Dynamic changes of the immune microenvironment in the development of gastric cancer caused by inflammation.

Precancerous lesions typically precede gastric cancer (GC), but the molecular mechanisms underlying the transition from these lesions to GC remain unclear. Therefore, it is urgent to understand this transition from precancerous lesions to GC, which is crucial for the early diagnosis and treatment of GC. In this study, we merged multiple single-cell RNA sequencing datasets to investigate the molecular changes in distinct cell types associated with the progression of GC. First, we observed an increasing abundance of immune cells and a decrease in non-immune cells from non-atrophic gastritis to GC. Five immune cell types were significantly enriched in GC compared to precancerous lesions. Moreover, we found that the interleukin (IL)-17 signaling pathway and Th17 cell differentiation were significantly up-regulated in immune cell subsets during GC progression. Some genes in these processes were predominantly expressed at the GC stage, highlighting their potential as diagnostic markers. Furthermore, we validated our findings using bulk RNA sequencing data from The Cancer Genome Atlas and confirmed consistent immune cell changes during GC progression. Our study provides insights into the immune infiltration and signaling pathways involved in the development of GC, contributing to the development of early diagnosis and targeted treatment strategies for this malignancy.

Key genes involved with prognosis were identified in lung adenocarcinoma by integrated bioinformatics analysis.

Objective: By screening the core genes in lung adenocarcinoma (LUAD) with bioinformatics, our study evaluated its prognosis value and role in infiltration process of immune cells. Methods: Using GEO database, we screened 5 gene chips, including GSE11072, GSE32863, GSE43458, GSE115002, and GSE116959. Then, we obtained the corresponding differentially expressed genes by analyzed 5 gene chips online by GEO2R (P < 0.05, |logFC| > 1). Then, through DAVID online platform, Cytoscape 3.6.1 software and PPI network analysis, the network was visualized and obtain the final core genes. Next, we plan to use the GEPIA, UALCAN, Kaplan-Meier plotter and Time 2.0 database for corresponding analysis. The GEPIA database was used to verify the expression of core genes in LUAD and normal lung tissues, and survival analysis was used to evaluate the value of core genes in the prognosis of LUAD patients. UALCAN was used to verify the expression of the LUAD core gene and promoter methylation status, and the predictive value of core genes was evaluated in LUAD patients by the Kaplan-Meier plotter online tool. Then, we used the Time 2.0 database to identify the relationship to immune infiltration in LUAD. Finally, we used the human protein atlas (HPA) database for online immunohistochemical analysis of the expressed proteins. Results: The expression of CCNB2 and CDC20 in LUAD were higher than those in normal lung tissues, their increased expression was negatively correlated with the overall survival rate of LUAD, and they were involved in cell cycle signal transduction, oocyte meiosis signal transduction as well as the infiltration process of immune cells in LUAD. The expression proteins of CCNB2 and CDC20 were also different in lung cancer tissue and normal lung tissue. Therefore, CCNB2 and CDC20 were identified as the vital core genes. Conclusion: CCNB2 and CDC20 are essential genes that may constitute prognostic biomarkers in LUAD, they also participate the immune infiltration process and protein expression process of LUAD, and might provides basis for clinical anti-tumor drug research.

Identification of Potential Key Genes and Prognostic Biomarkers of Lung Cancer Based on Bioinformatics.

Objective: To analyze and identify the core genes related to the expression and prognosis of lung cancer including lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) by bioinformatics technology, with the aim of providing a reference for clinical treatment. Methods: Five sets of gene chips, GSE7670, GSE151102, GSE33532, GSE43458, and GSE19804, were obtained from the Gene Expression Omnibus (GEO) database. After using GEO2R to analyze the differentially expressed genes (DEGs) between lung cancer and normal tissues online, the common DEGs of the five sets of chips were obtained using a Venn online tool and imported into the Database for Annotation, Visualization, and Integrated Discovery (DAVID) database for Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. The protein-protein interaction (PPI) network was constructed by STRING online software for further study, and the core genes were determined by Cytoscape software and KEGG pathway enrichment analysis. The clustering heat map was drawn by Excel software to verify its accuracy. In addition, we used the University of Alabama at Birmingham Cancer (UALCAN) website to analyze the expression of core genes in P53 mutation status, confirmed the expression of crucial core genes in lung cancer tissues with Gene Expression Profiling Interactive Analysis (GEPIA) and GEPIA2 online software, and evaluated their prognostic value in lung cancer patients with the Kaplan-Meier online plotter tool. Results: CHEK1, CCNB1, CCNB2, and CDK1 were selected. The expression levels of these four genes in lung cancer tissues were significantly higher than those in normal tissues. Their increased expression was negatively correlated with lung cancer patients (including LUAD and LUSC) prognosis and survival rate. Conclusion: CHEK1, CCNB1, CCNB2, and CDK1 are the critical core genes of lung cancer and are highly expressed in lung cancer. They are negatively correlated with the prognosis of lung cancer patients (including LUAD and LUSC) and closely related to the formation and prediction of lung cancer. They are valuable predictors and may be predictive biomarkers of lung cancer.

miR-574-5p mediates epithelial-mesenchymal transition in small cell lung cancer by targeting vimentin via a competitive endogenous RNA network.

Numerous studies have suggested that non-coding RNAs mediate tumorigenesis via the epithelial-mesenchymal transition (EMT). However, whether the long non-coding RNA (lncRNA) HOXA transcript at the distal tip (HOTTIP) plays a role in the EMT of small cell lung cancer (SCLC) remains unclear. The results of the present study suggest that HOTTIP-knockdown may lead to a significant increase in E-cadherin expression and a decrease in vimentin (VIM) expression; these proteins are two key markers of EMT. Furthermore, a notable morphological change in SCLC cells with HOTTIP-knockdown was observed: After upregulation of microRNA (miR)-574-5p, the cells exhibited a long, fusiform morphology. Investigating these phenomena further revealed that HOTTIP may participate in EMT by binding to miR-574-5p. In addition, using bioinformatics technology and a dual luciferase reporter assay, it was found that miR-574-5p inhibited VIM expression via direct binding and interaction. In summary, the present results indicate that HOTTIP may be involved in the EMT of SCLC by binding to miR-574-5p, and that miR-574-5p may act through VIM, which is a key marker of EMT.

Prediction Biomarkers Associated with Lymph Node Metastasis and Prognosis were Identified in Papillary Thyroid Carcinoma via Integrated Bioinformatics Analysis.

BACKGROUND: Prediction biomarkers associated with prognosis and lymph node metastasis (LNM) in papillary thyroid carcinoma (PTC) are needed to facilitate clinicians in choosing appropriate therapies. OBJECTIVE: We hope to identify key genes associated with LNM and prognosis in PTC. METHODS: GSE29265, GSE33630, GSE3467, GSE3678 and GSE58545 gene expression profiles were acquired from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) between PTC tissues and normal thyroid tissues were selected with the GEO2R tool, and common DEGs among the five datasets were integrated with Venn software online. A proteinprotein interaction (PPI) network of the common DEGs was visualized. We analyzed the PPI network and determined core genes using the Cytoscape software. Furthermore, we employed UALCAN to verify the expression and promoter methylation status of the core genes in thyroid carcinoma (THCA). Additionally, the Kaplan-Meier plotter online tool was used to analyze the relationship between overall survival and core gene expressions in THCA. RESULTS: TNS3, DUSP6, DUSP4 and PTPRE were identified as core genes. Expression of these 4 genes and the promoter methylation status of DUSP4 and PTPRE were strongly associated with LNM (P<0.05). High expression of 3 genes (DUSP6, DUSP4 and PTPRE) was related to a significantly better survival than low expression of the 3 genes in THCA. In contrast, high TNS3 expression was related to significantly worse survival (P<0.05). CONCLUSION: TNS3, DUSP6, DUSP4, PTPRE and DUSP4 and PTPRE promoter methylation status might be useful predictive biomarkers of LNM in PTC. Additionally, these genes may be prognostic biomarkers in PTC.

New insights into long non-coding RNAs in non-small cell lung cancer.

Lung cancer is a malignant tumor that seriously threatens human life and health. Non-small cell lung cancer (NSCLC) accounts for 85 % of all lung cancer cases, and its global 5-year survival rate is only approximately 5%. Thus, the identification of new prognostic biomarkers has become one of the most urgent challenges in NSCLC research. Long noncoding RNAs (LncRNAs) are a kind of noncoding RNA whose length exceeds 200 nucleotides (nt). LncRNAs are transcribed by RNA pol II and can be subjected to posttranscriptional modifications such as blocking, polyadenylation and splicing; moreover, their expression profiles are more specific than those of mRNAs. Emerging evidence confirms that lncRNAs are associated with the occurrence and development of NSCLC and play an important role in NSCLC drug resistance. The purpose of this review was to describe the roles of lncRNAs in the development, diagnosis and prognosis of NSCLC and to explore new evidence of lncRNAs in the treatment of NSCLC drug resistance. This review provides a new perspective of lncRNAs in the treatment of NSCLC.

Identification of key differentially expressed genes between ER-positive/HER2-negative breast cancer and ER-negative/HER2-negative breast cancer using integrated bioinformatics analysis.

BACKGROUND: Treatment strategies for various subtypes of breast cancer (BC) are different based on their distinct molecular characteristics. Therefore, it is very important to identify key differentially expressed genes (DEGs) between ER-positive/HER2-negative BC and ER-negative/HER2-negative BC. METHODS: Gene expression profiles of GSE22093 and GSE23988 were obtained from the Gene Expression Omnibus database. There were 74 ER-positive/HER2-negative BC tissues and 85 ER-negative/HER2-negative BC tissues in the two profile datasets. DEGs between ER-positive/HER2-negative tissues and ER-negative/HER2-negative BC tissues were identified by the GEO2R tool. The common DEGs among the two datasets were detected with Venn software online. Next, we made use of the Database for Annotation, Visualization and Integrated Discovery to analyze enriched Kyoto Encyclopedia of Gene and Genome (KEGG) pathways and gene ontology terms. Then, the protein-protein interactions (PPIs) of these DEGs were visualized by Cytoscape with the Search Tool for the Retrieval of Interacting Genes. Of the proteins in the PPI network, Molecular Complex Detection plug-in analysis identified nine core upregulated genes and one core downregulated gene. UALCAN and Gene Expression Profiling Interactive Analysis were applied to determine the expression of these 10 genes in BC. Furthermore, for the analysis of overall survival among those genes, the Kaplan-Meier method was implemented. RESULTS: Ninety-three common DEGs (63 upregulated and 30 downregulated) were identified. KEGG pathway enrichment analysis showed that upregulated DEGs were particularly enriched in the progesterone-mediated oocyte maturation pathway. In addition, PGR might be a prognostic biomarker for ER-positive/HER2-negative BC. CCND1 is a poor prognostic biomarker for ER-positive/HER2-negative BC and ER-negative/HER2-negative BC. Moreover, TFF1, AGR2 and EGFR might be predictive biomarkers of node metastasis in ER-positive/HER2-negative BC and ER-negative/HER2-negative BC. CONCLUSIONS: CCND1, AGR2, PGR, TFF1 and EGFR are the key DEGs between ER-positive/HER2-negative BC and ER-negative/HER2-negative BC. Further studies are required to confirm the functions of the identified genes.

Key genes involved in cell cycle arrest and DNA damage repair identified in anaplastic thyroid carcinoma using integrated bioinformatics analysis.

BACKGROUND: Since anaplastic thyroid carcinoma (ATC) has rapid progression and a poor outcome, identification of the key genes and underlying mechanisms of ATC is required. METHODS: Gene expression profiles of GSE29265 and GSE33630 were available from the Gene Expression Omnibus database. The two profile datasets included 19 ATC tissues, 55 normal thyroid tissues and 59 papillary thyroid cancer (PTC) tissues. Differentially expressed genes (DEGs) between ATC tissues and normal thyroid tissues as well as ATC tissues and PTC tissues were identified using the GEO2R tool. Common DEGs between the two datasets were selected via Venn software online. Then, we applied the Database for Annotation, Visualization and Integrated Discovery for Kyoto Encyclopedia of Gene and Genome pathway and gene ontology (GO) analyses. Additionally, protein-protein interactions (PPIs) of these DEGs were visualized via Cytoscape with Search Tool for the Retrieval of Interacting Genes. In the PPI networks analyzed by the Molecular Complex Detection plug-in, all 54 upregulated core genes were selected. Furthermore, Kaplan-Meier analysis was applied to analyze overall survival based on these 54 genes. Then, we used the DrugBank database to identify drug relationships for the 54 genes. Additionally, we validated the correlations between genes enriched in pathways and genes identified as prognosis biomarkers of THCA by Gene Expression Profiling Interactive Analysis. RESULTS: Four genes (CCNB1, CCNB2, CDK1 and CHEK1) involved cell cycle arrest and DNA repair were significantly enriched in the G2/M phase of the cell cycle pathway and before G2 phase arrest of the P53 pathway. Inhibitors of CHEK1, CDK1 and TOP2A were identified in the DrugBank database. ANLN, DEPDC1, KIF2C, CENPN, TACC3 CCNB2 and CDC6 were hypothesized to be prognostic biomarkers of ATC. Furthermore, CCNB1, CCNB2, CDK1 and CHEK1 were significantly positively associated with these prognosis genes. CONCLUSIONS: CCNB1, CCNB2, CDK1 and CHEK1 may be key genes involved cell cycle arrest and DNA damage repair in ATC. Further studies are required to confirm the contributions of the identified genes to ATC progression and survival.

Investigation of differentially expressed genes in nasopharyngeal carcinoma by integrated bioinformatics analysis.

Nasopharyngeal carcinoma (NPC) is a common malignancy of the head and neck. The aim of the present study was to conduct an integrated bioinformatics analysis of differentially expressed genes (DEGs) and to explore the molecular mechanisms of NPC. Two profiling datasets, GSE12452 and GSE34573, were downloaded from the Gene Expression Omnibus database and included 44 NPC specimens and 13 normal nasopharyngeal tissues. R software was used to identify the DEGs between NPC and normal nasopharyngeal tissues. Distributions of DEGs in chromosomes were explored based on the annotation file and the CYTOBAND database of DAVID. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were applied. Additionally, a protein-protein interaction (PPI) network, constructed using the STRING database and visualized by Cytoscape, was used to identify hub genes, key modules and important transcription factors (TFs). A total of 906 DEGs were identified; 434 (47.90%) DEGs were upregulated and 472 (52.10%) were downregulated. The DEGs were demonstrated to be enriched in chromosome 7p15-p14, 2q31, 1q21-q22, 1q21, 4q21 and 1p31-p22. DEGs were mainly enriched for the following GO terms: 'Cilium movement', 'microtubule bundle formation' and 'axoneme assembly'. KEGG pathway enrichment analysis revealed that pathways for 'cell cycle', 'DNA replication', 'interleukin-17 signaling', 'amoebiasis' and 'glutathione metabolism' were enriched. In addition, a PPI network comprising 867 nodes and 1,241 edges was constructed. Finally, five hub genes (aurora kinase A, cell division cycle 6, mitotic arrest deficient 2-like 1, DNA topoisomerase 2α and TPX2 microtubule nucleation factor), 8 modules, and 14 TFs were identified. Modules analysis revealed that cyclin-dependent kinase 1 and exportin 1 were involved in the pathway of Epstein-Barr virus infection. In summary, the hub genes, key modules and TFs identified in this study may promote our understanding of the pathogenesis of NPC and require further in-depth investigation.

Short-term stimulation with histone deacetylase inhibitor trichostatin a induces epithelial-mesenchymal transition in nasopharyngeal carcinoma cells without increasing cell invasion ability.

BACKGROUND: Epithelial-mesenchymal transition (EMT) may be one of the reasons for the failure in some clinical trials regarding histone deacetylase inhibitors (HDACIs)-treated solid tumors. We investigated the effects of a pan-HDACI trichostatin A (TSA) on the proliferation and EMT of nasopharyngeal carcinoma (NPC) cells. METHODS: Poorly-differentiated NPC cell line CNE2 and undifferentiated C666-1 were treated with various concentrations of TSA, the cell viability was assessed by CCK-8 assay, the morphology was photographed, and the mRNA level of HDACs was assessed by semiquantitative PCR. After determination the cell cycle distributions, cells were subjected to western blotting analysis of cell cycle and EMT-associated genes expression. And the changes in migration ability were assessed by transwell migration assay and scratch wound healing assay. Finally, histone deacetylases activator ITSA-1 was used to assess the reverse of TSA-induced changes in NPC cells. RESULTS: TSA inhibited the proliferation of CNE2 and C666-1 cells in a concentration-dependent manner and arrested the cell cycle at G1 phases. TSA reduced PCNA, cyclin D1, cyclin E1, CDK2, p16 and p21 expressions and stimulated CDK6 levels. TSA stimulation for 48 h could effectively induce the EMT in CNE2 and C666-1 cells, which showed an increase of spindle-like cells and promoted expression of Vimentin and Snail1 expression in a concentration-dependent manner. Surprisingly, this short period of TSA treatment that induced EMT also impeded the migration ability of CNE2 and C666-1 cells. Interestingly, ITSA-1 rescued TSA-impeded CNE2 and C666-1 cells' proliferation, migration and HDACs expression, also re-induced the cells to turn into epithelial cell phenotypes. CONCLUSIONS: These results indicate that short-term stimulation of TSA effectively inhibits cell proliferation and induce EMT-like changes in NPC cells but not increase its invasion ability.

Proliferative myositis and nodular fasciitis: a retrospective study with clinicopathologic and radiologic correlation.

Proliferative myositis (PM) and nodular fasciitis (NF) are two diseases easily misdiagnosed as cancer, often promoting unnecessary invasive procedures. To make accurate diagnoses of PM and NF and for the differential diagnosis between them, we performed a retrospective study to evaluate the roles of the clinical, radiologic, and pathologic characteristics of PM and NF. With an emphasis on the clinicopathologic and radiologic characteristics, we conducted a retrospective study of 8 cases of PM and 64 cases of NF that were diagnosed between 2012 and 2018. According to MRI findings, the lesions of PM and NF appeared as homogeneous masses with homogenous hypointensity or isointensity on T1-weighted images and as moderately or markedly hyperintense signals on T2-weighted images compared to skeletal muscle. In terms of histopathologic features, the differences between PM and NF mainly consisted of the presence of ganglion-like myofibroblasts with vesicular nuclei and basophilic cytoplasm in PM. The areas abundant in myxoid stroma with inflammatory infiltration that did not have abundant ganglion-like cells suggest NF. Immunohistochemically, the spindle-shaped cells of PM stained positive for smooth muscle actin (SMA), while the ganglion-like cells were negative. The spindle-shaped cells of NF showed diffuse expression of SMA, calponin, and vimentin. Our comprehensive study further demonstrated that PM and NF had a wide clinicopathologic and radiologic spectrum. Correlation with the clinical, radiologic and pathologic characteristics may help clinicians and pathologists make accurate diagnoses.

LncRNA HOTTIP-Mediated HOXA11 Expression Promotes Cell Growth, Migration and Inhibits Cell Apoptosis in Breast Cancer.

As the most common cause of cancer death in women, the pathogenesis of breast cancer still remains unclear. Here, we reported a long non-coding RNA (lncRNA), HOTTIP (HOXA transcript at the distal tip), that may play an important role in the pathogenesis of breast cancer. Using gain-and-loss-of experiments in vitro and in vivo, we observed the marked upregulation of HOTTIP/HOXA11 in the breast cancer cell line, MCF-7, and the downregulation of HOTTIP or HOXA11, which might inhibit cell proliferation and migration but promote cell apoptosis in breast cancer MCF-7 cells. In addition, by further rescue experiments with HOXA11 overexpression, we uncovered a novel potential regulatory mechanism between HOTTIP and one of its physical HOXA clusters, HOXA11. Hence, HOTTIP may mediate, at least partly, HOXA11 expression involved in cell growth, migration, and apoptosis of breast cancer MCF-7 cells.

High FMNL3 expression promotes nasopharyngeal carcinoma cell metastasis: role in TGF-ß1-induced epithelia-to-mesenchymal transition.

Formin-like 3 (FMNL3) plays a crucial role in cytoskeletal mediation and is potentially a biomarker for cell migration; however, its role in cancer metastasis remains unknown. In this study, we found elevated FMNL3 protein expression in clinical nasopharyngeal carcinoma (NPC) tissues. FMNL3 expression positively correlated to the clinical stage, T (tumour), N (lymph node metastasis) and M (distant metastasis) classification of NPC patients. Moreover, FMNL3 positively correlated to Vimentin expression and negatively correlated to E-cadherin expression in clinical NPC samples. In vitro experiments showed that FMNL3 expression was inversely related to NPC cell differentiation status. Overexpression of FMNL3 led to epithelial-to-mesenchymal transition (EMT) in well differentiated CNE1 cells. TGF-ß1-treated poorly differentiated CNE2 cells showed changes in EMT accompanied by enhanced FMNL3 expression and cell migration. On the contrary, knockdown of FMNL3 partially attenuated the TGF-ß1-promoted CNE2 cell migration, together with associated changes in EMT markers. Finally, knockdown of FMNL3 also weakened EMT in tumours in xenographs. Our study indicates for the first time that TGF-ß1/FMNL3 signalling may be a novel mechanism mediating EMT in NPC, which is closely associated with NPC metastasis.

Expression and significance of tumor drug resistance related proteins and beta-catenin in esophageal squamous cell carcinoma.

BACKGROUND AND OBJECTIVE: As chemotherapy is generally used in the clinical treatment of cancer, the problem of multidrug resistance (MDR) of tumors against the chemotherapeutic agents becomes more and more serious. It has been the major cause for the failure of the chemotherapy. We detected the expressions of beta-catenin and tumor drug resistance related proteins, MRP2, P-gp, and Bcl-2, in esophageal squamous cell carcinoma (ESCC) to explore their function and correlation in the occurrence and development of MDR in ESCC. METHODS: We used the tissue microarray technique, immunohistochemistry, and image analysis methods to detect the expressions of MRP2, P-gp, beta-catenin, and Bcl-2 proteins and analyze their relationships with clinical data in a ESCC tissue microarray consisting of 582 specimens of ESCC, 294 specimens of normal mucosa, 92 specimens of basal cell hyperplasia, and 87 specimens of dysplasia adjacent to cancer tissue. RESULTS: The integral optical density (IOD) of MRP2 and Bcl-2, which was 195.7 +/- 175.9 x 10(3)) and 90.5 +/- 112.5 x 10(3)), respectively, was significantly higher in ESCC than in normal mucosa, which was 104.8 +/- 86.1 x103) and 25.2 +/- 46.6 x 10(3)), respectively (P < 0.01). The IOD of P-gp and beta-catenin, which was 57.7 +/- 75.5 x 10(3)) and 32.0 +/- 47.0 x 10(3)) respectively, was significantly lower in ESCC than in normal mucosa, which was 114.8 +/- 106.6 x 10(3)) and 46.1 +/- 35.7 x 10(3)), respectively (P < 0.01). According to the following order, well differentiated moderately differentiated poorly differentiated, the IOD of MRP2 increased in ESCC (P < 0.01). The IOD of beta-catenin was higher in poorly differentiated ESCC than in well or moderately differentiated ESCC (P < 0.01). The IOD of Bcl-2 was lower in well differentiated ESCC than in poorly and moderately differentiated ESCC (P < 0.01). The IOD of beta-catenin and Bcl-2 was higher in the ESCC of specimens with infiltration depths that were in membrane mucosa than those in the muscular layer or serous coat (P < 0.01). The IOD of Bcl-2 was significantly higher in cases with lymph node metastasis than in cases without (P < 0.01). Positive correlations which were respectively between the expressions of P-gp and MRP2, the expressions of P-gp and Bcl-2 were found (r = 0.288 and r = 0.253, respectively, P < 0.01). CONCLUSIONS: MRP2, P-gp, and Bcl-2 may be taken as prognostic factors for MDR of ESCC. beta-catenin may play an important role in carcinogenesis and progression of ESCC.