Prognostic value of RNA methylation-related genes in gastric adenocarcinoma based on bioinformatics.

Background: Gastric cancer (GC) is a malignant tumor that originates from the epithelium of the gastric mucosa and has a poor prognosis. Stomach adenocarcinoma (STAD) covers 95% of total gastric cancer. This study aimed to identify the prognostic value of RNA methylation-related genes in gastric cancer. Methods: In this study, The Cancer Genome Atlas (TCGA)-STAD and GSE84426 cohorts were downloaded from public databases. Patients were classified by consistent cluster analysis based on prognosis-related differentially expressed RNA methylation genes Prognostic genes were obtained by differential expression, univariate Cox and least absolute shrinkage and selection operator (LASSO) analyses. The prognostic model was established and validated in the training set, test set and validation set respectively. Independent prognostic analysis was implemented. Finally, the expression of prognostic genes was affirmed by reverse transcription quantitative PCR (RT-qPCR). Results: In total, four prognostic genes (ACTA2, SAPCD2, PDK4 and APOD) related to RNA methylation were identified and enrolled into the risk signature. The STAD patients were divided into high- and low-risk groups based on the medium value of the risk score, and patients in the high-risk group had a poor prognosis. In addition, the RNA methylation-relevant risk signature was validated in the test and validation sets, and was authenticated as a reliable independent prognostic predictor. The nomogram was constructed based on the independent predictors to predict the 1/3/5-year survival probability of STAD patients. The gene set enrichment analysis (GSEA) result suggested that the poor prognosis in the high-risk subgroup may be related to immune-related pathways. Finally, the experimental results indicated that the expression trends of RNA methylation-relevant prognostic genes in gastric cancer cells were in agreement with the result of bioinformatics. Conclusion: Our study established a novel RNA methylation-related risk signature for STAD, which was of considerable significance for improving prognosis of STAD patients and offering theoretical support for clinical therapy.

Breast cancer-derived exosomal lncRNA SNHG14 induces normal fibroblast activation to cancer-associated fibroblasts via the EBF1/FAM171A1 axis.

BACKGROUND: Exosomes released from cancer cells can activate normal fibroblasts (NFs) into cancer-associated fibroblasts (CAFs), which promotes cancer development. Our study aims to explore the role and potential mechanisms of breast cancer exosomes-delivered long non-coding RNA (lncRNA) SNHG14 in regulating CAFs transformation. METHODS: Adjacent normal tissues, cancerous and serum specimens were gathered in breast cancer patients. Exosomes and NFs were separated from breast cancer cells (SKBR-3) and normal tissues of patients, respectively. Cell viability and migration were measured with CCK-8 and Transwell assays. CAFs markers, fibroblast activation protein (FAP) and a-smooth muscle actin (α-SMA) were detected for assessing CAFs activation. The interactions between molecules were evaluated using dual luciferase reporter assay, RNA immunoprecipitation and chromatin immunoprecipitation. RESULTS: SNHG14 and FAM171A1 were upregulated in breast cancer. Exosomes secreted by SKBR-3 cells induced NFs activation in CAFs, as indicated by upregulating CAFs marker levels and facilitated cell viability and migration. Exosomal SNHG14 silencing in SKBR-3 cells inhibited CAFs activation. SNHG14 positively regulated FAM171A1 expression through EBF1. FAM171A1 overexpression eliminated the inhibition effect of exosomal SNHG14 silencing in CAFs transformation. CONCLUSION: Breast cancer-derived exosomal SNHG14 contributed to NFs transformation into CAFs by the EBF1/FAM171A1 axis.

Exploration of prognostic genes and risk signature in breast cancer patients based on RNA binding proteins associated with ferroptosis.

Background: Breast cancer (BRCA) is a life-threatening malignancy in women with an unsatisfactory prognosis. The purpose of this study was to explore the prognostic biomarkers and a risk signature based on ferroptosis-related RNA-binding proteins (FR-RBPs). Methods: FR-RBPs were identified using Spearman correlation analysis. Differentially expressed genes (DEGs) were identified by the "limma" R package. The univariate Cox and multivariate Cox analyses were executed to determine the prognostic genes. The risk signature was constructed and verified with the training set, testing set, and validation set. Mutation analysis, immune checkpoint expression analysis in high- and low-risk groups, and correlation between risk signature and chemotherapeutic agents were conducted using the "maftools" package, "ggplot2" package, and the CellMiner database respectively. The Human Protein Atlas (HPA) database was employed to confirm protein expression trends of prognostic genes in BRCA and normal tissues. The expression of prognostic genes in cell lines was verified by Real-time quantitative polymerase chain reaction (RT-qPCR). Kaplan-meier (KM) plotter database analysis was applied to predict the correlation between the expression levels of signature genes and survival statuses. Results: Five prognostic genes (GSPT2, RNASE1, TIPARP, TSEN54, and SAMD4A) to construct an FR-RBPs-related risk signature were identified and the risk signature was validated by the International Cancer Genome Consortium (ICGC) cohort. Univariate and multivariate Cox regression analysis demonstrated the risk score was a robust independent prognostic factor in overall survival prediction. The Tumor Mutational Burden (TMB) analysis implied that the high- and low-risk groups responded differently to immunotherapy. Drug sensitivity analysis suggested that the risk signature may serve as a chemosensitivity predictor. The results of GSEA suggested that five prognostic genes might be related to DNA replication and the immune-related pathways. RT-qPCR results demonstrated that the expression trends of prognostic genes in cell lines were consistent with the results from public databases. KM plotter database analysis suggested that high expression levels of GSPT2, RNASE1, and SAMD4A contributed to poor prognoses. Conclusion: In conclusion, this study identified the FR-RBPs-related prognostic genes and developed an FR-RBPs-related risk signature for the prognosis of BRCA, which will be of great significance in developing new therapeutic targets and prognostic molecular biomarkers for BRCA.

[Retracted] Exosome-mediated transfer of lncRNA­SNHG14 promotes trastuzumab chemoresistance in breast cancer.

Following the publication of this paper, it was drawn to the Editor's attention by a concerned reader that the TUNEL assay data shown in Fig. 6C were strikingly similar to images that had already appeared in Fig. 8B in another article that appeared in the journal Oncotarget [Chen W, Xu X-K, Li J-L, Kong K-K, Li H, Chen C, He J, Wang F, Li P, Ge X-S and Li F-C: MALAT1 is a prognostic factor in glioblastoma multiforme and induces chemoresistance to temozolomide through suppressing miR-203 and promoting thymidylate synthase expression. Oncotarget 8: 22783-22799, 2017]. Owing to the fact that the contentious data in the above article had already been published elsewhere prior to its submission to International Journal of Oncology, the Editor has decided that this paper should be retracted from the Journal on account of a lack of confidence in the presented data. The authors did provide an explanation to account for the duplication of the data, although this was not accepted by the Editorial Board. The Editor apologizes to the readership for any inconvenience caused. [International Journal of Oncology 53: 1013-1026, 2018; DOI: 10.3892/ijo.2018.4467].

LINC01605 promotes aerobic glycolysis through lactate dehydrogenase A in triple-negative breast cancer.

Breast cancer is the most prevalent cancer diagnosed in women and the major malignancy that threatens women health, thus we explored the role of long noncoding RNA LINC01605 in triple-negative breast cancer (TNBC). We collected tissue samples from TNBC patients and cultured breast cancer cells to detect LINC01605 levels by RT-PCR. We then constructed LINC01605 knockdown and LINC01605 overexpressed TNBC cell lines, cell proliferation was measured by CCK-8 and colony formation assays, cell migration and invasion were measured by Transwell assay, and aerobic glycolysis of cells was detected. Furthermore, a downstream target gene was found, and its role was confirmed by mouse allogeneic tumor formation. It discovered that LINC01605 expression was significantly increased in TNBC patients, and its high expression predicted a low survival prognosis for TNBC patients. Stable knockdown of LINC01605 remarkably inhibited cell proliferation, migration, and invasion, as well as aerobic glycolysis by inhibiting lactate dehydrogenase A in TNBC cell lines. Notably, knockdown of LINC01605 suppressed in vivo tumor formation and migration in TNBC transplanted mice. In conclusion, targeting long noncoding RNA LINC01605 might serve as a therapeutic candidate strategy to treat patients with TNBC.

Circular RNA Circ-STIL Contributes to Cell Growth and Metastasis in Hepatocellular Carcinoma via Regulating miR-345-5p/AQP3 Axis.

BACKGROUND: Circular RNAs (circRNAs) are implicated in the pathogenesis and development of hepatocellular carcinoma (HCC). However, the function and latent mechanism of circ-STIL in HCC have not been elucidated. AIMS: This study was designed to explore the precise role and underlying molecular mechanism of circ-STIL in HCC advancement. METHODS: The expression levels of circ-STIL, SCL/TAL1 interrupting locus (STIL), miR-345-5p and aquaporin-3 (AQP3) were measured by quantitative real-time polymerase chain reaction or western blot. Cell proliferation was assessed by 3-(4,5-dimethylthizol-2-yl)-2,5-diphenyltetrazolium bromide assay and colony formation assay. Cell apoptosis was analyzed by flow cytometry. Transwell assay was conducted to analyze cell migratory and invasive capacities. The interactions among circ-STIL, miR-345-5p and AQP3 were confirmed by dual-luciferase reporter and RNA immunoprecipitation assays. Xenograft tumor model was established to analyze the role of circ-STIL in HCC in vivo. RESULTS: Circ-STIL was upregulated in HCC tissues and cells. Circ-STIL knockdown inhibited HCC cell progression by reducing cell proliferation, migration and invasion and promoting cell apoptosis. MiR-345-5p was a direct target of circ-STIL, and AQP3 was targeted by miR-345-5p in HCC. Circ-STIL knockdown or miR-345-5p overexpression impeded cell malignant behaviors in HCC cells, and the effects could be reversed by miR-345-5p silence or AQP3 enhancement, respectively. Meanwhile, circ-STIL regulated AQP3 expression by sponging miR-345-5p. Besides, circ-STIL downregulation retarded HCC tumor growth in vivo. CONCLUSION: Circ-STIL knockdown suppressed HCC development by regulating miR-345-5p/AQP3 pathway, which might provide a promising target for HCC therapy.

MiRNA-96-5p contributed to the proliferation of gastric cancer cells by targeting FOXO3.

Various microRNAs (miRNAs, miRs) and the forkhead box O (FOXO) family proteins have been shown to influence gastric cancer progression and development. Here, we aimed to identify the gastric cancer related miRNAs and their relationship with the FOXO family. MiRNA profiles were generated by miRNA microarray screening from pre-operative plasma samples. Quantitative reverse transcription PCR and western bolt were used to determine the expression levels of miR-96 and FOXO family. 3-(4,5-Dimethylthiazol-2-yl)-2,5-Diphenyltetrazolium Bromide assay and colony formation assay were used to test the cell viability. The miR-96-5p and FOXO3 interaction were confirmed by luciferase reporter assay. Our results demonstrated the excessive expression of miR-96-5p in gastric cancer cell lines and plasma samples from gastric cancer patients. In addition, the protein levels of FOXO3 were decreased in tissue samples from gastric cancer patients. Moreover, miR-96-5p accelerated the gastric cancer cell proliferation by directly targeting FOXO3. Therefore, we conclude that iR-96-5p might promote the progression of gastric cancer by directly targeting FOXO3 mRNA and downregulating the expression of FOXO3 protein, which provides new insights for the molecular mechanism of gastric cancer.

Long non-coding RNA SNHG14 induces trastuzumab resistance of breast cancer via regulating PABPC1 expression through H3K27 acetylation.

Currently, resistance to trastuzumab, a human epidermal growth factor receptor 2 (HER2) inhibitor, has become one major obstacle for improving the clinical outcome of patients with advanced HER2+ breast cancer. While cell behaviour can be modulated by long non-coding RNAs (lncRNAs), the contributions of lncRNAs in progression and trastuzumab resistance of breast cancer are largely unknown. To this end, the involvement and regulatory functions of lncRNA SNHG14 in human breast cancer were investigated. RT-qPCR assay showed that SNHG14 was up-regulated in breast cancer tissues and associated with trastuzumab response. Gain- and loss-of-function experiments revealed that overexpression of SNHG14 promotes cell proliferation, invasion and trastuzumab resistance, whereas knockdown of SNHG14 showed an opposite effect. PABPC1 gene was identified as a downstream target of SNHG14, and PABPC1 mediates the SNHG14-induced oncogenic effects. More importantly, ChIP assays demonstrated that lncRNA SNHG14 may induce PABPC1 expression through modulating H3K27 acetylation in the promoter of PABPC1 gene, thus resulting in the activation of Nrf2 signalling pathway. These data suggest that lncRNA SNHG14 promotes breast cancer tumorigenesis and trastuzumab resistance through regulating PABPC1 expression through H3K27 acetylation. Therefore, SNHG14 may serve as a novel diagnostic and therapeutic target for breast cancer patients.

Exosome-mediated transfer of lncRNA­SNHG14 promotes trastuzumab chemoresistance in breast cancer.

Currently, resistance to trastuzumab, a human epidermal growth factor receptor 2 (HER2) inhibitor, has become an important obstacle to improving the clinical outcome of patients with advanced HER2+ breast cancer. While cell behavior may be modulated by long non­coding RNAs (lncRNAs), the contributions of lncRNAs within extracellular vesicles (exosomes) are largely unknown. To this end, the involvement and regulatory functions of potential lncRNAs contained within exosomes during the formation of chemoresistance in human breast cancer were investigated. Trastuzumab-resistant cell lines were established by continuously grafting HER2+ SKBR-3 and BT474 cells into trastuzumab-containing culture medium. An lncRNA microarray assay followed by reverse transcription­quantitative polymerase chain reaction analysis identified that lncRNA-small nucleolar RNA host gene 14 (SNHG14) was upregulated in trastuzumab-resistant cells when compared with parental breast cancer cells. Functional experimentation demonstrated that knockdown of lncRNA­SNHG14 potently promoted trastuzumab-induced cytotoxicity. Furthermore, extracellular lncRNA­SNHG14 was able to be incorporated into exosomes and transmitted to sensitive cells, thus disseminating trastuzumab resistance. Treatment of sensitive cells with exosomes highly expressing lncRNA­SNHG14 induced trastuzumab resistance, while knockdown of lncRNA­SNHG14 abrogated this effect. The Signal Transduction Reporter Array indicated that lncRNA­SNHG14 may promote the effect of trastuzumab by targeting the apoptosis regulator Bcl­2 (Bcl­2)/apoptosis regulator BAX (Bax) signaling pathway. Furthermore, the expression level of serum exosomal lncRNA­SNHG14 was upregulated in patients who exhibited resistance to trastuzumab, compared with patients exhibiting a response. Therefore, lncRNA­SNHG14 may be a promising therapeutic target for patients with HER2+ breast cancer.