Candidate Prognostic Biomarker Research Articles

Competitive endogenous RNA network identifies four long non-coding RNA signature as a candidate prognostic biomarker for lung adenocarcinoma.

BackgroundLung adenocarcinoma (LUAD) is the most commonly histological subtype of lung cancer (LC) and the prognoses of the majority of LUAD patients are still very poor. The present study aimed at integrating long non-coding RNA (lncRNA), microRNA (miRNA) and messenger RNA (mRNA) expression data to construct lncRNA-miRNA-mRNA competitive endogenous RNA (ceRNA) network and identify importantly potential lncRNA signature in ceRNA network as a candidate prognostic biomarker for LUAD patients.MethodslncRNA, miRNA and mRNA expression data as well as clinical characteristics of LUAD patients were retrieved from The Cancer Genome Atlas (TCGA) database. Differentially expressed lncRNAs (DElncRNAs), differentially expressed mRNAs (DEmRNAs) and differentially expressed miRNA (DEmiRNA) between LUAD and normal lung tissues samples were analyzed. A lncRNA-miRNA-mRNA ceRNA network was constructed and the biological functions of DEmRNAs in ceRNA network were analyzed using gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. Univariate and multivariate Cox regression analyses of DElncRNAs in ceRNA network were implemented to predict the overall survival (OS) in LUAD patients. The receiver operating characteristic (ROC) analysis was used to evaluate the performance of multivariate Cox regression model.ResultsA total of 1,664 DElncRNAs, 120 DEmiRNAs and 2,503 DEmRNAs was identified between LUAD and normal lung tissues samples. A lncRNA-miRNA-mRNA ceRNA network including 140 DElncRNAs, 33 DEmiRNAs and 57 DEmRNAs was established. Kaplan-Meier (KM) [Log-rank (LR) test] and univariate regression analysis of those 140 DElncRNAs revealed that 7 DElncRNAs (LINC00518, UCA1, NAV2-AS2, MED4-AS1, SYNPR-AS1, AC011483.1, AP002478.1) were simultaneously identified to be associated with OS of LUAD patients. A multivariate Cox regression analysis of those 7 DElncRNAs showed that a group of 4 DElncRNAs including AP002478.1 (Cox P=4.66E-03), LINC00518 (Cox P=2.34E-04), MED4-AS1 (Cox P=6.42E-03) and NAV2-AS2 (Cox P=6.66E-02) had significantly prognostic value in OS of LUAD patients. The cumulative risk score indicated that the 4-lncRNA signature was significantly associated with OS of LUAD patients (P=0). The area under the curve (AUC) of the 4-lncRNA signature related with 3-year survival was 0.669.ConclusionsThe present study provides novel insights into the lncRNA-related regulatory mechanisms in LUAD, and identifying 4-lncRNA signature may serve as a candidate prognostic biomarker in predicting the OS of LUAD patients.

Competitive endogenous RNA network identifies four long non-coding RNA signature as a candidate prognostic biomarker for lung adenocarcinoma

Background: Lung adenocarcinoma (LUAD) is the most commonly histological subtype of lung cancer (LC) and the prognoses of the majority of LUAD patients are still very poor. The present study aimed at integrating long non-coding RNA (lncRNA), microRNA (miRNA) and messenger RNA (mRNA) expression data to construct lncRNA-miRNA-mRNA competitive endogenous RNA (ceRNA) network and identify importantly potential lncRNA signature in ceRNA network as a candidate prognostic biomarker for LUAD patients. Methods: lncRNA, miRNA and mRNA expression data as well as clinical characteristics of LUAD patients were retrieved from The Cancer Genome Atlas (TCGA) database. Differentially expressed lncRNAs (DElncRNAs), differentially expressed mRNAs (DEmRNAs) and differentially expressed miRNA (DEmiRNA) between LUAD and normal lung tissues samples were analyzed. A lncRNA-miRNA-mRNA ceRNA network was constructed and the biological functions of DEmRNAs in ceRNA network were analyzed using gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. Univariate and multivariate Cox regression analyses of DElncRNAs in ceRNA network were implemented to predict the overall survival (OS) in LUAD patients. The receiver operating characteristic (ROC) analysis was used to evaluate the performance of multivariate Cox regression model. Results: A total of 1,664 DElncRNAs, 120 DEmiRNAs and 2,503 DEmRNAs was identified between LUAD and normal lung tissues samples. A lncRNA-miRNA-mRNA ceRNA network including 140 DElncRNAs, 33 DEmiRNAs and 57 DEmRNAs was established. Kaplan-Meier (KM) [Log-rank (LR) test] and univariate regression analysis of those 140 DElncRNAs revealed that 7 DElncRNAs (LINC00518, UCA1, NAV2-AS2, MED4-AS1, SYNPR-AS1, AC011483.1, AP002478.1) were simultaneously identified to be associated with OS of LUAD patients. A multivariate Cox regression analysis of those 7 DElncRNAs showed that a group of 4 DElncRNAs including AP002478.1 (Cox P=4.66E-03), LINC00518 (Cox P=2.34E-04), MED4-AS1 (Cox P=6.42E-03) and NAV2-AS2 (Cox P=6.66E-02) had significantly prognostic value in OS of LUAD patients. The cumulative risk score indicated that the 4-lncRNA signature was significantly associated with OS of LUAD patients (P=0). The area under the curve (AUC) of the 4-lncRNA signature related with 3-year survival was 0.669. Conclusions: The present study provides novel insights into the lncRNA-related regulatory mechanisms in LUAD, and identifying 4-lncRNA signature may serve as a candidate prognostic biomarker in predicting the OS of LUAD patients.

Gold nano-particles (AuNPs) carrying miR-326 targets PDK1/AKT/c-myc axis in hepatocellular carcinoma

Abnormal expression of microRNAs (miRNAs) contributes to tumour growth and invasion. MiR-326 expression often down-regulates in several kinds of cancer and low expression of miR-326 is linked with poor prognosis in cancer patients. In the present study, we aimed to explore the modulatory mechanism of miR-326 in hepatocellular carcinoma (HCC). miR-326 expression was significantly decreased in HCC cell lines and tissues. miR-326 decreased HCC cell growth by affecting cell-cycle progression and by promoting apoptosis. In addition, miR-326 inhibited HCC cell invasion by decreasing the EMT phenotype. We found that miR-326 functioned as a tumour suppressor by repressing its down-stream target PDK1. C-myc contributed to miR-326 down-regulation through binding at its promoter and inhibited its expression. Based on these results, we conducted a therapeutic experiment by using gold nano-particles (AuNPs) carrying miR-326. Restoration of miR-326 reduced tumour growth in vivo. Our findings suggest that miR-326 may be a candidate prognostic biomarker and a target for new therapies in HCC patients.

Identification of differentially expressed genes and functional annotations associated with metastases of the uveal melanoma

Uveal melanoma (UVM) is an adult intraocular malignancy which is the most frequent and has a high tendency for metastasis. This study aims to develop significant differential gene subnetwork between primary and metastatic UVM to identify potential prognostic biomarkers. Differentially expressed genes (DEGs) among three chip datasets were downloaded from Gene Expression Omnibus and identified according to standardization annotation information. Genetic enrichment analyses were utilized to describe biologic functions. The protein-protein interaction network of DEGs was developed and the module analysis was constructed by STRING and Cytoscape. Kaplan-Meier method of the integrated expression score was applied to analyze survival outcomes. Functional annotation was assessed to perform GO and Kyoto Encyclopedia of Genes and Genomes enrichment analysis. In addition, ClueGO and gene set enrichment analysis were analyzed to detect underlying significant genes and involved signaling pathways. A total of 103 DEGs with function enrichment were recognized and might be considered as candidate prognostic biomarkers between primary and metastatic UVM. Furthermore, Kaplan-Meier method suggested that SCD5, SPTBN1, FABP5, SQLE, PTPLA (HACD1), and CDC25B were independent prognostic factors in UVM. Functional annotations indicated that the most involved significant pathways including interferon-gamma response, IL-6 JAK STAT3 signaling, TNFA signaling via NFKB and inflammatory response. Significant DEGs between primary and metastatic UVM tissue were identified and might have involved in the metastasis of UVM. SCD5, SPTBN1, FABP5, SQLE, PTPLA (HACD1), and CDC25B transcription levels were of high prognostic value, which might assist us to understand the underlying carcinogenesis or advancement of UVM better.

LncRNA H19 binds VGF and promotes pNEN progression via PI3K/AKT/CREB signaling.

Pancreatic neuroendocrine neoplasms (pNENs) are endocrine tumors arising in pancreas and is the most common neuroendocrine tumors. Mounting evidence indicates lncRNA H19 could be a determinant of tumor progression. However, the expression and mechanism of H19 and the relevant genes mediated by H19 in pNENs remain undefined. Microarray analysis was conducted to identify the differentially expressed lncRNAs in pNENs. H19 expression was analyzed in 39 paired pNEN tissues by qPCR. The biological role of H19 was determined by functional experiments. RNA pulldown, mass spectroscopy and RNA immunoprecipitation were performed to confirm the interaction between H19 and VGF. RNA-seq assays were performed after knockdown H19 or VGF. H19 was significantly upregulated in pNEN tissues with malignant behaviors, and the upregulation predicted poor prognosis in pNENs. In vitro and in vivo data showed that H19 overexpression promoted tumor growth and metastasis, whereas H19 knockdown led to the opposite phenotypes. H19 interacted with VGF, which was significantly upregulated in pNENs, and higher VGF expression was markedly related to poor differentiation and advanced stage. Furthermore, VGF was downregulated when H19 was knocked down, and VGF promoted cell proliferation, migration and invasion. Mechanistic investigations revealed that H19 activated PI3K/AKT/CREB signaling and promoted pNEN progression by interacting with VGF. These findings indicate that H19 is a promising prognostic factor in pNENs with malignant behaviors and functions as an oncogene via the VGF-mediated PI3K/AKT/CREB pathway. In addition, our study implies that VGF may also serve as a candidate prognostic biomarker and therapeutic target in pNENs.

Identification of long non‑coding RNA‑mediated transcriptional dysregulation triplets reveals global patterns and prognostic biomarkers for ER+/PR+, HER2‑ and triple negative breast cancer.

Breast cancer (BRCA) is the most common type of cancer in adult females. Estrogen receptor (ER)+/progesterone receptor (PR)+, human epidermal-growth factor receptor 2 (HER2)− BRCA and triple-negative breast cancer (TNBC) are two important subtypes of this disease. Long non-coding RNA (lncRNA)-mediated transcriptional dysregulation triplets (lncTDTs) may contribute to the development of cancer; however, the precise functional roles of lncTDTs in ER+/PR+, HER2− BRCA and TNBC require further investigation. In the present study, an integrated and computational approach was conducted to identify lncTDTs based on transcription factor (TF), gene, lncRNA expression profiles and experimentally verified TF-gene interactions. The regulatory patterns of these lncTDTs are complex and differed in ER+/PR+, HER2− BRCA and TNBC. Of note, five common lncTDTs were reported for these BRCA subtypes. Functional analysis revealed lncTDTs to be enriched in the PI3K/AKT signaling pathway within the two BRCA subtypes. Additionally, certain lncTDTs were associated with survival and may be considered candidate prognostic biomarkers for BRCA subtypes. Collectively, the results of the present study provide novel insight into the functions and mechanisms of lncRNAs in ER+/PR+, HER2− BRCA and TNBC, and may aid the development of targeted treatments against certain subtypes of BRCA.

Long non-coding RNA LINC00526 represses glioma progression via forming a double negative feedback loop with AXL.

Glioma is the most common primary intracranial carcinoma with extremely poor prognosis. The significances of long non‐coding RNA (lncRNA) involved in glioma have been started revealed. However, the expression, roles and molecular mechanisms of most lncRNAs in glioma are still unknown. In this study, we identified a novel lncRNA LINC00526, which is significantly low expressed in glioma. Low expression of LINC00526 is correlated with aggravation and poor survival in glioma. Functional assays revealed that ectopic expression of LINC00526 inhibits glioma cell proliferation, migration, and invasion. LINC00526 silencing promotes glioma cell proliferation, migration and invasion. Mechanistically, we found that LINC00526 directly interacts with EZH2, represses the binding of EZH2 to AXL promoter, attenuates the transcriptional activating roles of EZH2 on AXL, and therefore represses AXL expression. Via repressing AXL, LINC00526 further represses PI3K/Akt/NF‐κB signalling. Intriguingly, we identified that NFKB1 and NFKB2 directly binds LINC00526 promoter and represses LINC00526 transcription. We further found that via activating NF‐κB signalling, AXL represses LINC00526 transcription. Therefore, LINC00526/EZH2/AXL/PI3K/Akt/NF‐κB form a feedback loop in glioma. Analysis of the TCGA data revealed that the expression of LINC00526 is inversely correlated with that of AXL in glioma tissues. In addition, functional rescue assays revealed that the tumour suppressive roles of LINC00526 are dependent on the negative regulation of AXL. Collectively, our data identified LINC00526 as a tumour suppressor in glioma via forming a double negative feedback loop with AXL. Our data also suggested LINC00526 as a potential prognostic biomarker and therapeutic candidate for glioma.

RNF128 Promotes Invasion and Metastasis Via the EGFR/MAPK/MMP-2 Pathway in Esophageal Squamous Cell Carcinoma

Background: The prognosis of esophageal squamous cell carcinoma (ESCC) is generally poor, and the identification of molecular markers related to the regulation of ESCC invasion and migration is important. Methods and Results: In this study, we report that ring finger protein-128 (RNF128) enhances the invasiveness and motility of ESCC cells by using transwell assays and Western blotting. A xenograft nude mouse model showed that RNF128 promotes the metastasis of ESCC cells in the lung. A signal pathway analysis identified the epidermal growth factor receptor (EGFR)/mitogen-activated protein kinase (MAPK)/matrix matalloproteinases 2 (MMP-2) cascade as a mediator of RNF128-induced enhancement of ESCC progression. Inhibition experiments using inhibitors of EGFR, ERK kinase (MEK)/extracellular-signal-regulated-kinase (ERK), and MMP-2 reversed this progression. Co-immunoprecipitation demonstrated that RNF128 promotes the activation of the EGFR/ERK/MMP-2 pathway by interacting with p53 and p53 interacting with EGFR. Conclusion: Our results establish the functional role of RNF128 in driving the invasion and metastasis of ESCC through the EGFR/MAPK/MMP-2 pathway, implicating its potential as a candidate therapeutic target and prognostic biomarker for ESCC.

Up-regulation of long non-coding RNA-PCAT-1 promotes invasion and metastasis in esophageal squamous cell carcinoma.

Long non-coding RNA prostate cancer associated transcript-1 ncRNA (lncRNA-PCAT-1) plays an important role in the progression of prostate cancer. The present investigation was aimed to evaluate the potential roles of the lncRNA-PCAT-1 gene expression changes in esophageal squamous cell carcinoma (ESCC) between Iranian population. In the case-control investigation, we have analyzed a total of 150 fresh tissue samples, compromising of 75 cancerous tissues and 75 adjacent normal tissues from patients with ESCC. We used quantitative Real-time polymerase chain reaction (qRT-PCR) to evaluate the lncRNA-PCAT-1 gene expression levels in ESCC patients and correlation between the lncRNA-PCAT-1 expression changes and clinical characteristics. Our findings showed that the lncRNA-PCAT-1 gene was up-regulated in cancerous tissues compared with the adjacent non-cancerous tissues (p=0.0016). In addition, the results revealed a significant correlation between up-regulating of lncRNA-PCAT-1 and hot liquid drinking (p =0.017). These findings offer the potential roles of lncRNA-PCAT-1 in the pathogenesis of ESCC and may consider as a candidate prognostic biomarker for ESCC in an Iranian population.

Linc00423 as a tumor suppressor in retroperitoneal liposarcoma via activing MAPK signaling pathway through destabilizing of NFATC3

Unraveling the noncoding RNA expression networks governing cancer initiation and development is essential while remains largely uncompleted in retroperitoneal liposarcoma (RLS). Through RNA-seq technologies and computational biology, deregulated long noncoding RNAs (lncRNAs) are being identified and reveal that lncRNAs are implicated in serial steps of RLS development. High-throughput sequencing with computational methods for assembling the transcriptome of five paired RLS patient’s tissues. We found that long intergenic noncoding RNA 423 (linc00423) was downregulated in RLS tissues. Gain-of-function assays revealed that overexpressed linc00423 obviously inhibited RLS cell growth in vitro and in vivo. Additionally, RNA sequence, RNA-pulldown and RIP assays evidenced that linc00423 involved in MAPK signaling pathway via destabilizing of nuclear factor of activated T-cells 3 (NFATC3). Summing up, our findings demonstrated that linc00423 acted as the tumor suppressor in RLS cells through regulating the protein level of NFATC3 at a post-transcriptional level and negatively regulated the MAPK signaling pathway at a transcriptional level. Linc00423 might serve as a candidate prognostic biomarker and a target for novel therapies of RLS patients.

An 11-lncRNA expression could be potential prognostic biomarkers in head and neck squamous cell carcinoma.

The aim of our study is to construct the competing endogenous RNA (ceRNA) network of head and neck squamous cell carcinoma (HNSCC) and identify key long noncoding RNAs (lncRNAs) to predict prognosis. The genes whose expression were differentially in HNSCC and normal tissues were explored by the Cancer Genome Atlas database. The ceRNA network was constructed by the Cytoscape software. The lncRNAs which could estimate the overall survival were explored from Cox proportional hazards regression. There are 1997, 589, and 82 mRNAs, lncRNAs, and miRNAs whose expression were statistically significant different, respectively. Then, the network between miRNA and mRNA or miRNA and lncRNA was constructed by miRcode, miRDB, TargetScan, and miRanda. Five mRNAs, 10 lncRNAs, and 3 miRNAs were associated with overall survival. Then, 11-lncRNAs were found to be prognostic factors. Therefore, our research analyzed the potential signature of novel 11-lncRNA as candidate prognostic biomarker from the ceRNA network for patients with HNSCC.

World Workshop on Oral Medicine VII: Prognostic biomarkers in oral leukoplakia: A systematic review of longitudinal studies

To identify the prognostic biomarker candidates for stratification and long-term surveillance of oral leukoplakia progressing to cancer via a systematic literature review. Systematic searches with no date restrictions were conducted on March 29, 2018, targeting the databases PubMed (Ovid), EMBASE (Ovid), EBM (Ovid), and Web of Science (ISI). Bias was assessed using the Quality in Prognosis Studies tool. Biomarkers were stratified based on hallmarks of cancer. Inclusion criteria were met by 25 of 3,415 studies. A range of biomarkers were evaluated experimentally for risk stratification, prognosis, and surveillance of oral leukoplakia in tissue, blood, and saliva. However, the studies were highly heterogeneous and require further validation. Biomarkers reported in these studies included inflammatory or oxidative markers, growth factors, ion channels, genetic and cellular regulatory factors, and epigenetic biomarkers. Studies tended to include small sample sizes, under-reported or variably reported histopathological data, did not address potential confounding, reported limited/variable follow-up data, or lacked a control group. Inclusion of subsets from chemoprevention trials may have introduced bias regarding reported malignant transformation rates and accuracy of prognostic biomarkers. This review identified insufficient longitudinal evidence to support validated prognostic biomarkers for oral leukoplakia. Further studies are needed to identify molecular targets with the potential to mitigate risk of malignant transformation.

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 have a poor prognosis. It is essential to search for promising diagnostic and prognostic biomarkers for OSCC. Methods: The differentially expressed genes (DEGs) were obtained using R language. Receiver operating characteristic curve analysis was performed to identify diagnostic markers for OSCC. 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. Weighted gene co-expression network analysis and function enrichment analysis demonstrated that genes positively associated with AUNIP were enriched in cell cycle and the module eigengene was significantly correlated with the survival rate of OSCC patients. In gene set enrichment analysis, the correlation between AUNIP expression and human papillomavirus status in OSCC was verified. 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 interrelated with the 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 prevent and treat OSCC. Funding Statement: Taishan Scholars Project in Shandong Province (ts201511106) and the National Natural Science Foundation of China (Nos. 61603218). Declaration of Interests: The authors declare no conflicts of interest. Ethics Approval Statement: The samples were approved by Taizhou hospital Ethics Committee in Zhejiang province.

Identification of candidate diagnostic and prognostic biomarkers for human prostate cancer: RPL22L1 and RPS21.

Prostate cancer (PCa) is one of the most common malignancies in men worldwide. This study was designed to investigate the potential of Ribosomal Protein L22-like1 (RPL22L1) and Ribosomal Protein S21 (RPS21) as diagnostic and prognostic biomarkers for PCa. First, RPL22L1 and RPS21 were screened as the key molecular of PCa by bioinformatics analysis. Subsequently, the prostate tissue samples were stained for antibodies against RPL22L1 and RPS21. The unbiased signal quantification was performed by ImageJ software, and the results showed that the expression of RPL22L1 and RPS21 exhibited significant differences between the PCa tissues and the normal prostate tissues. Receiver-operating characteristics (ROC) curves were prepared, and then the area under the curve (AUC) values of RPL22L1 and RPS21 were calculated as 0.798 and 0.768, and the likelihood ratio (LR) values of RPL22L1 and RPS21 were calculated as 2.86 and 2.53. These data implied that the over-expression of RPL22L1 and RPS21 is associated with the presence of PCa. The further analysis suggested that the expression of RPL22L1 and RPS21 were significantly higher in high Gleason grade than they were in low Gleason grade. In addition, in vitro studies were undertaken to evaluate the roles of RPL22L1 and RPS21 in PCa. The results revealed that these genes promote PCa cell proliferation, migration and invasion, and inhibit PCa cell apoptosis. Taken together, these data showed that RPL22L1 and RPS21 exhibited higher expression in human prostate cancer tissue, and involved in PCa cell proliferation and invasion. This research provided a novel insight into diagnostic and prognostic biomarkers for PCa.

Identification of LIFR, PIK3R1, and MMP12 as Novel Prognostic Signatures in Gallbladder Cancer Using Network-Based Module Analysis.

Background: Gallbladder cancer (GBC) is a rare and aggressive malignancy of the biliary tract with a dismal survival rate. Effective biomarkers and therapeutic targets are urgently needed.Methods: We analyzed gene expression profiles of GBC to identify differentially expressed genes (DEGs) and then used these DEGs to identify functional module biomarkers based on protein functional interaction (FI) networks. We further evaluated the module-gene protein expression and clinical significance with immunohistochemistry staining (IHC) in a tissue microarray (TMA) from 80 GBC samples.Results: Five functional modules were identified. Module 0 included classical cancer signaling pathways, such as Ras and PI3K-Akt; and modules 1–4 included genes associated with muscle cells, fibrinogen, extracellular matrix, and integrins, respectively. We validated the expression of LIFR, PIK3R1, and MMP12, which were hubs or functional nodes in modules. Compared with paired peritumoural tissues, we found that the expression of LIFR (P = 0.002) and PIK3R1 (P = 0.046) proteins were significantly downregulated, and MMP12 (P = 0.006) was significantly upregulated. Further prognostic analysis showed that patients with low expression of LIFR had shorter overall survival than those with high expression (log-rank test P = 0.028), the same trend as for PIK3R1 (P = 0.053) and MMP12 (P = 0.006). Multivariate analysis indicated that expression of MMP12 protein (hazard ratio [HR] = 0.429; 95% confidence interval [CI] 0.198, 0.930; P = 0.032) was one of the significant independent prognostic factors for overall survival.Conclusions: We found a highly reliable FI network, which revealed LIFR, PIK3R1, and MMP12 as novel prognostic biomarker candidates for GBC. These findings could accelerate biomarker discovery and therapeutic development in this cancer.

Overexpression of ASPM, CDC20, and TTK Confer a Poorer Prognosis in Breast Cancer Identified by Gene Co-expression Network Analysis.

Breast cancer is one of the most common malignancies among females, and its prognosis is affected by a complex network of gene interactions. In this study, we constructed free-scale gene co-expression networks using weighted gene co-expression network analysis (WGCNA). The gene expression profiles of GSE25055 were downloaded from the Gene Expression Omnibus (GEO) database to identify potential biomarkers associated with breast cancer progression. GSE42568 was downloaded for validation. A total of 9 modules were established via the average linkage hierarchical clustering. We identified 3 hub genes (ASPM, CDC20, and TTK) in the significant module (R2 = 0.52), which were significantly correlated with poor prognosis both in test and validation datasets. In the datasets GSE25055 and GSE42568, higher expression levels of ASPM, CDC20, and TTK correlated with advanced tumor grades. Immunohistochemistry data from the Human Protein Atlas also demonstrated that their protein levels were higher in tumor samples. According to gene set enrichment analysis, 4 commonly enriched pathways were identified: cell cycle pathway, DNA replication pathway, homologous recombination pathway, and P53 signaling pathway. In addition, strong correlations were found among their expression levels. In conclusion, our WGCNA analysis identified candidate prognostic biomarkers for further basic and clinical researches.

Prognostic utility and clinical significance of lysyl oxidase-like 2 protein expression in digestive system cancers.

Lysyl oxidase-like 2 (LOXL2) participates in the occurrence and development of digestive system cancers (DSCs). The aim of this study was to determine whether LOXL2 protein could serve as a prognostic biomarker in patients with DSCs. Relevant studies published before October 1,2018 were identified from a comprehensive literature review in PubMed, Web of Science, and Embase. This meta-analysis was conducted via STATA/SE 14.1 software. Finally, a total of 12 publications and 6 different kinds of DSCs were identified. Meta-analysis indicated that increased expression of LOXL2 protein was significantly correlated with reduced overall survival (hazard ratios [HR]: 1.52; 95% confidence interval [CI]: 1.32-1.72) and worse progression-free survival/disease-free survival (HR: 2.15; 95% CI: 1.48-2.83) in cases with DSCs. In addition, clinicopathological parameters, including tumor invasion, lymph node metastasis, distant metastasis, and clinical stage were significantly related to LOXL2 protein expression in DSCs. High LOXL2 protein expression is significantly associated with worse clinical outcomes in DSCs and its expression level may represent a candidate prognostic biomarker in these cancers.

Quantitative proteomics identifies brain acid soluble protein 1 (BASP1) as a prognostic biomarker candidate in pancreatic cancer tissue.

BackgroundPancreatic cancer is a heterogenous disease with a poor prognosis. This study aimed to discover and validate prognostic tissue biomarkers in pancreatic cancer using a mass spectrometry (MS) based proteomics approach.MethodsGlobal protein sequencing of fresh frozen pancreatic cancer and healthy pancreas tissue samples was conducted by MS to discover potential protein biomarkers. Selected candidate proteins were further verified by targeted proteomics using parallel reaction monitoring (PRM). The expression of biomarker candidates was validated by immunohistochemistry in a large tissue microarray (TMA) cohort of 141 patients with resectable pancreatic cancer. Kaplan-Meier and Cox proportional hazard modelling was used to investigate the prognostic utility of candidate protein markers.FindingsIn the initial MS-discovery phase, 165 proteins were identified as potential biomarkers. In the subsequent MS-verification phase, a panel of 45 candidate proteins was verified by the development of a PRM assay. Brain acid soluble protein 1 (BASP1) was identified as a new biomarker candidate for pancreatic cancer possessing largely unknown biological and clinical functions and was selected for further analysis. Importantly, bioinformatic analysis indicated that BASP1 interacts with Wilms tumour protein (WT1) in pancreatic cancer. TMA-based immunohistochemistry analysis showed that BASP1 was an independent predictor of prolonged survival (HR 0.468, 95% CI 0.257–0.852, p = .013) and predicted favourable response to adjuvant chemotherapy, whereas WT1 indicated a worsened survival (HR 1.636, 95% CI 1.083–2.473, p = .019) and resistance to chemotherapy. Interaction analysis showed that patients with negative BASP1 and high WT1 expression had the poorest outcome (HR 3.536, 95% CI 1.336–9.362, p = .011).InterpretationWe here describe an MS-based proteomics platform for developing biomarkers for pancreatic cancer. Bioinformatic analysis and clinical data from our study suggest that BASP1 and its putative interaction partner WT1 can be used as biomarkers for predicting outcomes in pancreatic cancer patients.

Silencing of SNHG6 induced cell autophagy by targeting miR-26a-5p/ULK1 signaling pathway in human osteosarcoma

BackgroundlncRNAs have been proved to play crucial parts in various human cytopathology and cell physiology, including tumorigenesis. Down-regulated lncRNAs SNHG6 have shown great cell proliferation inhibitory effects in cancer development. Here we investigated how SNHG6 effected human osteosarcoma (OS) development and progression. Methods: Reverse transcription-quantitative PCR was performed to detect SNHG6 mRNA level in both OS tissues and cell lines. MTT and colony formation assays were used to determine the growth impact of SNHG6. Wound healing and trans-well assay were performed to measure the invasion effect of SNHG6. Western blotting were utilized to dissect molecular mechanisms.ResultsWe identified SNHG6 as a lncRNAs that significantly up-regulated in OS tissues and cells, patients with high SNHG6 expression suffered more malignant metastasis and shorter survival times. Furthermore, silencing of SNHG6 in OS significantly inhibited OS cell growth, weakened cell invasion capacity, arrested cell cycle at G0/G1 phase, and induced cell apoptosis. Additionally, mechanism assays suggested that SNHG6 could competitively sponging miR-26a-5p thereby regulating ULK1, and induced cell apoptosis and autophagy by targeting caspase3 and ATF3. Conclusions: Our findings demonstrated that SNHG6 acted as an oncogene in osteosarcoma cells through regulating miR-26a-5p/ULK1 at a post-transcriptional level. SNHG6 might serve as a candidate prognostic biomarker and a target for novel therapies of osteosarcoma patients.

MicroRNA-665 inhibits the oncogenicity of retinoblastoma by directly targeting high-mobility group box 1 and inactivating the Wnt/β-catenin pathway.

Purpose: Previous studies have revealed that microRNA-665 (miR-665) is dysregulated in a variety of human cancers. However, little is known regarding its expression profiles and functions in retinoblastoma (RB). Therefore, the aims of our study were to evaluate miR-665 expression in RB and determine the precise roles of miR-665 in the progression of RB.Patients and methods: Herein, RT-qPCR was used to determine miR-665 expression levels in RB tissues and cell lines, and a series of functional experiments were performed to explore the influence of miR-665 on RB cell proliferation, colony formation, apoptosis, migration, and invasion as well as tumor growth. The molecular mechanisms underlying the tumor-suppressive action of miR-665 in RB were also explored.Results: We found that miR-665 was markedly reduced in RB tissues and cell lines and that lower miR-665 expression was strongly associated with tumor size, TNM stage, and differentiation in patients with RB. Exogenous expression of miR-665 suppressed cell proliferation, colony formation, migration, and invasion, and induced cell apoptosis in RB cells, while silencing miR-665 expression had the opposite effects. In addition, upregulation of miR-665 decreased the tumor growth of RB cells in vivo. High-mobility group box 1 (HMGB1) was identified as a direct target of miR-665 in RB cells, and decreasing the expression of HMGB1 simulated the regulatory effects of miR-665 overexpression in RB cells, while knockdown of HMGB1 expression counteracted the miR-665-mediated antitumor effects in RB cells. Moreover, miR-665 was shown to regulate the Wnt/β-catenin signaling pathway by targeting HMGB1 in vitro and in vivo.Conclusion: Taken together, our in vitro and in vivo results suggest that miR-665 acts as a tumor-suppressive miRNA in RB by directly targeting HMGB1 and inactivating the Wnt/β-catenin pathway. Hence, this miRNA is a candidate prognostic biomarker and therapeutic target in patients with RB.