (neurexin-1) was investigated using knock-down studies and immunohistochemistry of two independent tumour cohorts.

Results

ES-CSCs were isolated from all primary cell cultures, consistent with the premise that ES is a CSC driven cancer. Transcriptional profiling confirmed that these cells were of mesenchymal origin, revealed novel cell surface targets for therapy that regulate cell-extracellular matrix interactions and identified candidate drivers of progression and relapse. High expression of neurexin-1 and low levels of regulators of its activity, APBA1 and NLGN4X, were associated with poor event-free and overall survival rates. Knock-down of neurexin-1 decreased viable cell numbers and spheroid formation.

Conclusions

Genes that regulate extracellular interactions, including neurexin-1, are candidate therapeutic targets in ES. High levels of neurexin-1 at diagnosis are associated with poor outcome and identify patients with localised disease that will relapse. These patients could benefit from more intensive or novel treatment modalities. The prognostic significance of neurexin-1 should be validated independently.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13402-021-00619-8.

Diseasome and comorbidities complexities of SARS-CoV-2 infection with common malignant diseases

With the increasing number of immunoinflammatory complexities, cancer patients have a higher risk of serious disease outcomes and mortality with SARS-CoV-2 infection which is still not clear. In this study, we aimed to identify infectome, diseasome and comorbidities between COVID-19 and cancer via comprehensive bioinformatics analysis to identify the synergistic severity of the cancer patient for SARS-CoV-2 infection. We utilized transcriptomic datasets of SARS-CoV-2 and different cancers from Gene Expression Omnibus and Array Express Database to develop a bioinformatics pipeline and software tools to analyze a large set of transcriptomic data and identify the pathobiological relationships between the disease conditions. Our bioinformatics approach revealed commonly dysregulated genes (MARCO, VCAN, ACTB, LGALS1, HMOX1, TIMP1, OAS2, GAPDH, MSH3, FN1, NPC2, JUND, CHI3L1, GPNMB, SYTL2, CASP1, S100A8, MYO10, IGFBP3, APCDD1, COL6A3, FABP5, PRDX3, CLEC1B, DDIT4, CXCL10 and CXCL8), common gene ontology (GO), molecular pathways between SARS-CoV-2 infections and cancers. This work also shows the synergistic complexities of SARS-CoV-2 infections for cancer patients through the gene set enrichment and semantic similarity. These results highlighted the immune systems, cell activation and cytokine production GO pathways that were observed in SARS-CoV-2 infections as well as breast, lungs, colon, kidney and thyroid cancers. This work also revealed ribosome biogenesis, wnt signaling pathway, ribosome, chemokine and cytokine pathways that are commonly deregulated in cancers and COVID-19. Thus, our bioinformatics approach and tools revealed interconnections in terms of significant genes, GO, pathways between SARS-CoV-2 infections and malignant tumors.

Changes in protein expression due to metformin treatment and hyperinsulinemia in a human endometrial cancer cell line

The incidence of endometrial cancer (EC) has increased over the past years and mainly affects women above the age of 45 years. Metabolic diseases such as obesity and type II diabetes mellitus as well as associated conditions like polycystic ovary syndrome (PCOS), insulin resistance and hyperinsulinemia lead to elevated levels of circulating estrogens. Increased estrogen concentrations, in turn, further trigger the proliferation of endometrial cells and thus promote EC development and progression, especially in the absence of progesterone as seen in postmenopausal women. Elevated blood glucose levels in diabetic patients further contribute to the risk of EC development. Metformin is an insulin-sensitizing biguanide drug, commonly used in the treatment of type II diabetes mellitus, especially in obese patients. Besides its effects on glucose metabolism, metformin displayed anti-cancer effects in various cancer types, including EC. Direct anti-cancer effects of metformin target signaling pathways that are involved in cellular growth and proliferation, e.g. the AKT/PKB/mTOR pathway. Further proteins and pathways have been suggested as potential targets, but the underlying mechanism of action of metformin's anti-cancer activity is still not completely understood. In the present study, the effects of metformin on protein expression were investigated in the human EC cell line HEC-1A using an affinity proteomic approach. Cells were treated with 0.5 mmol/L metformin over a period of 7 days and changes in the expression pattern of 1,300 different proteins were compared to the expression in untreated control cells as well as insulin-treated cells. Insulin treatment (100 ng/mL) was incorporated into the study in order to implement a model for insulin resistance and associated hyperinsulinemia, conditions that are often observed in obese and diabetic patients. Furthermore, the culture medium was supplemented with 10 nmol/L ß-estradiol (E2) during treatments to mimic increased estrogen levels, a common risk factor for EC development. Based on the most prominent and significant changes in expression, a set of 80 proteins was selected and subjected to a more detailed analysis. The data revealed that metformin and insulin targeted similar pathways in the present study and mostly acted on proteins related to proliferation, migration and tumor immune response. These pathways may be affected in a tumor-promoting as well as a tumor-suppressing way by either metformin treatment or insulin supplementation. The consequences for the cells resulting from the detected expression changes were discussed in detail for several proteins. The presented data helps identify potential targets affected by metformin treatment in EC and allows for a better understanding of the mechanism of action of the biguanide drug's anti-cancer activity. However, further investigations are necessary to confirm the observations and conclusions drawn from the presented data after metformin administration, especially for proteins that were regulated in a favorable way, i.e. AKT3, CCND2, CD63, CD81, GFAP, IL5, IL17A, IRF4, PI3, and VTCN1. Further proteins might be of interest, where metformin counteracted unfavorable effects that have been induced by hyperinsulinemia.

GLI3 Promotes Invasion and Predicts Poor Prognosis in Colorectal Cancer

Purpose

The epithelial–mesenchymal transition (EMT) is a key hallmark of cancer which promotes malignant progression, especially during the process of cancer invasion. A better understanding of EMT will help elucidate the molecular mechanism underlying colorectal cancer (CRC) metastasis and may provide new insights into the identification of potential biomarkers and therapeutic targets.

Methods

A series of bioinformatic approaches were combined and identify GLI3 as a potential key regulator in EMT. In vitro experiments were performed to knockdown GLI3 expression in two CRC cell lines and to reveal the oncogenic role of GLI3 in CRC. qRT-PCR and western blot were performed to show the influence of GLI3 in EMT and downstream pathways. The Kaplan-Meier analysis and log-rank test were used to evaluate the prognostic value of GLI3 in CRC patients.

Results

GLI3 was identified as a key regulator in coexpression and protein-protein interaction (PPI) networks involved in EMT. Bioinformatic analyses indicated that GLI3 had a high correlation with EMT markers in CRC. In vitro experiments showed that GLI3 knockdown attenuated the migratory and invasive capacities of CRC cells via influencing EMT property, especially by regulating phosphorylation of ERK signaling pathway. In addition, higher expression of GLI3 predicts worse prognosis in CRC patients.

Conclusions

In summary, we presented the first evidence that GLI3 could promote the migratory and invasive capacities of CRC cells by regulating the EMT process. Our study might provide some useful clues to a better understanding of GLI3 in EMT during CRC progression.

Biomarker discovery in highly invasive lung cancer cell through proteomics approaches

Lung cancer is one of the leading causes of cancer-related death worldwide. The most common type of lung cancer is non-small cell lung cancer (NSCLC). When NSCLC is detected, patients are typically already in a metastatic stage. Metastasized cancer is a major obstacle of effective treatment and understanding the mechanisms underlying metastasis is critical to treat cancer. Herein, we selected an invasive subpopulation from the human lung cancer cell line A549 using the transwell system and named it as A549-I5. Invasive and migratory activities of this cell line were analysed using wound healing, invasion, and migration assays. In addition, epithelial-mesenchymal transition (EMT) markers, such as Snail 1, Twist, Vimentin, N-cadherin and E-cadherin, were assessed through immunoblotting. In comparison to A549 cells, the invasive A549-I5 lung cancer cells had enhanced invasiveness, motility and EMT marker expression. Proteomic analysis identified 83 significantly differentially expressed proteins in A549-I5 cells. These identified proteins were classified according to their cellular functions and most were involved in cytoskeleton, redox regulation, protein degradation and protein folding. In summary, our results provide potential diagnostic markers and therapeutic candidates for the treatment of NSCLC metastasis. SIGNIFICANCE OF THE STUDY: When NSCLC is detected, most patients are already in a metastatic stage. Herein, we selected an invasive subpopulation from a human lung cancer cell line which had increased EMT markers as well as high wound healing, invasion and migration abilities. Proteomic analysis identified numerous proteins associated with functions in cytoskeleton, redox regulation, protein degradation and protein folding that were differentially expressed in these cells. These results may provide potential diagnostic markers and therapeutic candidates for the treatment of NSCLC metastasis.

A novel prognostic models for identifying the risk of hepatocellular carcinoma based on epithelial-mesenchymal transition-associated genes

Several epithelial-mesenchymal transition (EMT)-associated genes (EAGs) have been confirmed to correlate with the prognosis of hepatocellular carcinoma (HCC) patients. Herein, we explored the value of EAGs in the prognosis of HCC relying on data from The Cancer Genome Atlas (TCGA) database. A total of 200 EMT-associated genes were downloaded from the Gene set enrichment analysis (GSEA) website. Moreover, 96 differentially expressed EAGs were identified. Using Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, we forecasted the potential molecular mechanisms of EAGs. To identify prognostic EAGs, Cox regression was used in developing a prognostic risk model. Then, the Kaplan-Meier and receiver operating characteristic (ROC) curves were plotted to validate the prognostic significance of the model. A total of 5 prognostic correlated EAGs (P3H1, SPP1, MMP1, LGALS1, and ITGB5) were screened via Cox regression, which provided the basis for developing a novel prognostic risk model. Based on the risk model, patients were subdivided into high-risk and low-risk groups. The overall survival of the low-risk group was better compared to the high-risk group (P < 0.00001). The ROC curve of the risk model showed a higher AUC (Area under Curve) (AUC = 0.723) compared to other clinical features (AUC ≤ 0.511). A nomogram based on this model was constructed to predict the 1-year, 2-year, and 3-year overall survival rates (OS) of patients. Conclusively, we developed a novel HCC prognostic risk model based on the expression of EAGs, which help advance the prognostic management of HCC patients. Abbreviations: HCC: hepatocellular carcinoma; TCGA: The Cancer Genome Atlas; EMT: epithelial-mesenchymal transition; EAGs: EMT-associated genes; GSEA: gene set enrichment analysis; GO: Gene Ontology; KEGG: Kyoto Encyclopedia of Genes and Genomes; PPI: protein-protein interaction; TF: transcription factor; ROC: receiver operating characteristic; K-M: Kaplan-Meier; AUC: the area under the ROC curve; FDR: false discovery rate; TNM: Tumor size/lymph nodes/distance metastasis.

The Role of Transforming Growth Factor-Beta in Retinal Ganglion Cells with Hyperglycemia and Oxidative Stress

A characteristic of diabetes mellitus is hyperglycemia, which is considered with an emphasis on the diabetic retinopathy of progressive neurodegenerative disease. Retinal ganglion cells (RGCs) are believed to be important cells affected in the pathogenesis of diabetic retinopathy. Transforming growth factor-beta (TGF-β) is a neuroprotective protein that helps to withstand various neuronal injuries. To investigate the potential roles and regulatory mechanisms of TGF-β in hyperglycemia-triggered damage of RGCs in vitro, we established RGCs in 5.5, 25, 50, and 100 mM D-glucose supplemented media and focused on the TGF-β-related oxidative stress pathway in combination with hydrogen peroxide (H₂O₂). Functional experiments showed that TGF-β1/2 protein expression was upregulated in RGCs with hyperglycemia. The knockdown of TGF-β enhanced the accumulation of reactive oxygen species (ROS), inhibited the cell proliferation rate, and reduced glutathione content in hyperglycemia. Furthermore, the results showed that the TGF-β-mediated enhancement of antioxidant signaling was correlated with the activation of stress response proteins and the antioxidant pathway, such as aldehyde dehydrogenase 3A1 (ALDH3A1), heme oxygenase-1 (HO-1), nuclear factor erythroid 2-related factor (Nrf2), and hypoxia-inducible factor (HIF-1α). Summarizing, our results demonstrated that TGF-β keeps RGCs from hyperglycemia-triggered harm by promoting the activation of the antioxidant pathway, suggesting a potential anti-diabetic therapy for the treatment of diabetic retinopathy.

Proteomic analysis of Antrodia Cinnamomea-induced ER stress in liver cancer cells

Antrodia Cinnamomea is a fungus species widely used as a herb medicine for hypertension, cancer and handover. Nevertheless, the biological roles of Antrodia Cinnamomea on the molecular mechanism of liver cancer are not entirely understood. To determine whether Antrodia Cinnamomea is able to be used for the treatment of liver cancer and its molecular mechanism, we examined the effect of Antrodia Cinnamomea on the differential proteomic patterns in liver cancer cell lines HepG2 and C3A as well as in Chang's liver cell, a normal liver cell, using quantitative proteomic approach. The proteomic analysis demonstrated that abundance of 82, 125 and 125 proteins was significantly altered in Chang's liver cells, C3A and HepG2, respectively. The experimental outcomes also demonstrated that Antrodia Cinnamomea-induced cytotoxicity in liver cancer cells mostly involved dysregulation of protein folding, cytoskeleton regulation, redox-regulation, glycolysis pathway as well as transcription regulation. Further analysis also revealed that Antrodia Cinnamomea promoted misfolding of intracellular proteins and dysregulate of cellular redox-balance resulting in ER-stress. To sum up our studies demonstrated that the proteomic strategy used in this study offered a tool to investigate the molecular mechanisms of Antrodia Cinnamomea-induced liver cancer cytotoxicity. The proteomic results might be further evaluated as prospective targets in liver cancer treatment.

Identification of a Glucose Metabolism-related Signature for prediction of Clinical Prognosis in Clear Cell Renal Cell Carcinoma

Background: Clear cell renal cell carcinoma (ccRCC) is one of the most prevalent and invasive histological subtypes among all renal cell carcinomas (RCC). Cancer cell metabolism, particularly glucose metabolism, has been reported as a hallmark of cancer. However, the characteristics of glucose metabolism-related gene sets in ccRCC have not been systematically profiled.

Methods: In this study, we downloaded a gene expression profile and glucose metabolism-related gene set from TCGA (The Cancer Genome Altas) and MSigDB, respectively, to analyze the characteristics of glucose metabolism-related gene sets in ccRCC. We used a multivariable Cox regression analysis to develop a risk signature, which divided patients into low- and high- risk groups. In addition, a nomogram that combined the risk signature and clinical characteristics was created for predicting the 3- and 5-year overall survival (OS) of ccRCC. The accuracy of the nomogram prediction was evaluated using the area under the receiver operating characteristic curve (AUC) and a calibration plot.

Results: A total of 231 glucose metabolism-related genes were found, and 68 differentially expressed genes (DEGs) were identified. After screening by univariate regression analysis, LASSO regression analysis and multivariable Cox regression analysis, six glucose metabolism-related DEGs (FBP1, GYG2, KAT2A, LGALS1, PFKP, and RGN) were selected to develop a risk signature. There were significant differences in the clinical features (Fuhrman nuclear grade and TNM stage) between the high- and low-risk groups. The multivariable Cox regression indicated that the risk score was independent of the prognostic factors (training set: HR=3.393, 95% CI [2.025, 5.685], p<0.001; validation set: HR=1.933, 95% CI [1.130, 3.308], p=0.016). The AUCs of the nomograms for the 3-year OS in the training and validation sets were 0.808 and 0.819, respectively, and 0.777 and 0.796, respectively, for the 5- year OS.

Conclusion: We demonstrated a novel glucose metabolism-related risk signature for predicting the prognosis of ccRCC. However, additional in vitro and in vivo research is required to validate our findings.

Hybrid Stem Cell States: Insights Into the Relationship Between Mammary Development and Breast Cancer Using Single-Cell Transcriptomics

Similarities between stem cells and cancer cells have implicated mammary stem cells in breast carcinogenesis. Recent evidence suggests that normal breast stem cells exist in multiple phenotypic states: epithelial, mesenchymal, and hybrid epithelial/mesenchymal (E/M). Hybrid E/M cells in particular have been implicated in breast cancer metastasis and poor prognosis. Mounting evidence also suggests that stem cell phenotypes change throughout the life course, for example, through embryonic development and pregnancy. The goal of this study was to use single cell RNA-sequencing to quantify cell state distributions of the normal mammary (NM) gland throughout developmental stages and when perturbed into a stem-like state in vitro using conditional reprogramming (CR). Using machine learning based dataset alignment, we integrate multiple mammary gland single cell RNA-seq datasets from human and mouse, along with bulk RNA-seq data from breast tumors in the Cancer Genome Atlas (TCGA), to interrogate hybrid stem cell states in the normal mammary gland and cancer. CR of human mammary cells induces an expanded stem cell state, characterized by increased expression of embryonic stem cell associated genes. Alignment to a mouse single-cell transcriptome atlas spanning mammary gland development from in utero to adulthood revealed that NM cells align to adult mouse cells and CR cells align across the pseudotime trajectory with a stem-like population aligning to the embryonic mouse cells. Three hybrid populations emerge after CR that are rare in NM: KRT18+/KRT14+ (hybrid luminal/basal), EPCAM+/VIM+ (hybrid E/M), and a quadruple positive population, expressing all four markers. Pseudotime analysis and alignment to the mouse developmental trajectory revealed that E/M hybrids are the most developmentally immature. Analyses of single cell mouse mammary RNA-seq throughout pregnancy show that during gestation, there is an enrichment of hybrid E/M cells, suggesting that these cells play an important role in mammary morphogenesis during lactation. Finally, pseudotime analysis and alignment of TCGA breast cancer expression data revealed that breast cancer subtypes express distinct developmental signatures, with basal tumors representing the most “developmentally immature” phenotype. These results highlight phenotypic plasticity of normal mammary stem cells and provide insight into the relationship between hybrid cell populations, stemness, and cancer.

Antrodia cinnamomea Confers Obesity Resistance and Restores Intestinal Barrier Integrity in Leptin-deficient Obese Mice

Obesity is associated with metabolic disorders. Thus, obesity prevention and treatment are essential for health. Antrodia cinnamomea (AC) is a multifunctional medicinal fungus used for the treatment of various diseases and for preventing diet-induced obesity. Leptin deficiency causes over-eating and spontaneous obesity. The concomitant metabolic symptoms are more severe than diet-induced obesity. Here, we used leptin-deficient (ob/ob) mice as an animal model for over-feeding to study the effect of AC on obesity. We fed C57BL/6 mice (WT, ob+/+) and ob/ob mice with AC for four weeks before performing qRT-PCR and immunoblot analysis to elaborate AC-modulated mechanisms. Further, we used Caco-2 cells as a human intestinal epithelial barrier model to examine the effect of AC on intestinal permeability. Our results suggested that AC reduces lipid deposits of the liver and epididymal white adipose tissue (EWAT) by promoting lipid metabolism and inhibiting lipogenesis-associated genes and proteins in ob/ob mice. Moreover, AC effectively repaired intestinal-barrier injury caused by leptin deficiency and enhanced intestinal barrier integrity in Caco-2 cells. Interestingly, AC significantly reduced body weight and EWAT with no compromise on food intake in ob/ob mice. Thus, AC effectively reduced obesity caused by leptin-deficiency and can potentially be used as a nutraceutical for treating obesity.

Inferring novel genes related to oral cancer with a network embedding method and one-class learning algorithms

Oral cancer (OC) is one of the most common cancers threatening human lives. However, OC pathogenesis has yet to be fully uncovered, and thus designing effective treatments remains difficult. Identifying genes related to OC is an important way for achieving this purpose. In this study, we proposed three computational models for inferring novel OC-related genes. In contrast to previously proposed computational methods, which lacked the learning procedures, each proposed model adopted a one-class learning algorithm, which can provide a deep insight into features of validated OC-related genes. A network embedding algorithm (i.e., node2vec) was applied to the protein-protein interaction network to produce the representation of genes. The features of the OC-related genes were used in the training of the one-class algorithm, and the performance of the final inferring model was improved through a feature selection procedure. Then, candidate genes were produced by applying the trained inferring model to other genes. Three tests were performed to screen out the important candidate genes. Accordingly, we obtained three inferred gene sets, any two of which were different. The inferred genes were also different from previous reported genes and some of them have been included in the public Oral Cancer Gene Database. Finally, we analyzed several inferred genes to confirm whether they are novel OC-related genes.

Identification of AUNIP as a candidate diagnostic and prognostic biomarker for oral squamous cell carcinoma

Background

Oral squamous cell carcinoma (OSCC) is one of the most common malignant tumors worldwide. Patients with poorly differentiated OSCC often exhibit a poor prognosis. AUNIP (Aurora Kinase A and Ninein Interacting Protein), also known as AIBp, plays a key role in cell cycle and DNA damage repair. However, the function of AUNIP in OSCC remains elusive.

Methods

The differentially expressed genes (DEGs) were obtained using R language. Receiver operating characteristic curve analysis was performed to identify diagnostic markers for OSCC. The effectiveness of AUNIP in diagnosing OSCC was evaluated by machine learning. AUNIP expression was analyzed in publicly available databases and clinical specimens. Bioinformatics analysis and in vitro experiments were conducted to explore biological functions and prognostic value of AUNIP in OSCC.

Findings

The gene integration analysis revealed 90 upregulated DEGs. One candidate biomarker, AUNIP, for the diagnosis of OSCC was detected, and its expression gradually increased along with malignant differentiation of OSCC. Bioinformatics analysis demonstrated that AUNIP could be associated with tumor microenvironment, human papillomavirus infection, and cell cycle in OSCC. The suppression of AUNIP inhibited OSCC cell proliferation and resulted in G0/G1 phase arrest in OSCC cells. The survival analysis showed that AUNIP overexpression predicted poor prognosis of OSCC patients.

Interpretation: AUNIP could serve as a candidate diagnostic and prognostic biomarker for OSCC and suppression of AUNIP may be a potential approach to preventing and treating OSCC.

Fund

Taishan Scholars Project in Shandong Province (ts201511106) and the National Natural Science Foundation of China (Nos. 61603218).