Gene-microRNA network module analysis for ovarian cancer

Non-Coding RNAs Extended Omnigenic Module of Cancers

The emergence of cancers involves numerous coding and non-coding genes. Understanding the contribution of non-coding RNAs (ncRNAs) to the cancer neighborhood is crucial for interpreting the interaction between molecular markers of cancer. However, there is a lack of systematic studies on the involvement of ncRNAs in the cancer neighborhood. In this paper, we construct an interaction network which encompasses multiple genes. We focus on the fundamental topological indicator, namely connectivity, and evaluate its performance when applied to cancer-affected genes using statistical indices. Our findings reveal that ncRNAs significantly enhance the connectivity of affected genes and mediate the inclusion of more genes in the cancer module. To further explore the role of ncRNAs in the network, we propose a connectivity-based method which leverages the bridging function of ncRNAs across cancer-affected genes and reveals the non-coding RNAs extended omnigenic module (NeOModule). Topologically, this module promotes the formation of cancer patterns involving ncRNAs. Biologically, it is enriched with cancer pathways and treatment targets, providing valuable insights into disease relationships.

E2F1-induced microRNA-224-5p expression is associated with hepatocellular carcinoma cell migration, invasion and epithelial-mesenchymal transition via MREG

MicroRNA (miR)-224-5p has been reported to be associated with multiple types of cancer. However, its biological role and underlying mechanism in hepatocellular carcinoma (HCC) has yet to be fully elucidated. The aim of the present study was to investigate whether miR-224-5p mRNA expression level was increased in hepatocellular carcinoma and whether it was associated with poor prognosis. Decreased mRNA expression level of miR-224-5p was shown to suppress liver cancer cell migration, invasion and epithelial-mesenchymal transition (EMT). Mechanistically, E2F1 was found to regulate miR-224-5p expression by binding to its promoter region. Melanoregulin (MREG) was identified as the direct target of miR-224-5p by searching the TargetScan, miRDB and StarBase databases. Overexpression of MREG could attenuate liver cancer cell migration, invasion and EMT. Rescue experiments further confirmed that MREG was associated with the regulation of miR-224-5p in liver cancer. In addition, the E2F1/miR-224-5p axis was shown to promote liver cancer cell migration, invasion and EMT by regulating MREG expression. These results suggested that E2F1-induced upregulation of miR-224-5p may serve an important role in MREG-induced liver cancer cell migration, invasion and EMT, and highlights the regulatory function of miR-224-5p in liver cancer. Therefore, the E2F1/miR-224-5p/MREG axis may provide a theoretical basis for the clinical treatment of hepatocellular carcinoma.

Micro-RNA Regulation on Oct4 Gene Expression and Functional Differentiation in Skin Cancer Cells

Micro-RNA has a very important role in gene regulation. The stem gene Oct4 is related with the growth, mobility, and infiltration of skin cancer cells. Studying the regulatory mechanism of micro-RNAs of Oct4 in skin cancer cells is of important clinical significance. Oct4 gene was analyzed using bioinformatics methods to find mir-RNA with regulatory functions. mir-RNA high-expression vector and suppression vector with pcDNA3.1-EGFP was transfected to skin cancer cell line HS-4 followed analysis of Oct4 expression 24 h and 48 h after transfection and transwell in-vitro cell invasion assay. Bioinformatics showed that mir-335 has relationship with the Oct4 gene. pcDNA3.1-EGFP-335-up and pcDNA3.1-EGFP-335-down were successfully constructed. 24 and 48 hours after transfection, the Oct4 expression in the high-expression group was gradually and significantly decreased (P < 0.05). Meanwhile, the cell migration and infiltration capacity was decreased significantly and showed time dependence with significant differences between groups (P < 0.05). mir-335 expression in suppression group was reduced without change of Oct4 (P > 0.05). Increased mir-335 can decrease the performance of Oct4 in skin cancer cells and inhibit the infiltration ability of cells without affecting cell infiltration capability.

Gene co-expression network analysis reveals mechanisms underlying ozone-induced carbamazepine toxicity in zebrafish (Danio rerio) embryos

Sewage effluent ozonation can reduce concentrations of chemical pollutants including pharmaceutical residues. However, the formation of potentially toxic ozonation byproducts (OBPs) is a matter of concern. This study sought to elucidate toxicity mechanisms of ozonated carbamazepine (CBZ), an anti-epileptic drug frequently detected in sewage effluents and surface water, in zebrafish embryos (Danio rerio). Embryos were exposed to ozonated and non-ozonated CBZ from 3 h post-fertilization (hpf) until 144 hpf. Embryotoxicity endpoints (proportion of dead and malformed embryos) were assessed at 24, 48, and 144 hpf. Heart rate was recorded at 48 hpf. Exposure to ozonated CBZ gave rise to cardiovascular-related malformations and reduced heart rate. Moreover, embryo-larvae exposed to ozonated CBZ displayed a lack of swim bladder inflation. Hence, the expression patterns of CBZ target genes involved in cardiovascular and embryonal development were investigated through a stepwise gene co-expression analysis approach. Two co-expression networks and their upstream transcription regulators were identified, offering mechanistic explanations for the observed toxicity phenotypes. The study presents a novel application of gene co-expression analysis elucidating potential toxicity mechanisms of an ozonated pharmaceutical with environmental relevance. The resulting data was used to establish a putative adverse outcome pathway (AOP).

Integrated microRNA and mRNA signatures associated with overall survival in epithelial ovarian cancer

Ovarian cancer (OC), the eighth-leading cause of cancer-related death among females worldwide, is mainly represented by epithelial OC (EOC) that can be further subdivided into four subtypes: serous (75%), endometrioid (10%), clear cell (10%), and mucinous (3%). Major reasons for high mortality are the poor biological understanding of the OC mechanisms and a lack of reliable markers defining each EOC subtype. MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate gene expression primarily by targeting messenger RNA (mRNA) transcripts. Their aberrant expression patterns have been associated with cancer development, including OC. However, the role of miRNAs in tumorigenesis is still to be determined, mainly due to the lack of consensus regarding optimal methodologies for identification and validation of miRNAs and their targets. Several tools for computational target prediction exist, but false interpretations remain a problem. The experimental validation of every potential miRNA-mRNA pair is not feasible, as it is laborious and expensive. In this study, we analyzed the correlation between global miRNA and mRNA expression patterns derived from microarray profiling of 197 EOC patients to identify the signatures of miRNA-mRNA interactions associated with overall survival (OS). The aim was to investigate whether these miRNA-mRNA signatures might have a prognostic value for OS in different subtypes of EOC. The content of our cohort (162 serous carcinomas, 15 endometrioid carcinomas, 11 mucinous carcinomas, and 9 clear cell carcinomas) reflects a real-world scenario of EOC. Several interaction pairs between 6 miRNAs (hsa-miR-126-3p, hsa-miR-223-3p, hsa-miR-23a-5p, hsa-miR-27a-5p, hsa-miR-486-5p, and hsa-miR-506-3p) and 8 mRNAs (ATF3, CH25H, EMP1, HBB, HBEGF, NAMPT, POSTN, and PROCR) were identified and the findings appear to be well supported by the literature. This indicates that our study has a potential to reveal miRNA-mRNA signatures relevant for EOC. Thus, the evaluation on independent cohorts will further evaluate the performance of such findings.

The antitumor effect of miR-448 in epithelial ovarian cancer

BACKGROUND

Ovarian cancer (OC) is the seventh most commonly diagnosed cancer in the world and the tenth most common in China. Target agents such as bevacizumab and poly (ADP-ribose) polymerase (PARP) inhibitors show efficacy only in the early stages of some cases; therefore, more effective molecular targeting agents need to be developed. microRNAs (miRNA) have emerged as new biomarkers in the clinical diagnosis and treatment of OC. Among these, miRNA-448 has been shown to exert a tumor-suppressor role in numerous cancer types. However, the function of miR-448 in OC remains poorly understood.

METHODS

The miR-448 in cancer tissues and cell lines was tested by quantitative real-time polymerase chain (qRT-PCR). The miR-448 levels were altered by miR-448 mimics (UUGCAUAUGUAGGAUGUCCCAU) or miR-448 antisense oligonucleotide transfection (miR20001532-1-5). Cell growth was evaluated by MTT assay, and cell apoptosis was assayed by annexin V-FITC (detecting apoptotic cells by binding to phosphatidylserine) and propidium iodide (PI, detecting death cells by binding to DNA) (Cat. No. ab54775, Abacam). The target gene of miR-448 was confirmed by dual-luciferase reporter assays.

RESULTS

In this study, we found that miR-448 showed low expression in epithelial ovarian cancer (EOC) tissues and that the low expression of miR-448 was related to low survival rate. miR-448 may thus inhibit cellular proliferation and promote apoptosis by binding the 3'UTR of zinc finger E-box-binding homeobox 2 (ZEB2) and inhibiting the expression of ZEB2.

CONCLUSIONS

Our study suggests that miR-448 has an inhibitory role in OC.

Multi-Domain Networks Association for Biological Data Using Block Signed Graph Clustering

Multi-domain biological network association and clustering have attracted a lot of attention in biological data integration and understanding, which can provide a more global and accurate understanding of biological phenomenon. In many problems, different domains may have different cluster structures. Due to rapid growth of data collection from different sources, some domains may be strongly or weakly associated with the other domains. A key challenge is how to determine the degree of association among different domains, and to achieve accurate clustering results by data integration. In this paper, we propose an unsupervised learning approach for multi-domain network association by using block signed graph clustering. In particular, with consistency weights calculation, the proposed algorithm automatically identify domains relevant to each other strongly (or weakly) by assigning them larger (or smaller) weights. This approach not only significantly improve clustering accuracy but also understand multi-domain networks association. In each iteration of the proposed algorithm, we update consistency weights based on cluster structure of each domain, and then make use of different sets of eigenvectors to obtain different cluster structures in each domain. Experimental results on both synthetic data sets and real data sets (including neuron activity data and gene expression data) empirically demonstrate the effectiveness of the proposed algorithm in clustering performance and in domain association capability.

Gene Coexpression Networks Drive and Predict Reproductive Effects in Daphnia in Response to Environmental Disturbances

Increasing effects of anthropogenic stressors and those of natural origin on aquatic ecosystems have intensified the need for predictive and functional models of their effects. Here, we use gene expression patterns in combination with weighted gene coexpression networks and generalized additive models to predict effects on reproduction in the aquatic microcrustacean Daphnia. We developed models to predict effects on reproduction upon exposure to different cyanobacteria, different insecticides and binary mixtures of cyanobacteria and insecticides. Models developed specifically for groups of stressors (e.g., either cyanobacteria or insecticides) performed better than general models developed on all data. Furthermore, models developed using in silico generated mixture gene expression profiles from single stressor data were able to better predict effects on reproduction compared to models derived from the mixture exposures themselves. Our results highlight the potential of gene expression data to quantify effects of complex exposures at higher level organismal effects without prior mechanistic knowledge or complex exposure data.

Ancient and modern: hints of a core post-transcriptional network driving chemotherapy resistance in ovarian cancer

RNA-binding proteins (RBPs) and noncoding (nc)RNAs (such as microRNAs, long ncRNAs, and others) cooperate within a post-transcriptional network to regulate the expression of genes required for many aspects of cancer behavior including its sensitivity to chemotherapy. Here, using an RBP-centric approach, we explore the current knowledge surrounding contributers to post-transcriptional gene regulation (PTGR) in ovarian cancer and identify commonalities that hint at the existence of an evolutionarily conserved core PTGR network. This network regulates survival and chemotherapy resistance in the contemporary context of the cancer cell. There is emerging evidence that cancers become dependent on PTGR factors for their survival. Further understanding of this network may identify innovative therapeutic targets as well as yield crucial insights into the hard-wiring of many malignancies, including ovarian cancer. WIREs RNA 2018, 9:e1432. doi: 10.1002/wrna.1432 This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Translation > Translation Mechanisms RNA in Disease and Development > RNA in Disease.

Clinical value of peripheral blood microRNA detection in evaluation of SOX regimen as neoadjuvant chemotherapy for gastric cancer

BACKGROUND

Neoadjuvant chemotherapy has been widely applied in treating advanced gastric cancer (GC). However, little research has been conducted on evaluating the effect of neoadjuvant chemotherapy. Purpose of this study was to evaluate the effect of SOX regimen as neoadjuvant chemotherapy by detecting some microRNAs.

METHODS

Total 120 GC patients who had received neoadjuvant chemotherapy (SOX regimen) were recruited with 100 healthy participants as control contemporarily. Age and gender have no significant difference in both groups (P > .05). The effect of chemotherapy was evaluated by the results of CT scan and surgery. Also, adverse effects of chemotherapy were documented. Peripheral blood of GC patients was collected twice: one day before chemotherapy and surgery, respectively, whereas healthy controls' peripheral blood was collected once. Quantitative real-time PCR (qPCR) was utilized to detect expression of miR-145, miR-185, miR-381, and miR-195 of peripheral blood in both groups.

RESULTS

One hundred and twenty patients with advanced GC completed a total of 386 cycles of neoadjuvant chemotherapy with effective rate at 84.17% (101 of 120). Expression of miR-145, miR-185, and miR-381 of patients with GC was lower than that in the control group before chemotherapy commence (all P < .05), while the expressions of miR-145 and miR-185 elevated noticeably in CG patients after neoadjuvant chemotherapy (P < .05). The differences in the expression of miR-145 and miR-185 in advanced GC patients with different chemotherapy outcomes were detected.

CONCLUSION

Patients with GC at advanced stages had aberrant miRs expressions. Detection of miR-145 and miR-185 expression may assist to predict effectiveness and adverse effects of SOX regimen as neoadjuvant chemotherapy.

Knockdown of miR-629 Inhibits Ovarian Cancer Malignant Behaviors by Targeting Testis-Specific Y-Like Protein 5

Ovarian cancer (OC) is the most lethal gynecological cancer. The molecular mechanism of it is complicated, and numerous researches suggest that microRNAs are key regulators for it. This study was to investigate the pivotal role of miR-629 in the progression of OC and to reveal the possible molecular mechanism of its action. Testis-specific Y-like protein 5 (TSPYL5) is a tumor suppressor gene in various cancers, but there is little for its role in OC. OC OVCAR3 cells were transfected with the miR-629 vector, miR-629 inhibitor, and/or small interfering RNA (siRNA) targeting TSPYL5 (si-TSPYL5), respectively. After transfection, cell apoptosis, the ability of migration, and invasion were explored, as well as the level of miR-629 and TSPYL5 protein expression were detected by quantitative polymerase chain reaction and western blot. Compared with the control, there was increasing of miR-629, and decreasing of TSPYL5 and caspase 3 in OC tissue. Overexpression of miR-629 promoted the cell ability of migration and invasion and reduced OC cell apoptosis. In addition, elevated cancer inhibition ability of TSPYL5 induced by the miR-629 inhibitor was significantly blocked by inhibition of TSPYL5 (si-TSPYL5). All the above results suggested that miR-629 could promote OC proliferation, migration, and invasion by directly suppressing TSPYL5 expression, and inhibition of miR-629 might serve as a therapeutic target for OC.

MiR-218 suppresses the metastasis and EMT of HCC cells via targeting SERBP1

Hepatocellular carcinoma (HCC) is the leading cause of cancer-related deaths worldwide. Although many efforts for treating HCC have been made, the survival rate remains unsatisfied. Accumulating evidence indicates that microRNA-218 (miR-218) functions as a tumor suppressor and involves in many biological processes such as tumor initiation, development, and metastasis in certain types of human cancers. However, the potential function and underlying molecular mechanism of miR-218 in HCC still remains to be elucidated. Since HCC is a genetic disease, exploring the mechanisms of the pathogeny and integration are essential for the discovery of novel treatment targets for HCC. Therefore, the aim of the present study was to investigate the abnormal expression level of miR-218 in clinical HCC tissues and HCC cells, and to evaluate its function and underlying mechanisms in HCC. Our results revealed that miR-218 expression was significantly downregulated in HCC tissues and cell lines. Gain-of-function and loss-of-function assays indicated that forced expression of miR-218 in HCC cells inhibited cell migration/invasion and reversed epithelial-mesenchymal transition (EMT) to mesenchymal-epithelial transition (MET), while deletion of miR-218 promoted cell migration/invasion and contributed to the EMT phenotype formation. Bioinformatics analysis and luciferase reporter assay confirmed that serpine mRNA binding protein 1 (SERBP1) was a target gene of miR-218 and rescue assay further confirmed that SERBP1 involved in the function of miR-218 in HCC. All these results suggested that miR-218/SERBP1 signal pathway could inhibit the malignant phenotype formation and that targeting this pathway may be a potential novel way for HCC therapeutics.