microRNA-messenger RNA regulatory network of esophageal squamous cell carcinoma and the identification of miR-1 as a biomarker of patient survival

Identification of hub genes and microRNAs with prognostic values in esophageal cancer by integrated analysis

Esophageal cancer (EC) is the eighth most common cancer in the world, and the sixth most common cause of cancer-related mortality. The aim of the present study was to identify cell and molecular mechanisms involved in EC, and to provide the potential targets for diagnosis and treatment. Here, a microarray dataset (GSE20347) was screened to find differentially expressed genes (DEGs). Different bioinformatic methods were used to analyze the identified DEGs. The up-regulated DEGs were significantly involved in different biological processes and pathways including extracellular matrix organization and ECM-receptor interaction. FN1, CDK1, AURKA, TOP2A, FOXM1, BIRC5, CDC6, UBE2C, TTK, and TPX2 were identified as the most important genes among the up-regulated DEGs. Our analysis showed that has-miR-29a-3p, has-miR-29b-3p, has-miR-29c-3p, and has-miR-767-5p had the largest number of common targets among the up-regulated DEGs. These findings strengthen the understanding of EC development and progression, as well as representing potential markers for EC diagnosis and treatment.

Integrative analysis of negatively regulated miRNA-mRNA axes for esophageal squamous cell carcinoma

BACKGROUND

MicroRNAs regulating mRNA expression by targeting at mRNAs is known constructive in tumor occurrence, immune escape, and metastasis.

OBJECTIVE

This research aims at finding negatively regulatory miRNA-mRNA pairs in esophageal squamous cell carcinoma (ESCC).

METHODS

GENE expression data of The Cancer Genome Atlas (TCGA) and GEO database were employed in differently expressed RNA and miRNA (DE-miRNAs/DE-mRNAs) screening. Function analysis was conducted with DAVID-mirPath. MiRNA-mRNA axes were identified by MiRTarBase and TarBase and verified in esophageal specimen by real-time reverse transcription polymerase chain reaction (RT-qPCR). Receiver operation characteristic (ROC) curve and Decision Curve Analysis (DCA) were applied in miRNA-mRNA pairs predictive value estimation. Interactions between miRNA-mRNA regulatory pairs and immune features were analyzed using CIBERSORT.

RESULTS

Combining TCGA database, 4 miRNA and 10 mRNA GEO datasets, totally 26 DE-miRNAs (13 up and 13 down) and 114 DE-mRNAs (64 up and 50 down) were considered significant. MiRTarBase and TarBase identified 37 reverse regulation miRNA-mRNA pairs, 14 of which had been observed in esophageal tissue or cell line. Through analysis of RT-qPCR outcome, miR-106b-5p/KIAA0232 signature was chosen as characteristic pair of ESCC. ROC and DCA verified the predictive value of model containing miRNA-mRNA axis in ESCC. Via affecting mast cells, miR-106b-5p/KIAA0232 may contribute to tumor microenvironment.

CONCLUSIONS

The diagnostic model of miRNA-mRNA pair in ESCC was established. Their complex role in ESCC pathogenesis especially tumor immunity was partly disclosed.

Circ_0008285 knockdown represses tumor development by miR-384/RRM2 axis in hepatocellular carcinoma

INTRODUCTION AND OBJECTIVES

Circular RNA (circRNA) has attracted extensive attention in studies related to the malignant progression of cancer, including hepatocellular carcinoma (HCC). Therefore, its molecular mechanism in HCC needs to be further explored.

MATERIALS AND METHODS

The expression levels of circ_0008285, microRNA (miR)-384 and ribonucleotide reductase subunit M2 (RRM2) mRNA were detected by quantitative real-time polymerase chain reaction (qRT-PCR). Cell proliferation was analyzed using cell counting kit-8 assay and 5-ethynyl-2'-deoxyuridine assay, cell apoptosis was analyzed by flow cytometry, and cell migration and invasion were detected by transwell assay. Protein level was detected by western blot. The relationships between miR-384 and circ_0008285 or RRM2 were predicted by bioinformatics software and validated by dual luciferase reporter assay and RNA immunoprecipitation (RIP) assay.

RESULTS

Circ_0008285 expression is elevated to HCC tissues and cell lines. Silencing of circ_0008285 inhibited the proliferation, migration and invasion of HCC cells but accelerated cell apoptosis in vitro and impeded HCC tumorigenesis in vivo. Mechanistically, circ_0008285 directly interacted with miR-384, and miR-384 silencing attenuated the effects of circ_0008285 interference on cell proliferation, migration, invasion, and apoptosis. RRM2 was a direct target of miR-384, and RRM2 overexpression reversed the effects of miR-384 overexpression on cell proliferation, migration, invasion, and apoptosis. In addition, circ_0008285 regulated RRM2 expression by sponging miR-384.

CONCLUSION

In this study, circ_0008285 could promote the malignant biological behaviors of HCC cells through miR-384/RRM2 axis and has the potential to become a therapeutic target for HCC, providing a new idea for targeted therapy of HCC.

Relationship of expression of heat shock transcription factor 1 with sensitivity to radiotherapy and chemotherapy in esophageal squamous cell carcinoma

BACKGROUND

The morbidity and mortality of esophageal cancer are extremely high all over the world, and the treatment effect is not good. As the pathogenesis of esophageal cancer is not yet fully understood, this is not conducive to the study of specific therapeutic drugs for esophageal cancer. Heat shock transcription fact 1 (HSF1) is closely related to the occurrence and development of a variety of malignant tumors. Is HSF1 also closely related to the occurrence and development of esophageal squamous cell carcinoma (ESCC)? Will HSF1 become a biological target for the treatment of ESCC? Different patients with advanced ESCC have different sensitivity to radiotherapy and chemotherapy. Studies have shown that in hepatocellular carcinoma, HSF1 can weaken the toxic effect of radiotherapy and chemotherapy on tumors and reduce the curative effect. Does HSF1 affect the sensitivity of ESCC to radiotherapy and chemotherapy?

AIM

To investigate the expression of HSF1 in ESCC and its effect on the sensitivity of ESCC to radiotherapy and chemotherapy.

METHODS

Ninety-two patients were divided into four groups: 20 stage Ⅰ/Ⅱ ESCC patients undergoing surgical resection, 18 stage Ⅲ/Ⅱ ESCC patients undergoing surgical resection, and 44 stage Ⅲ/Ⅱ ESCC patients undergoing radiotherapy and chemotherapy. Among the 44 stage Ⅲ/Ⅱ ESCC patients undergoing radiotherapy and chemotherapy, 16 had low HSF1 expression and 28 had high expression. Ten cases of esophageal dysplasia. Ten esophagitis tissues were used as a control group. The expression of HSF1 in each group was detected by immunohistochemistry. The changes of non-tumorous lesion size, tumor diameter, and CEA value were compared between the HSF1 low expression group and high expression group before and after radiotherapy and chemotherapy to assess the sensitivity of patients to radiotherapy and chemotherapy. Factors that might affect the 3-year survival of ESCC patients were identified, and the 3-year overall survival rate of ESCC patients was calculated.

RESULTS

HSF1 was highly expressed in each ESCC group, but lowly expressed in esophagitis group and esophageal dysplasia group, and there was a significant difference in the expression of HSF1 between each ESCC group and esophagitis group and esophageal dysplasia group (P = 0.001). HSF1 expression was not significantly associated with age, gender, tumor location , tumor size, degree of differentiation, T stage, N stage, or M stage (P > 0.05). In the HSF1 low expression group, the non-tumor lesion was more significantly relieved, the tumor diameter was more significantly reduced, and the CEA value was more significantly decreased after radiotherapy and chemotherapy compared with those in the HSF1 high expression group (P < 0.05). In the ESCC surgical resection group, the 3-year survival period was significantly related to age (P = 0.019), HSF1 expression (P = 0.028), T stage (P = 0.007), and N stage (P = 0.016), but not related to gender, tumor location, tumor diameter, or degree of differentiation (P > 0.05). In stage Ⅲ/Ⅱ ESCC patients undergoing radiotherapy and chemotherapy, the HSF1 low expression group had a significantly higher 3-year overall survival rate than the HSF1 high expression group (P = 0.016). The 1-, 2-, and 3-year survival rates of the HSF1 low expression group were significantly higher than those of the HSF1 high expression group (P < 0.05). The HSF1 low expression group had a significantly higher 3-year overall survival rate than the HSF1 high expression group (P = 0.03).

CONCLUSION

HSF1 is highly expressed in ESCC and the higher the HSF1 expression, the worse the prognosis of patients. HSF1 expression is not related to patients' clinical characteristics. In stage Ⅲ/Ⅳ ESCC patients receiving radiotherapy and chemotherapy, the higher the expression of HSF1, the worse the sensitivity of patients to radiotherapy and chemotherapy. In ESCC patients undergoing surgical resection and stage Ⅲ/Ⅳ ESCC patients receiving radiotherapy and chemotherapy, the 3-year overall survival rate is higher in the HSF1 low expression group than in the HSF1 high expression group.

MicroRNA-1: Diverse role of a small player in multiple cancers

The process of cancer initiation and development is a dynamic and complex mechanism involving multiple genetic and non-genetic variations. With the development of high throughput techniques like next-generation sequencing, the field of cancer biology extended beyond the protein-coding genes. It brought the functional role of noncoding RNAs into cancer-associated pathways. MicroRNAs (miRNAs) are one such class of noncoding RNAs regulating different cancer development aspects, including progression and metastasis. MicroRNA-1 (miR-1) is a highly conserved miRNA with a functional role in developing skeletal muscle precursor cells and cardiomyocytes and acts as a consistent tumor suppressor gene. In humans, two discrete genes, MIR-1-1 located on 20q13.333 and MIR-1-2 located on 18q11.2 loci encode for a single mature miR-1. Downregulation of miR-1 has been demonstrated in multiple cancers, including lung, breast, liver, prostate, colorectal, pancreatic, medulloblastoma, and gastric cancer. A vast number of studies have shown that miR-1 affects the hallmarks of cancer like proliferation, invasion and metastasis, apoptosis, angiogenesis, chemosensitization, and immune modulation. The potential therapeutic applications of miR-1 in multiple cancer pathways provide a novel platform for developing anticancer therapies. This review focuses on the different antitumorigenic and therapeutic aspects of miR-1, including how it regulates tumor development and associated immunomodulatory functions.

miR-1: A comprehensive review of its role in normal development and diverse disorders

MicroRNA-1 (miR-1) is a conserved miRNA with high expression in the muscle tissues. In humans, two discrete genes, MIRN1-1 and MIRN1-2 residing on a genomic region on 18q11.2 produce a single mature miRNA which has 21 nucleotides. miR-1 has a regulatory role on a number of genes including heat shock protein 60 (HSP60), Kruppel-like factor 4 (KLF4) and Heart And Neural Crest Derivatives Expressed 2 (HAND2). miR-1 has critical roles in the physiological processes in the smooth and skeletal muscles as well as other tissues, thus being involved in the pathogenesis of a wide range of disorders. Moreover, dysregulation of miR-1 has been noted in diverse types of cancers including gastric, colorectal, breast, prostate and lung cancer. In the current review, we provide the summary of the data regarding the role of this miRNA in the normal development and the pathogenic processes.

miR-424-5p regulates cell proliferation and migration of esophageal squamous cell carcinoma by targeting SIRT4

Objective: The present research is aimed to elucidate the expression patterns of miR-424-5p and its role in tumorigenesis and progression of esophageal squamous cell carcinoma (ESCC).

Methods: Both starBase and TCGA were utilized to assess miR-424-5p expression status in ESCC. The endogenous mRNA expression levels of miR-424-5p in ESCC and normal esophagus cell lines were detected by qRT-PCR. CCK8 and colony-forming assays were applied to determine the effects of miR-424-5p on ESCC proliferation. Transwell migration and wound healing assays were carried out to observe the changes of ESCC cell mobility after miR-424-5p mimic or inhibitor transfection. Impact of miR-424-5p on malignancy growth in vivo was further verified in a mouse xenograft model. The regulatory relationships between miR-424-5p and SIRT4 were validated by dual luciferase reporter assay, qRT-PCR and Western blot.

Results: miR-424-5p expression was found upregulated in ESCC. miR-424-5p overexpression dramatically facilitated ESCC cells proliferation and migration capacity in vitro, while downregulation of miR-424-5p displayed the opposite trend. Inhibition of xenograft tumor growth was further evidenced in vivo. Moreover, SIRT4 was confirmed to be a specific target gene of miR-424-5p in ESCC and negatively modulated by miR-424-5p. Finally, SIRT4 overexpression strongly rescued the promoting influence of miR-424-5p on the proliferative and migratory capacity of ESCC cells.

Conclusions: miR-424-5p had tumor promoting functions in proliferation and migration of ESCC by targeting SIRT4, suggesting that miR-424-5p may serve as a potential diagnostic biomarker and manipulation of miR-424-5p/SIRT4 axis could provide a novel therapeutic strategy for further ESCC treatment.

The miR-1224-5p/TNS4/EGFR axis inhibits tumour progression in oesophageal squamous cell carcinoma

Oesophageal squamous cell carcinoma (ESCC) is a common and aggressive malignancy. Although many molecular alterations have been observed in ESCC, the mechanisms underlying the development and progression of this disease remain unclear. In the present study, miR-1224-5p was identified to be downregulated in ESCC tissues compared to normal tissues, and its low expression was correlated with shorter survival time in patients. In vitro experiments showed that miR-1224-5p inhibited the proliferation, colony formation, migration and invasion of ESCC cells. Mechanistic investigation revealed that miR-1224-5p directly targeted TNS4 and inhibited its expression, which led to the inactivation of EGFR-EFNA1/EPHA2-VEGFA (vascular endothelial growth factor A) signalling. Experiments in vivo confirmed the suppressive effect of miR-1224-5p on oesophageal cancer cells. By immunohistochemistry analysis of ESCC specimens, we found that TNS4 expression was positively correlated with that of VEGFA, and was significantly associated with lymph node metastasis and shorter survival time in patients. Together, our data suggest that miR-1224-5p downregulation is a frequent alteration in ESCC that promotes cell proliferation, migration, invasion and tumour growth by activating the EGFR-EFNA1/EPHA2-VEGFA signalling pathway via inhibition of TNS4 expression. Decreased miR-1224-5p and elevated TNS4 are unfavourable prognostic factors for ESCC patients.

miRNA-based biomarkers, therapies, and resistance in Cancer

MicroRNAs (miRNAs), small non-coding RNAs (ncRNAs) of about 22 nucleotides in size, play important roles in gene regulation, and their dysregulation is implicated in human diseases including cancer. A variety of miRNAs could take roles in the cancer progression, participate in the process of tumor immune, and function with miRNA sponges. During the last two decades, the connection between miRNAs and various cancers has been widely researched. Based on evidence about miRNA, numerous potential cancer biomarkers for the diagnosis and prognosis have been put forward, providing a new perspective on cancer screening. Besides, there are several miRNA-based therapies among different cancers being conducted, advanced treatments such as the combination of synergistic strategies and the use of complementary miRNAs provide significant clinical benefits to cancer patients potentially. Furthermore, it is demonstrated that many miRNAs are engaged in the resistance of cancer therapies with their complex underlying regulatory mechanisms, whose comprehensive cognition can help clinicians and improve patient prognosis. With the belief that studies about miRNAs in human cancer would have great clinical implications, we attempt to summarize the current situation and potential development prospects in this review.

Identification and validation of hub microRNAs dysregulated in esophageal squamous cell carcinoma

Esophageal squamous cell carcinoma (ESCC) is one of the deadliest cancers worldwide, and its morbidity is exacerbated by the lack of early symptoms. Bioinformatics analyses enable discovery of differentially expressed genes and non-protein-coding RNAs of potential prognostic and/or therapeutic relevance in ESCC and other cancers. Using bioinformatics tools, we searched for dysregulated miRNAs in two ESCC microarray datasets from the Gene Expression Omnibus (GEO) database. After identification of three upregulated and five downregulated miRNAs shared between databases, protein-protein interaction (PPI) network analysis was used to identify the top 10 hub-gene targets. Thereafter, a miRNA-gene interaction network predicted that most hub genes are regulated by miR-196a-5p and miR-1-3p, which are respectively upregulated and downregulated in ESCC. Functional enrichment analyses in the GO and KEGG databases indicated the potential involvement of these miRNAs in tumorigenesis-related processes and pathways, while both differential expression and correlation with T stage were demonstrated for each miRNA in a cohort of ESCC patients. Overexpression showed that miR-196a-5p increased, whereas miR-1-3p attenuated, proliferation and invasion in human ESCC cell lines grown in vitro. These findings suggest miR-196a-5p and miR-1-3p jointly contribute to ESCC tumorigenesis and are potential targets for diagnosis and treatment.

Integrated analysis of genome-wide miRNAs and targeted gene expression in esophageal squamous cell carcinoma (ESCC) and relation to prognosis

Background

Esophageal squamous cell carcinoma (ESCC) is a leading cause of cancer death worldwide and in China. We know miRNAs influence gene expression in tumorigenesis, but it is unclear how miRNAs affect gene expression or influence survival at the genome-wide level in ESCC.

Methods

We performed miRNA and mRNA expression arrays in 113 ESCC cases with tumor/normal matched tissues to identify dysregulated miRNAs, to correlate miRNA and mRNA expressions, and to relate miRNA and mRNA expression changes to survival and clinical characteristics.

Results

Thirty-nine miRNAs were identified whose tumor/normal tissue expression ratios showed dysregulation (28 down- and 11 up-regulated by at least two-fold with P < 1.92E-04), including several not previously reported in ESCC (miR-885-5p, miR-140-3p, miR-708, miR-639, miR-596). Expressions of 16 miRNAs were highly correlated with expressions of 195 genes (P < 8.42E-09; absolute rho values 0.51–0.64). Increased expressions of miRNA in tumor tissue for both miR-30e* and miR-124 were associated with increased survival (P < 0.05). Similarly, nine probes in eight of 818 dysregulated genes had RNA expression levels that were nominally associated with survival, including NF1, ASXL1, HSPA4, TGOLN2, BAIAP2, EZH2, CHAF1A, SUPT7L.

Conclusions

Our characterization and integrated analysis of genome-wide miRNA and gene expression in ESCC provides insights into the expression of miRNAs and their relation to regulation of RNA targets in ESCC tumorigenesis, and suggest opportunities for the future development of miRs and mRNAs as biomarkers for early detection, diagnosis, and prognosis in ESCC.

MicroRNA-301b and its target gene synaptosome-associated protein 91 as important modulators in esophageal cancer: functional experiments

The aim of this study was to probe the influence of microRNA-301b (miR-301b) in esophageal cancer pathogenesis. Based on the data acquired from The Cancer Genome Atlas database, we found that miR-301b was highly expressed in esophageal cancer tissues and high expression of miR-301b was related to worse prognosis in patients with esophageal cancer. Quantitative real-time PCR revealed that the expression of miR-301b was higher in all examined esophageal cancer cell lines (ECA109, KY-SE150, TE-1, and NEC) than that in a human esophageal epithelial cell line (HEEC). Upregulation/downregulation of miR-301b facilitated/suppressed the growth, migration, and invasion of ECA109/KY-SE150 cells. Synaptosome-associated protein 91 (SNAP91) was proved to be one of the target genes of miR-301b and was negatively modulated by miR-301b. Besides, SNAP91 was lowly expressed in human esophageal cancer tissues and cell lines. Meanwhile, low expression of SNAP91 was concerned with poor prognosis in patients with esophageal cancer. Furthermore, we discovered that overexpression/depletion of SNAP91 suppressed/facilitated the proliferation of KY-SE150/ECA109 cells. MiR-301b and SNAP91 had little impact on HEEC cell proliferation and this degree of influence was negligible compared with their impacts on esophageal cancer cell proliferation. By rescue assay, we showed that overexpression of SNAP91 restrained the growth, migration, and invasion of ECA109 cells with overexpressed miR-301b while knockdown of SNAP91 showed the contrary effects on KY-SE150 cells with downregulated miR-301b. These consequences indicated that miR-301b played an important effect on esophageal cancer cells through regulating SNAP91, insinuating that miR-301b/SNAP91 might be novel potential targets for esophageal cancer therapy and prognosis.

Esophageal Cancer Development: Crucial Clues Arising from the Extracellular Matrix

In the last years, the extracellular matrix (ECM) has been reported as playing a relevant role in esophageal cancer (EC) development, with this compartment being related to several aspects of EC genesis and progression. This sounds very interesting due to the complexity of this highly incident and lethal tumor, which takes the sixth position in mortality among all tumor types worldwide. The well-established increase in ECM stiffness, which is able to trigger mechanotransduction signaling, is capable of regulating several malignant behaviors by converting alteration in ECM mechanics into cytoplasmatic biochemical signals. In this sense, it has been shown that some molecules play a key role in these events, particularly the different collagen isoforms, as well as enzymes related to its turnover, such as lysyl oxidase (LOX) and matrix metalloproteinases (MMPs). In fact, MMPs are not only involved in ECM stiffness, but also in other events related to ECM homeostasis, which includes ECM remodeling. Therefore, the crucial role of distinct MMPs isoform has already been reported, especially MMP-2, -3, -7, and -9, along EC development, thus strongly associating these proteins with the control of important cellular events during tumor progression, particularly in the process of invasion during metastasis establishment. In addition, by distinct mechanisms, a vast diversity of glycoproteins and proteoglycans, such as laminin, fibronectin, tenascin C, galectin, dermatan sulfate, and hyaluronic acid exert remarkable effects in esophageal malignant cells due to the activation of oncogenic signaling pathways mainly involved in cytoskeleton alterations during adhesion and migration processes. Finally, the wide spectrum of interactions potentially mediated by ECM may represent a singular intervention scenario in esophageal carcinogenesis natural history and, due to the scarce knowledge on the cellular and molecular mechanisms involved in EC development, the growing body of evidence on ECM’s role along esophageal carcinogenesis might provide a solid base to improve its management in the future.