RETRACTED: Microarray analysis of microRNA expression in liver cancer tissues and normal control

CKS1B as Drug Resistance-Inducing Gene-A Potential Target to Improve Cancer Therapy

Cancer is a threat to human health and life. Although previously centered on chemical drug treatments, cancer treatment has entered an era of precision targeted therapy. Targeted therapy entails precise guidance, allowing the selective killing of cancer cells and thereby reducing damage to healthy tissues. Therefore, the need to explore potential targets for tumor treatment is vital. Cyclin-dependent kinase regulatory subunit 1B (CKS1B), a member of the conserved cyclin kinase subunit 1 (CKS1) protein family, plays an essential role in cell cycling. A large number of studies have shown that CKS1B is associated with the pathogenesis of many human cancers and closely related to drug resistance. Here, we describe the current understanding of the cellular functions of CKS1B and its underlying mechanisms, summarize a recent study of CKS1B as a target for cancer treatment and discuss the potential of CKS1B as a therapeutic target.

Alterations of MicroRNA Expression in the Liver, Heart, and Testis of Mice Upon Exposure to Repeated Low-Dose Radiation

MicroRNAs (miRs), which regulate target gene expression at the post-transcriptional level, play a crucial role in inducing biological effects upon high-dose ionizing radiation. Yet, the miR expression profiles in response to repeated low-dose radiation (LDR) in vivo have not been elucidated. This study investigated the response profiles of 11 miRs with functions involved in metabolism, DNA damage and repair, inflammation, and fibrosis in mouse liver, heart, and testis upon repeated LDR exposure for 4 months. The expression profiles were evaluated using stem-loop quantitative reverse transcription polymerase chain reaction immediately and at 2 months after LDR exposure. The expression profiles varied significantly at both time points. At the organ level, the heart was the most affected, followed by the liver and testis, in which significant miR upregulation related to DNA damage response was found. Metabolism-related miRs decreased in the liver and increased in the testis. The current results showed immediate and long-lasting alterations in the miR expression profiles in response to repeated LDR in different organs.

Dysregulated microRNA expression profiles in cholangiocarcinoma cell-derived exosomes

AIM

Cholangiocarcinoma (CCA) is a malignant tumor of bile duct epithelial cells. The prognosis of CCA is poor due to lack of effective therapeutic targets and detection at an advanced stage. Exosomes are secreted nano-sized vesicles and contribute to the malignancy of several cancers via transferring their miRNAs between cells. Thus, exosomal miRNAs may serve as new therapeutic targets and potential biomarkers for CCA.

MAIN METHODS

Exosomes were isolated from three different CCA cell lines and normal human cholangiocyte cells, followed by miRNA profiling analysis. Potential role of dysregulated miRNA was investigated by knockdown experiment.

KEY FINDINGS

We found that 38 and 460 miRNAs in CCA exosomes were significantly up- and down-regulated, respectively. Of these differentially expressed miRNAs, the hsa-miR-205-5p and miR-200 family members were markedly up-regulated for 600-1500 folds, whereas the miR-199 family members and their clustered miRNA, hsa-miR-214-3p, were down-regulated for 1000-2000 folds. The expression patterns of these representative exosomal miRNAs were similar to those observed in all types of CCA cells. The target genes of the top ten most up- and down-regulated miRNAs are significantly associated with well-characterized cancer-related pathways. Consistently, knockdown of the most up-regulated miRNA, miR-205-5p, reduced KKU-M213 cell invasion and migration.

SIGNIFICANCE

We have demonstrated the distinct miRNA signatures in exosomes released from CCA cells, compared to normal human cholangiocyte cells. These exosomal miRNAs may have the potential to be novel therapeutic targets and biomarkers for CCA.

MicroRNA Signatures for circulating CD133-positive cells in hepatocellular carcinoma with HCV infection

AIM

Molecular characterization of the CD133+ stem cells associated with hepatocarinogensis through identifying the expression patterns of specific microRNAs (miRNAs).

METHODS

We investigated the expression pattern of 13 miRNAs in purified CD133+ cells separated from the peripheral blood of healthy volunteers, chronic hepatitis C (CHC), liver cirrhosis (LC) and hepatocellular carcinoma (HCC) patients a long with bone marrow samples from the healthy volunteers and the LC patients using custom miScript miRNA PCR array.

RESULTS

The differential expression of the 13 studied miRNAs in CD133+ cells separated from the HCC patients' peripheral blood compared to the controls revealed that miR-602, miR-181b, miR-101, miR-122, miR-192, miR-125a-5p, and miR-221 were significantly up regulated (fold change = 1.8, 1.7, 2, 5.4, 1.6, 2.9 & 1.5 P value = 0.039, 0.0019, 0.0013, 0.0370, 00024, 0.000044 &0.000007 respectively). As for the HCC group compared to the CHC group; miR-602, miR-122, miR-181b, miR-125a-5p, and miR-192 were significantly up regulated (fold change = 13, 3.1, 2.8, 1.6 & 1.56, P value = 0.01, 0.001, 0.000004, 0.002 & 0.007 respectively). Upon comparing the HCC group to the LC group; miR-199a-3p, miR-192, miR-122, miR-181b, miR-224, miR-125a-5p, and miR-885-5p were significantly up regulated (fold change = 5, 6.7, 2.3, 3, 2.5, 4.2 & 39.5 P value = 0.001025, 0.000024, 0.000472, 0.000278, 0.000004, 0.000075 & 0.0000001 respectively) whereas miR-22 was significantly down regulated (fold change = 0.57 P value = 0.00002). Only, miR-192, miR-122, miR-181b and miR-125a-5p were significant common miRNAs in CD133+ cells of the HCC group compared to the other non-malignant groups.

CONCLUSION

We identified a miRNA panel comprised of four miRNAs (miR-192, miR-122, miR-181b and miR-125a-5p) that may serve as a molecular tool for characterization of the CD133+ cells associated with different stages of hepatocarinogensis. This panel may aid in developing a new target therapy specific for those CD133+ cells.

Integrated MicroRNA-mRNA Analysis Reveals miR-204 Inhibits Cell Proliferation in Gastric Cancer by Targeting CKS1B, CXCL1 and GPRC5A

Gastric cancer (GC) is the second most frequent cause of cancer-related deaths worldwide. MicroRNAs are single-stranded RNA molecules of 21–23 nucleotides that regulate target gene expression through specific base-pairing interactions between miRNA and untranslated regions of targeted mRNAs. In this study, we generated a multistep approach for the integrated analysis of miRNA and mRNA expression. First, both miRNA and mRNA expression profiling datasets in gastric cancer from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) identified 79 and 1042 differentially expressed miRNAs and mRNAs, respectively, in gastric cancer. Second, inverse correlations between miRNA and mRNA expression levels identified 3206 miRNA–mRNA pairs combined with 79 dysregulated miRNAs and their 774 target mRNAs predicted by three prediction tools, miRanda, PITA, and RNAhybrid. Additionally, miR-204, which was found to be down-regulated in gastric cancer, was ectopically over-expressed in the AGS gastric cancer cell line and all down-regulated targets were identified by RNA sequencing (RNA-seq) analysis. Over-expression of miR-204 reduced the gastric cancer cell proliferation and suppressed the expression of three targets which were validated by qRT-PCR and luciferase assays. For the first time, we identified that CKS1B, CXCL1, and GPRC5A are putative targets of miR-204 and elucidated that miR-204 acted as potential tumor suppressor and, therefore, are useful as a promising therapeutic target for gastric cancer.

Joint Covariate Detection on Expression Profiles for Identifying MicroRNAs Related to Venous Metastasis in Hepatocellular Carcinoma

Expression profiles of cancer are generally composed of three dimensions including gene probes, patients (e.g., metastasis or non-metastasis) and tissues (i.e., cancer or normal cells of a patient). In order to combine these three dimensions, we proposed a joint covariate detection that not only considered projections on gene probes and tissues simultaneously, but also concentrated on distinguishing patients into different groups. Due to highly lethal malignancy of hepatocellular carcinoma, we chose data GSE6857 to testify the effectiveness of our method. A bootstrap and accumulation strategy was introduced in, which could select candidate microRNAs to distinguish metastasis from non-metastasis patient group. Two pairs of microRNAs were further selected. Each component of either significant microRNA pair was derived from different cliques. Targets were sought and pathway analysis were made, which might reveal the mechanism of venous metastasis in primary hepatocellular carcinoma.

MicroRNA-505 suppresses proliferation and invasion in hepatoma cells by directly targeting high-mobility group box 1

AIMS

MicroRNA-505 (miR-505) expressions have been reported to be altered in the serum of HCC patients. However, the effect and underlying mechanism of miR-505 in hepatoma cells remains poorly understood. The present study intended to investigate the expression levels and the probable role and molecular basis of miR-505 in hepatoma cells.

MAIN METHODS

Real-time PCR was used to determine the miR-505 expressions in hepatoma cell lines QGY-7703, SMMC-7721 and MHCC97. Furthermore, an up-or down-regulation of miR-505 was performed in MHCC97 by transfected with miR-505 mimics or anti-miR-505, respectively. Cell proliferation, cell invasion, and epithelial-mesenchymal transition were determined. Moreover, the target gene of miR-505 was also investigated.

KEY FINDINGS

The expressions of miR-505 were down-regulated in three hepatoma cell lines. MHCC97 possessed the lowest miR-505 levels among the three hepatoma cell lines. Furthermore, the up-regulation of miR-505 suppressed, whereas the down-regulation of miR-505 promoted proliferation, invasion and epithelial-mesenchymal transition in MHCC97. Moreover, miR-505 could directly bind to the 3'-untranslated region of High-Mobility Group Box 1. Notably, High-Mobility Group Box 1 knockdown apparently promoted cell proliferation and invasion in MHCC97.

SIGNIFICANCE

We investigated that MiR-505 regulates proliferation and invasion in MHCC97 cells via targeting High-Mobility Group Box 1.

Construction of synergy networks from gene expression data related to disease

A few methods have been developed to determine whether genes collaborate with each other in relation to a particular disease using an information theoretic measure of synergy. Here, we propose an alternative definition of synergy and justify that our definition improves upon the existing measures of synergy in the context of gene interactions. We use this definition on a prostate cancer data set consisting of gene expression levels in both cancerous and non-cancerous samples and identify pairs of genes which are unable to discriminate between cancerous and non-cancerous samples individually but can do so jointly when we take their synergistic property into account. We also propose a very simple yet effective technique for computation of conditional entropy at a very low cost. The worst case complexity of our method is O(n) while the best case complexity of a state-of-the-art method is O(n(2)). Furthermore, our method can also be extended to find synergistic relation among triplets or even among a larger number of genes. Finally, we validate our results by demonstrating that these findings cannot be due to pure chance and provide the relevance of the synergistic pairs in cancer biology.

Serum microRNA-199a/b-3p as a predictive biomarker for treatment response in patients with hepatocellular carcinoma undergoing transarterial chemoembolization

Objective

The aim of this study was to investigate whether the level of serum microRNA-199a/b-3p (miR-199a/b-3p) can serve as a predictor of treatment response to transarterial chemoembolization (TACE) in patients with hepatocellular carcinoma (HCC).

Methods

Serum miR-199a/b-3p expression level was measured in 132 patients with HCC before TACE (t1) and 3–5 days after TACE (t2). Additionally, 126 patients of these 132 patients had levels measured 4 weeks after TACE (t3) and 3–5 days after second TACE (t4). Serum miR-199a/b-3p expression levels were compared with those of 50 healthy controls. Correlations between miR-199a/b-3p expression levels and clinicopathologic factors and tumor responsiveness were analyzed. The modified Response Evaluation Criteria in Solid Tumors assessment was conducted at t3.

Results

A lower mean baseline miR-199a/b-3p expression level was observed in patients with HCC compared with healthy controls (0.68±0.81 vs 2.50±2.16, P<0.001). A negative correlation between baseline miR-199a/b-3p expression levels and tumor size (P<0.001) was observed. The nonresponder group had significantly lower miR-199a/b-3p expression levels than the responder group at t1 (0.77±1.09 vs 1.96±1.32, P<0.001). In addition, the decrease in miR-199a/b-3p at t2 was greater in the responder group than in the nonresponder group (P=0.011). A higher proportion of the responder group achieved a >25% decrease in serum miR-199a/b-3p expression levels compared with the nonresponder group (64% vs 39%).

Conclusion

Serum miR-199a/b-3p may represent a novel biomarker for predicting efficacy of TACE in patients with HCC.

A transcriptional target of androgen receptor, miR-421 regulates proliferation and metabolism of prostate cancer cells

Prostate cancer is one of the most common malignancies, and microRNAs have been recognized to be involved in tumorigenesis of various kinds of cancer including prostate cancer (PCa). Androgen receptor (AR) plays a core role in prostate cancer progression and is responsible for regulation of numerous downstream targets including microRNAs. This study identified an AR-repressed microRNA, miR-421, in prostate cancer. Expression of miR-421 was significantly suppressed by androgen treatment, and correlated to AR expression in different prostate cancer cell lines. Furthermore, androgen-activated AR could directly bind to androgen responsive element (ARE) of miR-421, as predicted by bioinformatics resources and demonstrated by ChIP and luciferase reporter assays. In addition, over-expression of miR-421 markedly supressed cell viability, delayed cell cycle, reduced glycolysis and inhibited migration in prostate cancer cells. According to the result of miR-421 target genes searching, we focused on 4 genes NRAS, PRAME, CUL4B and PFKFB2 based on their involvement in cell proliferation, cell cycle progression and metabolism. The expression of these 4 downstream targets were significantly repressed by miR-421, and the binding sites were verified by luciferase assay. Additionally, we explored the expression of miR-421 and its target genes in human prostate cancer tissues, both in shared microarray data and in our own cohort. Significant differential expression and inverse correlation were found in PCa patients.

Use of miRNAs as biomarkers in sepsis

Sepsis is one of the most common causes of death in critical patients. Severe generalized inflammation, infections, and severe physiological imbalances significantly decrease the survival rate with more than 50%. Moreover, monitoring, evaluation, and therapy management often become extremely difficult for the clinician in this type of patients. Current methods of diagnosing sepsis vary based especially on the determination of biochemical-humoral markers, such as cytokines, components of the complement, and proinflammatory and anti-inflammatory compounds. Recent studies highlight the use of new biomarkers for sepsis, namely, miRNAs. miRNAs belong to a class of small, noncoding RNAs with an approximate content of 19-23 nucleotides. Following biochemical and physiological imbalances, the expression of miRNAs in blood or other body fluids changes significantly. Moreover, its stability, specificity, and selectivity make miRNAs ideal candidates for sepsis biomarkers. In conclusion, we can affirm that stable species of circulating miRNAs represent potential biomarkers for monitoring the evolution of sepsis.

Circulating MicroRNAs as Non-Invasive Biomarkers for Early Detection of Non-Small-Cell Lung Cancer

Background

Detection of lung cancer at an early stage by sensitive screening tests could be an important strategy to improving prognosis. Our objective was to identify a panel of circulating microRNAs in plasma that will contribute to early detection of lung cancer.

Material and Methods

Plasma samples from 100 early stage (I to IIIA) non–small-cell lung cancer (NSCLC) patients and 100 non-cancer controls were screened for 754 circulating microRNAs via qRT-PCR, using TaqMan MicroRNA Arrays. Logistic regression with a lasso penalty was used to select a panel of microRNAs that discriminate between cases and controls. Internal validation of model discrimination was conducted by calculating the bootstrap optimism-corrected AUC for the selected model.

Results

We identified a panel of 24 microRNAs with optimum classification performance. The combination of these 24 microRNAs alone could discriminate lung cancer cases from non-cancer controls with an AUC of 0.92 (95% CI: 0.87-0.95). This classification improved to an AUC of 0.94 (95% CI: 0.90-0.97) following addition of sex, age and smoking status to the model. Internal validation of the model suggests that the discriminatory power of the panel will be high when applied to independent samples with a corrected AUC of 0.78 for the 24-miRNA panel alone.

Conclusion

Our 24-microRNA predictor improves lung cancer prediction beyond that of known risk factors.

EGF induces microRNAs that target suppressors of cell migration: miR-15b targets MTSS1 in breast cancer

Growth factors promote tumor growth and metastasis. We found that epidermal growth factor (EGF) induced a set of 22 microRNAs (miRNAs) before promoting the migration of mammary cells. These miRNAs were more abundant in human breast tumors relative to the surrounding tissue, and their abundance varied among breast cancer subtypes. One of these miRNAs, miR-15b, targeted the 3' untranslated region of MTSS1 (metastasis suppressor protein 1). Although xenografts in which MTSS1 was knocked down grew more slowly in mice initially, longer-term growth was unaffected. Knocking down MTSS1 increased migration and Matrigel invasion of nontransformed mammary epithelial cells. Overexpressing MTSS1 in an invasive cell line decreased cell migration and invasiveness, decreased the formation of invadopodia and actin stress fibers, and increased the formation of cellular junctions. In tissues from breast cancer patients with the aggressive basal subtype, an inverse correlation occurred with the high expression of miRNA-15b and the low expression of MTSS1. Furthermore, low abundance of MTSS1 correlated with poor patient prognosis. Thus, growth factor-inducible miRNAs mediate mechanisms underlying the progression of cancer.

Circulating small noncoding RNAs as biomarkers of aging

Small noncoding RNAs (sncRNAs) mediate a variety of cellular functions in animals and plants. Deep sequencing has made it possible to obtain highly detailed information on the types and abundance of sncRNAs in biological specimens, leading to the discovery that sncRNAs circulate in the blood of humans and mammals. The most abundant types of circulating sncRNAs are microRNAs (miRNAs), 5' transfer RNA (tRNA) halves, and YRNA fragments, with minute amounts of other types that may nevertheless be significant. Of the more abundant circulating sncRNAs only miRNAs have well described functions, but characteristics of the others suggest specific processing and secretion as complexes that protect the RNA from degradation. The properties of circulating sncRNAs are consistent with their serving as signaling molecules, and investigations of circulating miRNAs support the view that they can enter cells and regulate cellular functions. The serum levels of specific sncRNAs change markedly with age, and these changes can be mitigated by calorie restriction (CR), indicating that levels are under physiologic control. The ability of circulating sncRNAs to transmit functions between cells and to regulate a broad spectrum of cellular functions, and the changes in their levels with age, implicate them in the manifestations of aging. Our understanding of the functions of circulating sncRNA, particularly in relation to aging, is currently at a very early stage; results to date suggest that more extensive investigation will yield important insights into mechanisms of aging.

MicroRNA-224 upregulation and AKT activation synergistically predict poor prognosis in patients with hepatocellular carcinoma

BACKGROUND AND AIM

Previous evidence has shown that microRNA (miR)-224 may function as an onco-miRNA in hepatocellular carcinoma (HCC) cells by activating AKT signaling. However, little is known about the clinical significance of the combined expression of miR-224 and phosphorylated-AKT (pAKT) on human HCC. The aim of this study was to investigate the synergistical influence of miR-224 and pAKT on clinical characteristics and prognosis in patients with HCC.

METHODS

One-hundred and thirty HCC patients who had undergone curative liver resection were selected. In situ hybridization and immunohistochemistry were respectively performed to detect the expression of miR-224 and pAKT in the respective tumors.

RESULTS

Compared with the adjacent nonneoplastic liver tissues, the expression levels of miR-224 and pAKT protein in HCC tissues were both significantly increased (both P<0.001). In addition, the combined upregulation of miR-224 and pAKT protein was significantly associated with serum AFP (P=0.01), tumor stage (P=0.002) and tumor grade (P=0.008). Moreover, HCC patients highly expressing both miR-224 and pAKT protein had worse 5-year disease-free survival and 5-year overall survival (both P<0.001). Furthermore, the Cox proportional hazards model showed that the combined upregulation of miR-224 and pAKT protein (miR-224-high/pAKT-high) may be independent poor prognostic factors for both 5-year disease-free survival (P=0.008) and 5-year overall survival (P=0.01) in HCC.

CONCLUSION

These results indicate for the first time that miR-224 upregulation and AKT activation may synergistically associate with tumor progression of HCC. The combined high expression of miR-224 and pAKT may be a potential indicator for predicting unfavorable prognosis in HCC patients.

MicroRNA expression profiling and functional annotation analysis of their targets in patients with type 1 diabetes mellitus

Type 1 diabetes mellitus (T1DM) results from an autoimmune attack against the insulin-producing pancreatic β-cells, leading to elimination of insulin production. The exact cause of this disorder is still unclear. Although the differential expression of microRNAs (miRNAs), small non-coding RNAs that control gene expression in a post-transcriptional manner, has been identified in many diseases, including T1DM, only scarce information exists concerning miRNA expression profile in T1DM. Thus, we employed the microarray technology to examine the miRNA expression profiles displayed by peripheral blood mononuclear cells (PBMCs) from T1DM patients compared with healthy subjects. Total RNA extracted from PBMCs from 11 T1DM patients and nine healthy subjects was hybridized onto Agilent human miRNA microarray slides (V3), 8x15K, and expression data were analyzed on R statistical environment. After applying the rank products statistical test, the receiver-operating characteristic (ROC) curves were generated and the areas under the ROC curves (AUC) were calculated. To examine the functions of the differentially expressed (p-value<0.01, percentage of false-positives <0.05) miRNAs that passed the AUC cutoff value ≥ 0.90, the database miRWalk was used to predict their potential targets, which were afterwards submitted to the functional annotation tool provided by the Database for Annotation, Visualization, and Integrated Discovery (DAVID), version 6.7, using annotations from the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. We found 57 probes, corresponding to 44 different miRNAs (35 up-regulated and 9 down-regulated), that were differentially expressed in T1DM and passed the AUC threshold of 0.90. The hierarchical clustering analysis indicated the discriminatory power of those miRNAs, since they were able to clearly distinguish T1DM patients from healthy individuals. Target prediction indicated that 47 candidate genes for T1DM are potentially regulated by the differentially expressed miRNAs. After performing functional annotation analysis of the predicted targets, we observed 22 and 12 annotated KEGG pathways for the induced and repressed miRNAs, respectively. Interestingly, many pathways were enriched for the targets of both up- and down-regulated miRNAs and the majority of those pathways have been previously associated with T1DM, including many cancer-related pathways. In conclusion, our study indicated miRNAs that may be potential biomarkers of T1DM as well as provided new insights into the molecular mechanisms involved in this disorder.

MicroRNA-429 Modulates Hepatocellular Carcinoma Prognosis and Tumorigenesis

MicroRNA-429 (miR-429) may modify the development and progression of cancers; however, the role of this microRNA in the hepatocellular carcinoma (HCC) has not been well elaborated. Here, we tested miR-429 expression in 138 pathology-diagnosed HCC cases and SMMC-7721 cells. We found that miR-429 was upregulated in HCC tumor tissues and that the high expression of miR-429 was significantly correlated with larger tumor size (odd ratio (OR), 2.70; 95% confidence interval (CI), 1.28–5.56) and higher aflatoxin B1-DNA adducts (OR = 3.13, 95% CI = 1.47–6.67). Furthermore, this microRNA overexpression modified the recurrence-free survival and overall survival of HCC patients. Functionally, miR-429 overexpression progressed tumor cells proliferation and inhibited cell apoptosis. These results indicate for the first time that miR-429 may modify HCC prognosis and tumorigenesis and may be a potential tumor therapeutic target.