Non-tumor Tissue Samples Research Articles

RAB31 is targeted by miR-26b and serves a role in the promotion of osteosarcoma.

Ras-related protein Rab-31 (RAB31), a small guanosine 5'-triphosphate-binding protein, is a member of the Rab family and has been demonstrated to serve an oncogenic role in several common types of human cancer. However, the function of RAB31 in osteosarcoma (OS) has not been previously studied. The present study identified that the expression levels of RAB31 were significantly higher in OS tissue samples compared with matched adjacent non-tumor tissue samples, and high RAB31 expression was associated with malignant progression and a poor prognosis for patients with OS. Furthermore, it was identified that the expression levels of RAB31 were increased in OS cell lines compared with normal osteoblast cells. Silencing of RAB31 expression significantly inhibited OS cell proliferation, cell cycle progression, migration and invasion, and significantly increased the rate of cell apoptosis. In addition, the present study used a luciferase reporter assay to demonstrate that RAB31 was a direct target gene of microRNA-26b (miR-26b), which is a known tumor suppressor in OS. The expression levels of RAB31 were negatively associated with miR-26b expression in OS cells. Finally, miR-26b was demonstrated to be significantly decreased in OS tissues compared with adjacent non-tumor tissues, and an inverse correlation was observed between the expression levels of RAB31 and miR-26b in OS tissues. In summary, to the best of our knowledge, the present study is the first to report that RAB31 is a target gene of miR-26b, and silencing of RAB31 may inhibit OS growth and progression.

MiR-4461 Inhibits Tumorigenesis of Renal Cell Carcinoma by Targeting PPP1R3C.

Background: Renal cell carcinoma (RCC) is one of the most common and malignant tumors in the urinary system. The aim of this research was to investigate the mechanism and clinical significance of miR-4461 in the RCC progression. Materials and Methods: Twenty-eight (28) paired RCC tissue samples and adjacent nontumor tissue samples, as well as RCC cell lines were used to measure the expression of miR-4461 and protein phosphatase 1 regulatory subunit 3C (PPP1R3C) transcript by real-time quantitative PCR. The target relationship between miR-4461 and PPP1R3C was predicted by TargetScan and further verified by dual-luciferase reporter gene assay and RNA pull-down assay. Cell Counting Kit-8 (CCK-8) assay and BrdU ELISA assay were performed to measure RCC cell viability and proliferation. In addition, caspase-3 activity assay and cell adhesion assay were implemented to measure RCC cell apoptosis and adhesion. Results: MiR-4461 was lowly expressed both in RCC tissues and cells, while upregulated PPP1R3C was tested in RCC tissues and cells. In addition, miR-4461 was validated to directly target PPP1R3C, thereby negatively regulating PPP1R3C. Particularly, miR-4461 exerted a clear inhibitory effect on the malignant phenotypes of RCC cells by binding and inhibiting PPP1R3C. Conclusion: MiR-4461, which served as a tumor suppressor, inhibited RCC progression by targeting and downregulating PPP1R3C.

High ADAMTS18 expression is associated with poor prognosis in stomach adenocarcinoma.

Stomach adenocarcinoma (STAD) is the most pathological type of gastric cancer. ADAM metallopeptidase with thrombospondin type 1 motif 18 (ADAMTS18) plays an essential role in organ development and tumorigenesis; however, its function in STAD, and its impact on clinical outcome remain unclear. Thus, the present study aimed to investigate the association between ADAMTS18 expression and the prognosis of patients with STAD. Data from 300 patients with STAD in The Cancer Genome Atlas (TCGA) database were analyzed, and the median survival time and overall survival (OS) rate of these patients were assessed. Subsequently, 40 paired tumor and non-tumor tissue samples from patients with STAD were collected, and the relative ADAMTS18 mRNA expression levels were determined. Results from TCGA database demonstrated that high tumor ADAMTS18 expression was associated with a poorer prognosis in patients with STAD. Similarly, results from the assessed patient cohort indicated that ADAMTS18 expression was significantly higher in STAD tissues compared with non-tumor tissues. Furthermore, ADAMTS18 expression was significantly associated with tumor differentiation, lymph node metastasis and tumor node metastasis stage. Taken together, these results suggest that ADAMTS18 is highly expressed in STAD tissues, and thus may act as a potential indicator of poor prognosis in patients with STAD.

Circular RNA cir-ITCH Is a Potential Therapeutic Target for the Treatment of Castration-Resistant Prostate Cancer.

cir-ITCH, a well-known tumor-suppressive circular RNA, plays a critical role in different cancers. However, its expression and functional role in prostate cancer (PCa) are unclear. Herein, we explored the potential mechanism and tumor-inhibiting role of cir-ITCH in PCa. Using reverse transcriptase polymerase chain reaction assay, we analyzed the expression of cir-ITCH in PCa and paired adjacent nontumor tissue samples resected during surgical operation, as well as in two cell lines of human PCa (LNCaP and PC-3) and the immortalized normal prostate epithelial cell line (RWPE-1). Cell viability and migration of PCa cell lines were evaluated using CCK-8 and wound-healing assays. Expression of key proteins of the Wnt/β-catenin and PI3K/AKT/mTOR pathways was detected using western blotting. We found that cir-ITCH expression was typically downregulated in the tissues and cell lines of PCa compared to that in the peritumoral tissue and in RWPE-1 cells, respectively. The results showed that cir-ITCH overexpression significantly inhibits the proliferation, migration, and invasion of human PCa cells and that reciprocal inhibition of expression occurred between cir-ITCH and miR-17. Proteins in the Wnt/β-catenin and PI3K/AKT/mTOR pathways were downregulated by overexpression of cir-ITCH both in androgen receptor-positive LNCaP cells and androgen receptor-negative PC-3 cells. Taken together, these data demonstrated that cir-ITCH plays a tumor-suppressive role in human PCa cells, partly through the Wnt/β-catenin and PI3K/AKT/mTOR pathways. Thus, cir-ITCH may serve as a novel therapeutic target for the treatment of PCa, especially castration-resistant prostate cancer.

Optimized protocol for metabolomic and lipidomic profiling in formalin-fixed paraffin-embedded kidney tissue by LC-MS

Formalin-fixed and paraffin-embedded (FFPE) tissue represents a valuable resource to examine cancer metabolic alterations and to identify potential markers of disease. Protocols commonly used for liquid-chromatography mass spectrometry (LC-MS)-based FFPE metabolomics have not been optimized for lipidomic analysis and pre-analytical factors, that potentially affect metabolite levels, were scarcely investigated. We here demonstrate the assessment and optimization of sample preparation procedures for comprehensive metabolomic and lipidomic profiling in FFPE kidney tissue by LC-QTOF-MS. The optimized protocol allows improved monitoring of lipids including ceramides (Cer), glycosphingolipids (GSL) and triglycerides (TAGs) while the profiling capability for small polar molecules is maintained. Further, repeatable sample preparation (CVs < 20%) along with high analytical (CVs < 10%) and inter-day precision (CVs < 20%) is achieved. As proof of concept, we analyzed a set of clear cell renal cell carcinoma (ccRCC) and corresponding non-tumorous FFPE tissue samples, achieving phenotypic distinction. Investigation of the impact of tissue fixation time (6 h, 30 h and 54 h) on FFPE tissue metabolic profiles revealed metabolite class-dependent differences on their detection abundance. Whereas specific lipids (e.g. phosphatidylinositoles, GSLs, saturated fatty acids and saturated lyso-phosphatidytlethanolamines [LPE]) remained largely unaffected (CVs < 20% between groups of fixation time), neutral lipids (e.g. Cer and TAGs) exhibited high variability (CVs > 80%). Strikingly, out of the lipid classes assigned as unaffected, fatty acids 18:0, 16:0 and LPE 18:0 were detectable by high-resolution MALDI-FT-ICR MS imaging in an independent cohort of ccRCC tissues (n = 64) and exhibited significant differences between tumor and non-tumor regions.

Whole genomic copy number variation score: an indicator of potential diagnostic and prognostic value for lung adenocarcinoma

Objective: To verify the value of whole genomic copy number variation (WGCNV) detection and scoring system in the diagnosis and prognosis of lung adenocarcinoma. Methods: Seventy-six lung adenocarcinoma specimens including ninety-one tumor samples and twenty adjacent non-tumor lung tissue samples were collected using Laser capture microdissection (LCM). Whole genomic amplification (WGA) was used to enrich DNA and construct a sequencing library for next generation sequencing (NGS). Changes of larger than 5Mb CNV in this study were analyzed and scored. The nuclear grading and score of tumor cells in the surgery and pleural effusion cytology of lung adenocarcinoma specimens were evaluated separately. For each case, we evaluated (1) nuclear size, (2) mitotic counts, (3) nuclear atypia, (4) atypical mitoses. The data of disease-free survive (DFS) and overall survive (OS) were collected for assessing the prognostic value of WGCNV score. Meanwhile, receiver operating characteristic (ROC) and area under curve (AUC) were used to define a cut-off value and evaluate the diagnostic significance in lung adenocarcinoma. Results: The WGCNV scores of twenty adjacent non-tumor lung tissue samples were treated as normal control and all of WGCNV scores of tumor samples range from 0 to 9.95, the median score was 2.7. The WGCNV scores were divided into three groups: low score group <1.74, medium score grade 1.74~4.23, high score grade >4.23. The WGCNV score was positively associated with the nuclear grade scoring (r=0.780 90, P<0.001). The result for evaluation of prognostic value of the WGCNV scores showed that comparing with low WGCNV score group, Hazard Ratio (HR) of medium score group was 4.11 (95%CI=0.72~23.57) and high score group was 2.07 (95%CI=0.30~14.12). These results suggested that the risks of the medium and high WGCNV score group elevated. According to the analysis results of ROC curve, when the cut off value was 0.01, the sensitivity and specificity for lung adenocarcinoma diagnosis were 97.8% and 95.0% respectively, the positive predictive value (PPV) and negative predictive value (NPV) were 99.0% and 90.1%, respectively, the AUC was 0.981. In the differentiation of adenocarcinoma in situ (AIS) and minimally invasive adenocarcinoma (MIA) group and invasive adenocarcinoma group, when the cut off value was 1.8, the sensitivity and specificity between the two groups were 78.1% and 94.4%, and the PPV and NPV were 98.0% and 52.0%, respectively, the AUC was 0.896. Conclusion: This study verifies that WGCNV scoring system has a potential diagnostic and prognostic value in lung adenocarcinoma.

Identification of Key mRNAs and Pathways in Colorectal Cancer

Colorectal cancer (CRC) is the third most cancer-related death worldwide. This work aimed to identify potential hub genes and dysregulated pathways in the CRC by bioinformatics analysis. Three gene expression datasets were collected from GEO datasets, including tumor sample (N = 242) and adjacent nontumor tissue sample (N = 59). RankProd was used to discover the differential expressed genes between tumor and adjacent nontumor tissues for datasets generated by different laboratories. The gene set enrichment analysis conducted on the DE genes, followed by the protein–protein interaction (PPI) network. In total, 2,007 significant differential expression (DE) genes between tumor and adjacent nontumor tissues, include 1,090 upregulated genes and 917 downregulated genes in the tumor. The DE mRNAs are involved in cancer-related pathways. We comprehensively identified the CRC-related key mRNAs. Our data demonstrated combined different resources of transcriptomes will promote the understanding of the molecular mechanisms underlying CRC development and may be useful in discovering candidate molecular biomarkers for diagnosing, prognosis, and treating of CRC.

LINC00461 Overexpression Can Induce Docetaxel Resistance in Breast Cancer by Interacting with miR-411-5p.

PurposeBreast cancer (BC) is the most common malignant cancer in women worldwide. Recently, long non-coding RNAs (LncRNAs) have been reported to have essential roles in BC tumorigenesis.Patients and MethodsTumor and adjacent non-tumor tissue samples were collected from patients with BC (n = 168) for comparison of LncRNA and miRNA expression levels. Patient clinical, demographic, and molecular data were analyzed by univariate and multivariate methods to identify factors associated with patient survival, and a nomogram was generated using significant risk/protective factors. Further, analyses of LINC00461 and miR-411-5p expression and function were conducted in BC and normal breast epithelial cell lines, by quantitative RT-PCR, cell proliferation, wound-healing, RNA pull-down, RNA immunoprecipitation, and luciferase assays. Docetaxel (DTX)-resistant BC cell lines were also generated and used to assess the roles of LINC00461 and miR-411-5p in drug resistance.ResultsLINC00461 was up-regulated in BC tissues relative to adjacent non-tumor samples, and expression of LINC00461 was correlated with poor patient prognosis. LINC00461 knockdown could inhibit proliferation of BC cells in vitro. Further, LINC00461 expression was higher in DTX-resistant than in non-resistant BC cell lines. Our data support a role for LINC00461 as a competitive endogenous RNA sponge involved in regulation of miR-411-5p expression in BC. miR-411-5p was down-regulated in both BC tissues and cell lines, with levels negatively correlated with those of LINC00461. Moreover, miR-411-5p was down-regulated in DTX-resistant BC cell lines compared with non-resistant cell lines.ConclusionIn conclusion, LINC00461 promotes proliferation, migration, and DTX-resistance in BC by acting as a sponge for miR-411-5p. This process represents a potential therapeutic target for patients with BC.

MP17-10 N 6 -METHYLADENOSINE MODIFICATION OF CIRCANKS1A ACCELERATES CYTOPLASMIC EXPORT AND STABILIZES RACGAP1 TO PROMOTE BLADDER CANCER CELL PROLIFERATION AND METASTASIS

You have accessJournal of UrologyBladder Cancer: Basic Research & Pathophysiology II (MP17)1 Apr 2020MP17-10 N6-METHYLADENOSINE MODIFICATION OF CIRCANKS1A ACCELERATES CYTOPLASMIC EXPORT AND STABILIZES RACGAP1 TO PROMOTE BLADDER CANCER CELL PROLIFERATION AND METASTASIS Qiangqiang Ge*, Yang Xun, Junlin Lu, and Shaogang Wang Qiangqiang Ge*Qiangqiang Ge* More articles by this author , Yang XunYang Xun More articles by this author , Junlin LuJunlin Lu More articles by this author , and Shaogang WangShaogang Wang More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000000842.010AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract INTRODUCTION AND OBJECTIVE: Circular RNAs (circRNAs) have been identified to serve as significant regulators in cancer progression. However, the role of circRNA in bladder cancer (BCa) remains largely unknown. Herein, we investigate the expression profiles of circRNA in 20 paired samples of BCa. METHODS: To investigate the the expression profiles of circRNA, we performed high-throughput CircRNA Microarray using 20 pairs of BCa and matched adjacent non-tumor tissue samples. To explore crucial circRNAs that involved in BCa, co-expression network analysis was performed between the top 100 mostly changed circRNAs. The network represented that 15 circRNAs might involve in BCa progression. Analysis of the correlation between the expression level of 15 circRNAs and clinical data was conducted and circANKS1A was chosen. Gain-of-function and loss-of-function experiments were used to analyze the effect of circANKS1A on cell proliferation and metastasis in vitro and in vivo. m6A-containing RNAs were precipitated from methylated RNA immunoprecipitation (MeRIP) assays. The role of m6A methylation of circANKS1A in BCa proliferation and metastasis was investigated. To explore the potential molecular mechanisms of circANKS1A in regulating BCa malignance, RNA pull-down assays and mass spectrometry analysis were performed to screen circANKS1A-interacting proteins. RESULTS: By evaluating the co-expression network of differentially expressed circRNAs, we identify an N6-methyladenosine (m6A) modified circRNA, circANKS1A, upregulated in serum samples and tumor tissues from BCa patients with muscle invasive bladder Cancer (MIBC). What's more, circANKS1A upregulation is correlated with higher TNM stage and larger tumor size in BCa patients, and predicts poorer patient survival. Elevated circANKS1A promotes cell proliferation both in vitro and in vivo. The upregulated expression of circANKS1A facilitates cancer cells migration in vitro and promotes lung metastasis and liver metastasis in PDX metastasis models in vivo. Of note, N6-methyladenosine modification of circANKS1A accelerates export to the cytoplasm. By forming a circANKS1A/FOXM1/RACGAP1 RNA-protein ternary complex in the cytoplasm, circANKS1A enhances the stability of RACGAP1 mRNA to promote BCa cell proliferation and metastasis progression. Clinically, the upregulated expressions of circANKS1A and RACGAP1 are more prevalent in MIBC tissues than in non-muscle invasive bladder Cancer (NMIBC) tissues. CONCLUSIONS: N6-methyladenosine modification of circANKS1A modulates cytoplasmic export, stabilizes RACGAP1 to promote BCa cell proliferation and metastasis, and indicate that circANKS1A could serve as a significant prognostic marker and therapeutic target for BCa. Source of Funding: National Foundation Committee of Natural Sciences of China (grant numbers 81570631 and 81770704) © 2020 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 203Issue Supplement 4April 2020Page: e229-e230 Advertisement Copyright & Permissions© 2020 by American Urological Association Education and Research, Inc.MetricsAuthor Information Qiangqiang Ge* More articles by this author Yang Xun More articles by this author Junlin Lu More articles by this author Shaogang Wang More articles by this author Expand All Advertisement PDF downloadLoading ...

Long Non-Coding RNA NANCI/NKX2-1 Duplex Impacts Prognosis in Stage I Non-Small-Cell Lung Cancer

BackgroundNANCI, an intergenic long non-coding RNA (lncRNA) is essential for buffering NKX2-1 expression during embryonic development and in adult tissue. We analyzed NANCI and NKX2-1 in human lung embryonic samples and adult lung tissues and evaluated their potential as prognostic markers in stage I non-small cell lung cancer (NSCLC). Methods and resultsNANCI and NKX2-1 expression was assessed by TaqMan assays in 18 human embryonic samples from 8 to 13 weeks, 59 non-tumoral (NT) lung tissue samples, and 98 stage I NSCLC tumor samples. NANCI and NKX2-1 expression in embryonic and NSCLC samples were downregulated in comparison to adult NT tissue. Patients with low expression of NANCI had shorter disease-free survival (DFS) and overall survival (OS) than those with high levels (47.6 vs 69.3 months, P=0.032 and 57.7 vs 77.6 months, P=0.021, respectively). When the expression levels of NANCI and NKX2-1 were evaluated in combination, four groups were identified (high NANCI/high NKX2-1, low NANCI/high NKX2-1, high NANCI/low NKX2-1 and low NANCI/low NKX2-1) with differential impact on DFS (P=0.042) and OS (P=0.024). Interestingly, the high NANCI/high NKX2-1 duplex group had longer DFS and OS than the other three groups (71.25 vs 46.3 months, P=0.009 and 81.3 vs 56.1 months, P=0.004, respectively). In the multivariate analysis, the high NANCI/high NKX2-1 duplex was identified as an independent prognostic factor for longer DFS (HR 0.346, 95% CI, 0.169–0.709; P=0.004) and OS (HR 0.309, 95% CI, 0.121–0.786; P=0.014). ConclusionsNANCI and the NANCI-NKX2-1 duplex impacts prognosis in stage I NSCLC patients.

MiR-150 is a negative independent prognostic biomarker for primary gastrointestinal diffuse large B-cell lymphoma.

A number of studies suggest an association between miRNAs and diffuse large B-cell lymphoma (DLBCL). The present study aimed to investigate the prognostic value of microRNA (miR-150) in primary gastrointestinal (PGI)-DLBCL, by assessing the association between miR-150 expression and clinicopathological characteristics in patients with PGI-DLBCL. A total of 84 patients diagnosed with PGI-DLBCL were recruited and both tumor and adjacent non-tumor tissue samples were collected. miR-150 expression was assessed via reverse transcription-quantitative (RT-q)PCR analysis. The results demonstrated that miR-150 expression was significantly lower in PGI-DLBCL tissues compared with adjacent non-tumor tissues. Furthermore, receiver operating characteristic (ROC) curve analysis indicated that the optimal cut-off value of miR-150 for predicting survival was 8.965 with high sensitivity (79.8%) and specificity (77.1%). Patients were divided into two groups according to this cut-off value, as follows: High (n=18) and low expression (n=66) groups. Low miR-150 expression was significantly associated with clinical stage, International Prognostic Index (IPI), Eastern Cooperative Oncology Group status and use of rituximab. RT-qPCR analysis demonstrated that miR-150 expression was significantly lower in patients with high IPI scores compared with patients with low IPI scores. Downregulated miR-150 expression was significantly associated with shorter overall survival (OS) time and progression-free survival (PFS) time in patients with PGI-DLBCL. Furthermore, miR-150 level and IPI score were identified as two risk factors for OS and PFS. The diagnostic value of miR-150 was evaluated via ROC curve analysis, with an area under the curve value of 0.882. Taken together, the results of the present study suggest that miR-150 is a potential diagnostic marker of PGI-DLBCL, and may also serve as a useful prognostic factor for survival outcomes in patients with PGI-DLBCL.

Connective tissue growth factor as an unfavorable prognostic marker promotes the proliferation, migration, and invasion of gliomas.

BackgroundIn consideration of the difficulty in diagnosing high heterogeneous glioma, valuable prognostic markers are urgent to be investigated. This study aimed to verify that connective tissue growth factor (CTGF) is associated with the clinical prognosis of glioma, also to analyze the effect of CTGF on the biological function.MethodsIn this study, glioma and non-tumor tissue samples were obtained in 2012 to 2014 from the Department of Neurosurgery of Nanfang Hospital of Southern Medical University, Guangzhou, China. Based on messenger RNA (mRNA) data from the Cancer Genome Atlas (TCGA) and CCGA dataset, combined with related clinical information, we detected the expression of CTGF mRNA in glioma and assessed its effect on the prognosis of glioma patients. High expression of CTGF mRNA and protein in glioma were verified by reverse transcription-polymerase chain reaction, immunohistochemistry, and Western blotting. The role of CTGF in the proliferation, migration, and invasion of gliomas were respectively identified by methylthiazoletetrazolium assay, Transwell and Boyden assay in vitro. The effect on glioma cell circle was assessed by flow cytometry. For higher expression of CTGF in glioblastoma (GBM), the biological function of CTGF in GBM was investigated by gene ontology (GO) analysis.ResultsIn depth analysis of TCGA data revealed that CTGF mRNA was highly expressed in glioma (GBM, n = 163; lowly proliferative glioma [LGG], n = 518; non-tumor brain tissue, n = 207; LGG, t = 2.410, GBM, t = 2.364, P < 0.05). CTGF mRNA and protein expression in glioma (86%) was significantly higher than that in non-tumor tissues (18%) verified by collected samples. Glioma patients with higher expression of CTGF showed an obviously poorer overall survival (35.4 and 27.0 months compared to 63.3 and 55.1 months in TCGA and Chinese Glioma Genome Atlas (CGGA) databases separately, CGGA: χ2 = 7.596, P = 0.0059; TCGA: χ2 = 10.46, P = 0.0012). Inhibiting CTGF expression could significantly suppress the proliferation, migration, and invasion of gliomas. CTGF higher expression had been observed in GBM, and GO analysis demonstrated that the function of CTGF in GBM was mainly associated with metabolism and energy pathways (P < 0.001).ConclusionsCTGF is highly expressed in glioma, especially GBM, as an unfavorable and independent prognostic marker for glioma patients and facilitates the progress of glioma.

LncRNA DCST1-AS1 Was Upregulated in Endometrial Carcinoma and May Sponge miR-92a-3p to Upregulate Notch1.

IntroductionThe functions of DCST1-AS1 have been investigated in liver cancer, while its role in endometrial carcinoma (EC) remains hardly known. This study aimed to analyze the role of DCST1-AS1 in EC.MethodsPaired EC and non-tumor tissue samples were obtained from 62 EC patients. These patients were followed up for 5 years since their admission to record their survival conditions. HEC-1 cells were transfected with DCST1-AS1, Notch1 vectors, miRNA negative control or miR-92a-3p mimic. Luciferase activity was measured. QPCR and Western blot were applied to determine the RNA level and protein expression, respectively. The invasion and migration of HEC-1 cells were analyzed by Transwell assay.ResultsWe in this study found that DCST1-AS1 was upregulated in EC. Survival analysis revealed that high levels of DCST1-AS1 expression predicted poor survival of EC patients. Bioinformatics analysis revealed that miR-92a-3p may bind DCST1-AS1 and the interaction between them was further confirmed by dual-luciferase activity assay. However, overexpression of miR-92a-3p and DCST1-AS1 failed to affect the expression of each other. Moreover, DCST1-AS1 overexpression led to upregulated Notch1 and increased cancer cell invasion and migration rates. Overexpression of miR-92a-3p played an opposite role and attenuated the effects of DCST1-AS1 overexpression.DiscussionDCST1-AS1 is downregulated in EC and may sponge miR-92a-3p, thereby promoting cancer cell invasion and migration.

LncRNA HCP5 Stimulates the Proliferation of Non-Small Cell Lung Cancer Cells by Up-Regulating Survivin Through the Down-Regulation of miR-320.

IntroductionWe explored the roles of lncRNA HCP5 in non-small cell lung cancer (NSCLC).MethodsLevels of HCP5 were measured by performing qPCR and data were compared between non-tumor and NSCLC tissue samples by performing a paired t-test. Expression levels of miR-320 and survivin mRNA in NSCLC tissues were also measured by performing qPCR. The effects of HCP5, miR-320 and survivin overexpression on the proliferation of H23 cells were analyzed by cell proliferation assay.ResultsWe found that HCP5 was up-regulated in NSCLC and predicted the poor survival of NSCLC patients. HCP5 was negatively correlated with miR-320 but positively correlated with survivin in NSCLC tissues. In NSCLC cells, HCP5 overexpression led to the up-regulated survivin and down-regulated miR-320. Moreover, miR-320 overexpression failed to affect HCP5 but down-regulated survivin. Cell proliferation assay showed that HCP5 and survivin overexpression led to increased, while miR-320 overexpression led to decreased cell proliferation rate. In addition, miR-320 overexpression reduced the effects of HCP5 overexpression.ConclusionTherefore, HCP5 may stimulate the proliferation of NSCLC cells by up-regulating survivin through the down-regulation of miR-320.

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/).

The clinicopathological and prognostic value of CD44 expression in bladder cancer: a study based on meta-analysis and TCGA data

ABSTRACT CD44 is reported to be involved in tumor invasion and metastasis. However, the role of cancer stem cell marker CD44 in bladder cancer still remains controversial. Hence, the correlations between CD44 expression and the clinicopathological features and the prognosis of bladder cancer were investigated. Publications using immunohistochemical methods were identified. The Cancer Genome Atlas (TCGA) data were also analyzed. The odds ratios (ORs) or hazard ratios (HRs) with their 95% confidence intervals (95% CIs) were calculated. 14 studies involving 1107 tissue samples were included. CD44 expression in bladder cancer was lower than in non-tumor tissue samples (OR = 0.14, P = 0.005), which was consistent with TCGA data. CD44 expression was correlated with advanced T stage (OR = 1.76, P = 0.029) and lymph node metastasis (OR = 4.09, P < 0.001). Multivariate survival analysis showed that CD44 expression was not linked to tumor-specific survival, overall survival, and recurrence/relapse-free survival, but was associated with disease failure (HR = 2.912, 95% CI = 1.51–5.61). No relationships of CD44 expression with the clinicopathological features and overall survival were found from TCGA data. Our finding suggested that CD44 expression may be correlated with progression, metastasis, and disease failure of bladder cancer. However, further large-scale studies are needed. Abbreviations: CD44: Cluster of Differentiation 44; CIs: Confidence Intervals; CSCs: Cancer Stem Cells; EMT: Epithelial-mesenchymal Transition; HRs: Hazard Ratios; ORs: Odds Ratios; TCGA: The Cancer Genome Atlas

LC3B in Malignant Cells Correlates With Immune Infiltrate in Hypopharyngeal Squamous Cell Carcinoma.

The objective of this study was to investigate the between autophagy activity and local immune response in hypopharyngeal squamous cell carcinoma (HSCC). Herein, we observed the expression of autophagy marker microtubule-associated protein light chain 3B (MAP1LC3B), CD8 cytotoxic T lymphocytes (CTLs), CD39 (regulatory T cells Tregs) and CD163 (tumor-associated macrophages TAMs) in HSCC, and determined the prognostic roles of CD8+/CD39+ and CD8+/CD163+ in patients with HSCC. The expression of light chain 3B (LC3B) and CD8+/CD39+ was found to be significantly lower in HSCC tissues than in adjacent non-tumor mucosa tissue samples; LC3B expression was positively correlated with the infiltration rate of CD8+/CD39+ in HSCC. Further studies revealed that the ratio of CD8+/CD39+ immune cells was negatively correlated with tumor lymph node metastasis and TNM classification, while the ratio of CD8+/CD163+ immune cells was negatively correlated with TNM classification. Moreover, the expression of LC3B was analyzed and the patients were grouped according to their immune infiltration characteristics. The 5-year cumulative survival rates of LC3B+, CD8+/CD39+, and CD8+/CD163+ patients were significantly higher than those of other group patients. Collectively, our studies indicated that the expression of LC3B in HSCC was correlated with the infiltration ratio of immune cells, and a change in autophagy activity may affect the cellular immunity in HSCC. The ratios of tCD8+/CD39+ and tCD8+/CD163+ may serve as prognostic factors for HSCC.

Postoperative standard chemoradiotherapy benefits primary glioblastoma patients of all ages.

BackgroundGlioblastoma is the most malignant tumor of the central nervous system. Several prediction models have been produced to aid in prognosis assessment. Age, a primary decision factor for prognosis, is associated with increased genomic alterations, however the exact link between increased age and poor prognosis is unknown.ObjectiveIn this study, we aimed to reveal the underlying cause of poor prognosis in elderly patients.MethodsThis study included data on 616 primary GBM tumor samples from the CGGA and TCGA databases and 41 nontumor brain tissue samples obtained from http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE53890. Hallmarks and clinicopathological characteristics were evaluated in both tumor and nontumor brain tissues. The association between choice of treatment regimen and age was measured using ANOVA and Student's t test.ResultsAge was a robust predictor of poor prognosis in glioma. No age‐related hallmarks of cancer were detected, including pathological characteristics or mutations. However, treatment choice was strongly significantly different between old and young patients. Combined chemo‐radiation therapy could benefit old and young GBM patients, however, old patients are currently less likely to choose it.ConclusionThe vast divergence in prognosis between young and old GBM patients is largely caused by choice of treatment rather than age‐related tumor genomic characteristics. Postoperative standard radio‐ and chemotherapy provide strong benefits to primary glioblastoma patients of all ages.

Identification of a new methylation site in the Sept9 promoter region for the diagnosis of hepatocellular carcinoma

Background. Over 600,000 people die from hepatocellular carcinoma (HCC) each year worldwide. The disease is often detected at advanced stages and in many cases is not curable. Early diagnostic and monitoring of HCC recurrences remains a substantial problem in clinical oncology. That determines the need for a search for highly sensitive and specific biomarkers for the non-invasive of HCC diagnostics. The objective of the study. Identification of the hypermethylated locus in the promoter region of the septin 9 (Sept9) gene based on the annotated methylomes from the public databases. Experimental validation of methylation on a pilot panel of paired clinical samples of patients with HCC, as well as tissue samples from patients with benign liver tumors and lymphocytes from healthy donors. Materials and methods. To analyze the methyl data, samples of HCC from TCGA, hepatocellular adenoma from GEO (Gene Expression Omnibus) depository, peripheral blood cells and tissues of healthy donors from Methbank were used. Experimental validation of methylation levels of the identified site was carried out on a pilot panel of clinical samples by bisulphite pyrosequencing using PyroMark Q24.Results. Based on the analysis of methylome data, we selected cg20275528 site, which is characterized by high level of methylation in HCC tissues and minimal levels of methylation in non-tumor liver tissue, hepatocellular adenoma and peripheral blood of healthy donors. Experimental testing on a pilot panel of clinical specimens showed that the level of marker site methylation in HCC (42 % median) is significantly higher than in non-tumor liver tissues (3 % median) and benign neoplasms (1.5 % median) and exceeds the threshold value in HCC compared to paired samples of adjacent non-tumor liver tissue in 20 out of 30 studied cases (66.6 %). The general possibility for cg20275528 methylation detection in circulating DNA of plasma in HCC patients was shown.Conclusion. The obtained results indicate that the approach to the detection and experimental verification of diagnostically significant markers developed and tested in this study can be used to identify new differentially methylated sites and to establish new approaches for non-invasive HCC diagnosis.

Decreased DC-SIGNR expression in hepatocellular carcinoma predicts poor patient prognosis.

Dendritic cell-specific intercellular adhesion molecule-grabbing non-integrin-related protein (DC-SIGNR) is a transmembrane receptor primarily involved in pathogen recognition by the innate immune system, with particular importance for viral recognition. DC-SIGNR may also be associated with tumorigenesis. The aim of the present study was to investigate the association between DC-SIGNR expression, development of hepatocellular carcinoma (HCC), and clinicopathological features. Immunohistochemistry was used to assess DC-SIGNR protein expression in HCC and paired non-cancerous tissue samples. DC-SIGNR expression was lower in HCC tissues compared with adjacent non-tumor tissue samples. The expression of DC-SIGNR was associated with small tumor size, low Edmondson grade and high patient long term survival rates. Bioinformatics analyses were performed on several datasets to assess the potential function of DC-SIGNR and related genes; the data revealed that DC-SIGNR mRNA expression was lower in HCC tissues compared with non-cancerous controls, and analyses of ten-year survival rates indicated patients with low DC-SIGNR expression exhibited shorter average survival times. In conclusion, decreased DC-SIGNR expression in HCC tissues may be a relevant predictive biomarker of clinical prognosis, in addition to being a viable therapeutic target for HCC treatment.