Study of MicroRNA Expression Profiles of Esophageal Cancer

Study on the Selection of the Targets of Esophageal Carcinoma and Interventions of Ginsenosides Based on Network Pharmacology and Bioinformatics

Background

Esophageal carcinoma (ESCA) is not only a threat to people's health but also the sixth most common cause of cancer-related mortality worldwide.

Methods

In this study, the key targets of ESCA are screened through GeneCards and DisGeNET databases combined with the Gene Expression Omnibus (GEO) database (GSE1420 and GSE20347). Then, data associated with ESCA samples are downloaded from The Cancer Genome Atlas (TCGA) database for integrated analysis. Moreover, the effect of epithelial cell adhesion molecule (EpCAM) expression on the survival of patients with ESCA is evaluated by Kaplan–Meier and Cox analyses. The virtual screening is carried out using a Suflex-Dock molecular docking module. The chemical components, which have been well bound to EpCAM, are screened out based on a total score >5 as a threshold. Ginsenosides and EpCAM are analyzed by LigPlot + v.2.2 software to identify the binding sites.

Results

Four ESCA targets are obtained from GeneCards, DisGeNET, and GEO databases. In this study, it is found that high EpCAM expression is associated with histologic grade, stage, patient age, N classification, T classification, and radiation therapy. The Kaplan–Meier curves for overall survival also show that the higher expression of EpCAM is associated with worse outcomes in patients with ESCA. Univariate and multivariate Cox analyses indicate that EpCAM mRNA expression might be a useful biomarker for ESCA(P < 0.05). Molecular docking technology suggests that ginsenoside Rg3 and ginsenoside Rh2 can easily establish good docking modes and have a high affinity with EpCAM. The 6′-hydroxyl and 6″-hydroxyl on the 3-glycosyl of ginsenoside Rg3 are prone to form hydrogen bonds (Lys151 and Lys221) with the active sites of EpCAM ligand binding domain. The hydroxyl groups on the 12 sites of the ginsenoside Rh2 glycoside framework are found to have hydrogen bonding with Leu240. The formation of hydrogen bonds plays an important role in binding of ginsenoside Rg3 and ginsenoside Rh2 to EpCAM, as well as the stability of EpCAM conformation.

Conclusion

EpCAM may be determined as a potential biomarker for early diagnosis and prognosis of ESCA. Ginsenoside Rg3 and ginsenoside Rh2 have potential antiesophageal cancer activities. This experiment provides a reference for the study of the chemical compositions of ginsenosides in the treatment of esophageal cancer.

Complex role of miR-130a-3p and miR-148a-3p balance on drug resistance and tumor biology in esophageal squamous cell carcinoma

miRNAs play a crucial role in cancer development and progression. However, results on the impact of miRNAs on drug sensitivity and tumor biology vary, and most studies to date focussed on either increasing or decreasing miRNA expression levels. Therefore, the current study investigated the role of different expression levels of miR-130a-3p and miR-148a-3p on drug resistance and tumor biology in four esophageal squamous cell carcinoma cell lines. Interestingly, up- and downregulation of both miRNAs significantly increased sensitivity towards chemotherapy. MiRNA modulation also reduced adherence and migration potential, and increased apoptosis rates. Target analyses showed that up- and downregulation of both miRNAs activated the apoptotic p53-pathway via increased expression of either BAX (miR-148a-3p) or Caspase 9 (miR-130a-3p). miR-148a-3p downregulation seemed to mediate its effects primarily via regulation of Bim rather than Bcl-2 levels, whereas we found the opposite scenario following miR-148a-3p upregulation. A similar effect was observed for miR-130a-3p regulating Bcl-2 and XIAP. Our data provide the first evidence that miRNA modulation in both directions may lead to similar effects on chemotherapy response and tumor biology in esophageal squamous cell carcinoma. Most interestingly, up- and downregulation seem to mediate their effects via modulating the balance of several validated or predicted targets.

miR-135 promotes proliferation and stemness of oesophageal squamous cell carcinoma by targeting RERG

MicroRNA (miRNA) plays an important role in tumourigenesis and cancer development by regulating oncogenes or tumour suppressor that are implicated in cell cycle, cell mobility and even cell senescence. Due to the resistance to enzymes that could degrade nucleotides, miRNAs have been considered proper for diagnosis and prognosis evaluation of cancer. The present study was designed to investigate miRNA associated with ESCC and identified effective miRNAs, which could serve as biomarker or targets. We first performed miRNA profiling to identify a subset of dysregulated miRNAs in ESCC. miR-135, miR-451 and miR-186 were the most differentially expressed miRNAs. Subsequent RT-PCR validated that miR-135 was upregulated in ESCC cell lines TE2 and TE9, implying the promise as a prognostic and diagnostic marker. The Cox regression analysis suggests the correlation of miR-135 expression and tumour stages. Survival analysis demonstrated metastatic samples largely have higher miR-135 expression. Downregulation of miR-135 suppressed proliferation and invasion of TE2 and TE9 cell lines. Subsequent target prediction combined with functional enrichment analysis identified "Small GTPase superfamily" that are possibly targeted by miR-135, which offers candidates for further investigation. Finally, RERG was identified as a target of miR-135. Downregulation of RERG could inhibit the cell proliferation and sphere formation ability of TE2 and TE9. Taken together, miR-135 was proved to promote tumour development of ESCC, which promises the prospect of using miR-135 as a biomarker indicator in diagnosis and prognosis.

microRNAs: Key regulators of chemotherapy response and metastatic potential via complex control of target pathways in esophageal adenocarcinoma

INTRODUCTION

Incidence of esophageal adenocarcinoma (EAC) increased significantly over the last decades. Lack of response to chemotherapy is a major problem in the treatment of this disease. This study aims to assess the biological relevance of characteristic microRNA profiles of chemotherapy resistant EAC cells with regards to response to chemotherapy and biological behavior.

METHODS

We selected 3 microRNAs from characteristic microRNA profiles of resistant EAC (miR-27b-3p, miR-200b-3p, and miR-148a-3p). Expression of microRNAs was modified in 6 EAC cell lines. Effects on chemotherapy, adhesion, migration, apoptosis and cell cycle were assessed using standard assays. Target analyses were performed using Western Blot and Luciferase techniques.

RESULTS

MiR-27b-3p significantly sensitized cells to 5FU and Cisplatin in 83% respectively in 33% of cell lines, miR-148a-3p in 67% respectively 33% of cases. MiR-200b-3p increased sensitivity only towards 5FU in 50% of cases. Co-transfections with miR-27b-3p/miR-148a-3p showed an additive effect on response to chemotherapy in 50% of cases. Upregulation of miR-148a-3p reduced protein expression levels of DNMT-1, MSK-1, Bcl-2 and Bim, and miR-27b upregulation led to downregulation of Sp1 and PPARy proteins implicating a potential negative post-transcriptional control via the respective microRNAs. Finally, we were able to confirm Bcl-2 for the first time as direct target of miR-148a-3p in EAC.

CONCLUSION

This study demonstrates that specific microRNA profiles of chemotherapy resistant EAC in fact determine their response to chemotherapy and biological behavior. Our data further show that microRNA-mediated regulation of chemotherapy resistance is complex, and several microRNAs seem to "co-operate" at various steps within a broad number of pathways what fits very well to our recently proposed understanding of microRNA-mediated regulation as function of cellular functional complexes. These data highlight the promising potential of microRNAs to predict or monitor treatment response to chemotherapy in EAC, and to potentially modulate tumor biology in a therapeutic approach.

Complex Epigenetic Regulation of Chemotherapy Resistance and Biohlogy in Esophageal Squamous Cell Carcinoma via MicroRNAs

Background: Resistance towards chemotherapy is a major obstacle in the treatment of esophageal squamous cell carcinoma (ESCC). We investigated the role of specific microRNAs in chemotherapy resistance and tumor biology. Methods: We selected three microRNAs from characteristic microRNA signatures of resistant ESCC (hsa-miR-125a-5p, hsa-miR-130a-3p, hsa-miR-1226-3p), and hsa-miR-148a-3p. Effects on chemotherapy, adhesion, migration, apoptosis and cell cycle were assessed in six ESCC cell lines. Target analyses were performed using Western blotting and luciferase techniques. Results: MiR-130a-3p sensitized cells towards cisplatin in 100% of cell lines, miR-148a-3p in 83%, miR-125a-5p in 67%, miR-1226-3p in 50% (p ≤ 0.04). MiR-130a-3p sensitized 83% of cell lines towards 5-FU, miR-148a-3p/miR-125a-5p/miR-1226-3p only 33% (p ≤ 0.015). Several resistance-relevant pathways seem to be targeted on various levels. Bcl-2 was confirmed as a direct target of miR-130a-3p and miR-148a-3p, and p53 as a target of miR-125a-5p. All microRNAs decreased migration and adhesion, except miR-130a-3p, and increased apoptosis. Simultaneous manipulation of two microRNAs exhibited additive sensitizing effects towards cisplatin in 50% (miR-125a-5p/miR-148a-3p), and 75% (miR-148a-3p/miR-130a-3p) of cell lines (p ≤ 0.006). Conclusion: Our data present strong evidence that specific microRNA signatures are responsible for drug resistance and aggressiveness of ESCC. Final functional readout of these complex processes appears to be more important than single microRNA-target interactions.

MiR-375 suppresses invasion and metastasis by direct targeting of SHOX2 in esophageal squamous cell carcinoma

Esophageal squamous cell carcinoma (ESCC) is the most common histological type in China. MicroRNAs are endogenously expressed in mammals and play a significant role in tumor invasion and metastasis by targeting potential downstream genes. In the present study, microarray analysis showed that miR-375 expression was distinctly downregulated in ESCC compared with that in normal esophageal epithelium tissues. Then, luciferase reporter assay showed that SHOX2 was the direct downstream target of miR-375 and this interaction was confirmed by the rescue experiments. Quantitative polymerase chain reaction results also showed that SHOX2 expression was upregulated in ESCC cells and tissues. Further analysis showed that SHOX2 induced proliferation, invasion, and metastasis of ESCC both in vivo and in vitro. Moreover, the interaction between miR-375 and SHOX2 affected the epithelial-to-mesenchymal transition. We conclude that miR-375 may suppress invasion and metastasis of ESCC by directly targeting SHOX2. The miR-375/SHOX2 axis may be a novel therapeutic target for ESCC.

Saliva supernatant miR-21: a novel potential biomarker for esophageal cancer detection

OBJECTIVE

To identify whether saliva supernatant miR-21 can serve as a novel potential biomarker in patients with esophageal cancer (EC).

METHODS

32 patients with EC and 16 healthy controls were recruited in this study. Total RNA was extracted from saliva supernatant samples for measurement of miR-21 levels using RT-qPCR and relationships between miR-21 levels and clinical characteristics of EC patients were analyzed.

RESULTS

miR-21 was significantly higher in the EC than control groups. The sensitivity and specificity were 84.4% and 62.5% respectively. Supernatant miR-21 levels showed no significant correlation with cancer stage, differentiation and nodal metastasis.

CONCLUSIONS

Saliva supernatant miR-21 may be a novel biomarker for EC.

Genomics, microRNA, epigenetics, and proteomics for future diagnosis, treatment and monitoring response in upper GI cancers

One major objective for our evolving understanding in the treatment of cancers will be to address how a combination of diagnosis and treatment strategies can be used to integrate patient and tumor variables with an outcome-oriented approach. Such an approach, in a multimodal therapy setting, could identify those patients (1) who should undergo a defined treatment (personalized therapy) (2) in whom modifications of the multimodal therapy due to observed responses might lead to an improvement of the response and/or prognosis (individualized therapy), (3) who might not benefit from a particular toxic treatment regimen, and (4) who could be identified early on and thereby be spared the morbidity associated with such treatments. These strategies could lead in the direction of precision medicine and there is hope of integrating translational molecular data to improve cancer classifications. In order to achieve these goals, it is necessary to understand the key issues in different aspects of biotechnology to anticipate future directions of personalized and individualized diagnosis and multimodal treatment strategies. Providing an overview of translational data in cancers proved to be a challenge as different methods and techniques used to obtain molecular data are used and studies are based on different tumor entities with different tumor biology and prognoses as well as vastly different therapeutic approaches. The pros and cons of the available methodologies and the potential response data in genomics, microRNA, epigenetics and proteomics with a focus on upper gastrointestinal cancers are considered herein to allow for an understanding of where these technologies stand with respect to cancer diagnosis, prognosis and treatment.

Temporal differences in microRNA expression patterns in astrocytes and neurons after ischemic injury

MicroRNAs (miRNAs) are small, non-protein-coding RNA molecules that modulate gene translation. Their expression is altered in many central nervous system (CNS) injuries suggesting a role in the cellular response to stress. Current studies in brain tissue have not yet described the cell-specific temporal miRNA expression patterns following ischemic injury. In this study, we analyzed the expression alterations of a set of miRNAs in neurons and astrocytes subjected to 60 minutes of ischemia and collected at different time-points following this injury. To mimic ischemic conditions and reperfusion in vitro, cortical primary neuronal and astrocytic cultures prepared from fetal rats were first placed in oxygen and glucose deprived (OGD) medium for 60 minutes, followed by their transfer into normoxic pre-conditioned medium. Total RNA was extracted at different time-points after the termination of the ischemic insult and the expression levels of miRNAs were measured. In neurons exposed to OGD, expression of miR-29b was upregulated 2-fold within 6 h and up to 4-fold at 24 h post-OGD, whereas induction of miR-21 was upregulated 2-fold after 24 h when compared to expression in neurons under normoxic conditions. In contrast, in astrocytes, miR-29b and miR-21 were upregulated only after 12 h. MiR-30b, 107, and 137 showed expression alteration in astrocytes, but not in neurons. Furthermore, we show that expression of miR-29b was significantly decreased in neurons exposed to Insulin-Like Growth Factor I (IGF-I), a well documented neuroprotectant in ischemic models. Our study indicates that miRNAs expression is altered in neurons and astrocytes after ischemic injury. Furthermore, we found that following OGD, specific miRNAs have unique cell-specific temporal expression patterns in CNS. Therefore the specific role of each miRNA in different intracellular processes in ischemic brain and the relevance of their temporal and spatial expression patterns warrant further investigation that may lead to novel strategies for therapeutic interventions.

Understanding bipolar disorder: the epigenetic perspective

Bipolar disease (BPD) is a complex major psychiatric disorder that affects between 1% and 2% of the population and exhibits ?85% heritability. This has made BPD an appealing target for genetic studies yet, despite numerous attempts, the genetic basis of this disease remains elusive. Recently, it has come to light that epigenetic factors may also influence the development of BPD. These factors act via stable but reversible modifications of DNA and chromatin structure. In this chapter, we revisit the epidemiological, clinical, and molecular findings in BPD and reanalyze them from the perspective of inherited and acquired epigenetic misregulation. Epigenetic research has great potential to enhance our understanding of the molecular basis of BPD.