Identification of miR-374a as a prognostic marker for survival in patients with early-stage nonsmall cell lung cancer

Investigating miR-9 and miR-222 in CSF and Plasma of Neuroblastoma Patients as Metastatic and Apoptotic-Related Markers

Neuroblastoma is a cancer that occurs due to abnormal development of the sympathetic nervous system. The dysregulation of miR-9 and miR-222 plays a crucial role in neuroblastoma development. These microRNAs have a significant relationship with PTEN, caspase-9, and MMP14, which can potentially form the basis for the specific diagnosis and treatment of this disease. In our study, two neuroblastoma cell lines were divided into three groups based on whether they had been treated with miR-9, anti-miR-9, miR-222, or both. We evaluated various parameters in these groups, including migration (through a wound healing assay), apoptosis (using flow cytometry), and gene expression (through qRT-PCR). Additionally, we measured the expression levels of MMP14, miR-9, and miR-222 in plasma and CSF samples from neuroblastoma patients using ELISA and qRT-PCR. We found that patients with neuroblastoma had higher levels of MMP14 and miR-222 mRNA expression but lower levels of miR-9 mRNA expression. Furthermore, after treating the cell lines with anti-miR-9 and anti-miR-222, we observed increased levels of MMP14 expression, as well as PTEN and caspase-9. Additionally, the treatment with anti-miR-222 and anti-miR-9 led to an increase in the frequency of apoptosis and migration of cancer cells. Our research shows that the dysregulation of miR-9, miR-222, and MMP14 could be key indicators in the pathogenesis of neuroblastoma. We also found that up-regulation of miR-9 was associated with decreased disease severity, whereas up-regulation of miR-222 and MMP14 was linked to increased disease severity.

The NcRNA/Wnt axis in lung cancer: oncogenic mechanisms, remarkable indicators and therapeutic targets

Early diagnosis of lung cancer (LC) is challenging, treatment options are limited, and treatment resistance leads to poor prognosis and management in most patients. The Wnt/β-catenin signaling pathway plays a vital role in the occurrence, progression, and therapeutic response of LC. Recent studies indicate that non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) function as epigenetic regulators that can promote or inhibit Wnt/β-catenin signaling by interacting with Wnt proteins, receptors, signaling transducers, and transcriptional effectors, thereby affecting LC cell proliferation, metastasis, invasion, and treatment resistance. Deepening our understanding of the regulatory network between ncRNAs and the Wnt/β-catenin signaling pathway will help overcome the limitations of current LC diagnosis and treatment methods. This article comprehensively reviews the regulatory mechanisms related to the functions of ncRNAs and the Wnt/β-catenin pathway in LC, examining their potential as diagnostic and prognostic biomarkers and therapeutic targets, aiming to offer new promising perspectives for LC diagnosis and treatment.

MicroRNAs in disease States

This review highlights the role of miRNAs in various diseases affecting major organ systems. miRNAs are small, non-coding RNA molecules that regulate numerous genes. Dysregulation of miRNAs is linked to many pathological conditions due to their involvement in gene silencing and cellular pathways. We discuss miRNA expression patterns, their physiological and pathological roles, and how changes in miRNA levels contribute to disease. Notably, miRNAs like miR-499 and miR-21 are implicated in heart failure and atherosclerosis. miRNA dysregulation is also associated with colorectal and gastric cancers, influencing tumorigenesis and chemoresistance. In neurological diseases, miRNAs exhibit diverse profiles that affect neurodevelopment and degeneration. Additionally, miRNAs modulate cell function in reproductive organs, impacting fertility and cancer progression. miRNAs such as miR-192 and miR-204 serve as biomarkers for nephropathy and acute kidney injury. These miRNAs are involved in skeletal muscle diseases, contributing to conditions like osteoporosis and sarcopenia. miRNAs function as oncogenes or tumor suppressors in cancer, highlighting their potential in diagnostics and therapy. Further research is needed to develop miRNA-based diagnostics and treatments.

MicroRNA Nobel Prize: Timely Recognition and High Anticipation of Future Products-A Prospective Analysis

MicroRNAs (miRNAs) maintain cellular homeostasis by blocking mRNAs by binding with them to fine-tune the expression of genes across numerous biological pathways. The 2024 Nobel Prize in Medicine and Physiology for discovering miRNAs was long overdue. We anticipate a deluge of research work involving miRNAs to repeat the history of prizes awarded for research on other RNAs. Although miRNA therapies are included for several complex diseases, the realization that miRNAs regulate genes and their roles in addressing therapies for hundreds of diseases are expected; but with advancement in drug discovery tools, we anticipate even faster entry of new drugs. To promote this, we provide details of the current science, logic, intellectual property, formulations, and regulatory process with anticipation that many more researchers will introduce novel therapies based on the discussion and advice provided in this paper.

Advancements in Personalized CAR-T Therapy: Comprehensive Overview of Biomarkers and Therapeutic Targets in Hematological Malignancies

Chimeric antigen receptor T-cell (CAR-T) therapy is a novel anticancer therapy using autologous or allogeneic T-cells. To date, six CAR-T therapies for specific B-cell acute lymphoblastic leukemia (B-ALL), non-Hodgkin lymphomas (NHL), and multiple myeloma (MM) have been approved by the Food and Drug Administration (FDA). Significant barriers to the effectiveness of CAR-T therapy include cytokine release syndrome (CRS), neurotoxicity in the case of Allogeneic Stem Cell Transplantation (Allo-SCT) graft-versus-host-disease (GVHD), antigen escape, modest antitumor activity, restricted trafficking, limited persistence, the immunosuppressive microenvironment, and senescence and exhaustion of CAR-Ts. Furthermore, cancer drug resistance remains a major problem in clinical practice. CAR-T therapy, in combination with checkpoint blockades and bispecific T-cell engagers (BiTEs) or other drugs, appears to be an appealing anticancer strategy. Many of these agents have shown impressive results, combining efficacy with tolerability. Biomarkers like extracellular vesicles (EVs), cell-free DNA (cfDNA), circulating tumor (ctDNA) and miRNAs may play an important role in toxicity, relapse assessment, and efficacy prediction, and can be implicated in clinical applications of CAR-T therapy and in establishing safe and efficacious personalized medicine. However, further research is required to fully comprehend the particular side effects of immunomodulation, to ascertain the best order and combination of this medication with conventional chemotherapy and targeted therapies, and to find reliable predictive biomarkers.

LncRNA GAS5 Modulates the Progression of Glioma Through Repressing miR-135b-5p and Upregulating APC

Purpose

The main purpose of this paper is to explore the interaction between GAS5 and miR-135b-5p to understand their function in the metastasis, invasion, and proliferation of glioma. This may provide new ideas for the pathogenesis and treatment of glioma.

Patients and Methods

Western blotting assays and RT‑qPCR were employed to investigate the expression of related genes in glioma tissues or cell lines. CCK-8 was used to examine the impact of GAS5 on cell viability. Motile activities were adopted by the transwell and wound healing experiments. A double luciferase experiment was performed to elucidate transcriptional regulation.

Results

GAS5 showed low expression in glioma cells and tissues, and up-regulation of GAS5 could depress the invasion, proliferation, and metastasis of glioma. GAS5 negatively regulates miR-135b-5p, which can counteract the cellular effects caused by GAS5. APC was the target of miR-135b-5p, and GAS5 can regulate the expression of APC by sponging miR-135b-5p. APC overexpression reversed the effects of miR-135b-5p promotion on glioma cells, while miR-135b-5p has the opposite function. As a downstream target gene of GAS5, miR-135b-5p was negatively regulated by GAS5. The restoration of miR-135b-5p can remarkably reverse the impact of GAS5 on glioma cells. In addition, GAS5 increased the expression of APC in glioma cells by inhibiting miR-135b-5p.

Conclusion

GAS5 increased APC expression by restraining miR-135b-5p and partially blocked the progression of glioma, suggesting that it could be an advantageous therapeutic target for glioma intervention.

Impact of Aging and Cellular Senescence in the Pathophysiology of Preeclampsia

The incidence of hypertensive disorders of pregnancy is increasing, which may be due to several factors, including an increased age at pregnancy and more comorbid health conditions during reproductive years. Preeclampsia, the most severe hypertensive disorder of pregnancy, has been associated with an increased risk of future disease, including cardiovascular and kidney diseases. Cellular senescence, the process of cell cycle arrest in response to many physiologic and maladaptive stimuli, may play an important role in the pathogenesis of preeclampsia and provide a mechanistic link to future disease. In this article, we will discuss the pathophysiology of preeclampsia, the many mechanisms of cellular senescence, evidence for the involvement of senescence in the development of preeclampsia, as well as evidence that cellular senescence may link preeclampsia to the risk of future disease. Lastly, we will explore how a better understanding of the role of cellular senescence in preeclampsia may lead to therapeutic trials. © 2023 American Physiological Society. Compr Physiol 13:5077-5114, 2023.

miR-429 Suppresses Endometrial Cancer Progression and Drug Resistance via DDX53

(1) Background: To examine miR-429-meditated DEAD (Asp-Glu-Ala-Asp) box polypeptide 53 (DDX53) function in endometrial cancer (EC). (2) Methods: DDX53 and miR-429 levels were measured using quantitative real-time polymerase chain reaction and western blotting assays, cell invasion and migration using Transwell invasion and wound healing assays, and cell proliferation using colony-forming/proliferation assays. A murine xenograft model was also generated to examine miR-429 and DDX53 functions in vivo. (3) Results: DDX53 overexpression (OE) promoted key cancer phenotypes (proliferation, migration, and invasion) in EC, while in vivo, DDX53 OE hindered tumor growth in the murine xenograft model. Moreover, miR-429 was identified as a novel miRNA-targeting DDX53, which suppressed EC proliferation and invasion. (4) Conclusions: DDX53 and miR-429 regulatory mechanisms could provide novel molecular therapies for EC.

Emerging roles of PHLPP phosphatases in lung cancer

Pleckstrin homologous domain leucine-rich repeating protein phosphatases (PHLPPs) were originally identified as protein kinase B (Akt) kinase hydrophobic motif specific phosphatases to maintain the cellular homeostasis. With the continuous expansion of PHLPPs research, imbalanced-PHLPPs were mainly found as a tumor suppressor gene of a variety of solid tumors. In this review, we simply described the history and structures of PHLPPs and summarized the recent achievements in emerging roles of PHLPPs in lung cancer by 1) the signaling pathways affected by PHLPPs including Phosphoinositide 3-kinase (PI3K)/AKT, RAS/RAF/mitogen-activated protein kinase (MEK)/extracellular signal-regulated kinase (ERK) and Protein kinase C (PKC) signaling cascades. 2) function of PHLPPs regulatory factor USP46 and miR-190/miR-215, 3) the potential roles of PHLPPs in disease prognosis, Epidermal growth factor receptors (EGFR)- tyrosine kinase inhibitor (TKI) resistance and DNA damage, 4) and the possible function of PHLPPs in radiotherapy, ferroptosis and inflammation response. Therefore, PHLPPs can be considered as either biomarker or prognostic marker for lung cancer treatment.

Contributions of Circulating microRNAs for Early Detection of Lung Cancer

There is unmet need to develop circulating biomarkers that would enable earlier interception of lung cancer when more effective treatment options are available. Here, a set of 30 miRNAs, selected from a review of the published literature were assessed for their predictive performance in identifying lung cancer cases in the pre-diagnostic setting. The 30 miRNAs were assayed using sera collected from 102 individuals diagnosed with lung cancer within one year following blood draw and 212 controls matched for age, sex, and smoking status. The additive performance of top-performing miRNA candidates in combination with a previously validated four-protein marker panel (4MP) consisting of the precursor form of surfactant protein B (Pro-SFTPB), cancer antigen 125 (CA125), carcinoembryonic antigen (CEA) and cytokeratin-19 fragment (CYFRA21-1) was additionally assessed. Of the 30 miRNAs evaluated, five (miR-320a-3p, miR-210-3p, miR-92a-3p, miR-21-5p, and miR-140-3p) were statistically significantly (Wilcoxon rank sum test p < 0.05) elevated in case sera compared to controls, with individual AUCs ranging from 0.57−0.62. Compared to the 4MP alone, the combination of 3-miRNAs + 4MP improved sensitivity at 95% specificity by 19.1% ((95% CI of difference 0.0−28.6); two-sided p: 0.006). Our findings demonstrate utility for miRNAs for early detection of lung cancer in combination with a four-protein marker panel.

Expression, Clinical Significance, Immune Infiltration, and Regulation Network of miR-3940-5p in Lung Adenocarcinoma Based on Bioinformatic Analysis and Experimental Validation

Background

Based on bioinformatics analysis and experimental validation, we investigated the expression, clinical significance, immune infiltration, and potential signaling pathways of miR-3940-5p in lung adenocarcinoma (LUAD).

Methods

521 LUAD tissue samples and 46 normal lung tissue samples from The Cancer Genome Atlas (TCGA) database. We evaluated the relationship between clinical features and miR-3940-5p expression using Kruskal–Wallis, Wilcoxon sign-rank, and logistic regression, explored the relationship between miR-3940-5p expression and the prognosis of LUAD patients using Kaplan–Meier survival curve analysis. Several databases were used to identify miRNA targets. MiR-3940-5p target genes were analyzed based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. The significant role of miR-3940-5p in function was evaluated using immune infiltration analysis. LUAD cell lines were tested for miR-3940-5p expression using QRT-PCR.

Results

There was a significant association between high miR-3940-5p expression in LUAD and T stage (P=0.005), pathologic stage (P=0.047), race (White vs Asian & Black or African American) (P=0.041), residual tumor (P=0.043), and anatomic neoplasm subdivision2 (P=0.030). MiR-3940-5p expression predicted poor overall survival (HR: 1.35; 95% CI: 1.01–1.81; P=0.045), disease-specific survival (HR: 1.53; 95% CI: 1.05–2.23; P=0.026), and progression-free survival (HR: 1.35; 95% CI: 1.03–1.77; P=0.032). BAP1, BBS1, CCR2, KCNE3, PEBP1, and RABL2A were all associated with poor OS in LUAD patients with low miR-3940-5p expression levels. According to GO and KEGG analyses, miR-3940-5p may play a role in LUAD development by regulating pathways such as measles, PI3K-Akt signaling pathway, and p53 signaling pathway. There was a correlation between the expression level of miR-3940-5p and immune infiltration. LUAD cell lines showed significantly higher levels of miR-3940-5p than Beas-2B cells.

Conclusion

A high expression of miR-3940-5p is significantly associated with a poor prognosis in patients with LUAD, suggesting that it could be used as a prognostic biomarker.

Biomarkers and the microbiome in the detection and treatment of early-stage non-small cell lung cancer

Lung cancer is one of the most common and deadly cancers in the world. However, over the last several years, research into lung cancer screening and novel therapeutic approaches have provided promise that earlier detection combined with new treatment strategies may result in significantly improved outcomes. Biomarkers will most certainly play a major role in identifying those who may benefit from, and how to apply, these new treatment strategies. Here we discuss potential biomarkers, including the microbiome, in both detection and treatment strategies for early stage lung cancer.

Molecular Pathology of Lung Cancer

This overview of the molecular pathology of lung cancer includes a review of the most salient molecular alterations of the genome, transcriptome, and the epigenome. The insights provided by the growing use of next-generation sequencing (NGS) in lung cancer will be discussed, and interrelated concepts such as intertumor heterogeneity, intratumor heterogeneity, tumor mutational burden, and the advent of liquid biopsy will be explored. Moreover, this work describes how the evolving field of molecular pathology refines the understanding of different histologic phenotypes of non-small-cell lung cancer (NSCLC) and the underlying biology of small-cell lung cancer. This review will provide an appreciation for how ongoing scientific findings and technologic advances in molecular pathology are crucial for development of biomarkers, therapeutic agents, clinical trials, and ultimately improved patient care.

ROLE OF MICRO RNA IN THE REGULATION OF CELL POLARIZATION IN HEPATOCELLULAR CARCINOMA

BACKGROUND

The occurrence of tissue scarring, and architecture-modifying signalling led to a tumorigenic microenvironment. Targeting specifically the biological mediators responsible for the physiological and morphological changes accommodating Hepatocellular carcinoma (HCC) growth may be the key for identifying a future HCC cure.

METHODS

Morphological and physiological features of cultured HepG2 cells in both stimulated recombinant human vascular endothelial growth factor (VEGF165), and unstimulated (control) conditions were assessed. Quantitative RT-PCR measured endogenous VEGF expression levels. The assessment of pro-angiogenic biological mediator (miR-296, miR-31, and miR-17) profiles was achieved by polarization-inducing VEGF165 stimulation followed by quantitative RT-PCR.

RESULTS

In-vitro conditions reproduced successfully the physiological environment leading to the occurrence of HCC, including the successful HepG2 polarization following VEGF stimulation. While endogenous VEGF production only occurs if complete polarization has been reached, the quantified biological mediator profiles determined here pointed at either possible early stages of depolarization or at the lack of tumorigenic potential of the HepG2 cells. All tested micro RNAs (miRs) displayed upregulated profiles, although the miR-296 was less amplified (3.78-fold as compared to control) than miR-31 or miR-17 (6.5- and 6.6-fold, respectively).

CONCLUSIONS

The findings surrounding miR-17 reproduce similar data reported in the literature; the unexpected high miR-31 expression was intriguing. Given HepG2 cells' minimal tumorigenic potential, the unexpected multi-fold upregulation of miR-31 may be a cause or a consequence of HepG2 cells' low tumorigenic potential. The exploration of miR-31 therapeutic potential may be a future rewarding endeavor.

MicroRNA -196b is related to the overall survival of patients with esophageal squamous cell carcinoma and facilitates tumor progression by regulating SOCS2 (Suppressor Of Cytokine Signaling 2)

Esophageal squamous cell carcinoma (ESCC) is common cancer in China. At the same time, microRNA-196b (miR-196b) has different promotion/inhibition effects in different cancers. The study aims to reveal the role of miR-196b in ESCC and explore its prognostic value. The expression of miR-196b in ESCC samples and cell lines was detected to explore the expression pattern of miR-196b in ESCC. Kaplan-Meier method was conducted for survival rate and Multivariate Cox analysis was used to explore the clinical significance of miR-196b in ESCC. The Cell Counting Kit-8 (CCK-8) assay, transwell migration and invasion tests were used to determine the biological function of miR-196b in ESCC. The relationship of miR-196b and SOCS2 in ESCC was detected by luciferase activity assay and RIP assay. Both in ESCC tissues and cell lines, miR-196b expression was up-regulated. miR-196b expression is related to TNM stage and lymph node metastasis. Combining with the results of Multivariate Cox regression analysis, miR-196b may be a potential independent prognostic marker for ESCC patients. The results of the functional analysis showed that miR-196b inhibitor can reduce cell proliferation, migration and invasion in ESCC cells. Besides, the suppressor of cytokine signaling 2 (SOCS2) is the target of miR-196b in ESCC. miR-196b may exist as a tumor-promoting factor in ESCC and enhance the proliferation abilities, migration capacities, and invasion potential of ESCC cells by targeting SOCS2. miR-196b and SOCS2 have a close negative correlation in ESCC, which may be used as a clinically poor prognostic biomarker and therapeutic target for ESCC.

Morphing projections: a new visual technique for fast and interactive large-scale analysis of biomedical datasets

MOTIVATION

Biomedical research entails analyzing high dimensional records of biomedical features with hundreds or thousands of samples each. This often involves using also complementary clinical metadata, as well as a broad user domain knowledge. Common data analytics software makes use of machine learning algorithms or data visualization tools. However, they are frequently one-way analyses, providing little room for the user to reconfigure the steps in light of the observed results. In other cases, reconfigurations involve large latencies, requiring a retraining of algorithms or a large pipeline of actions. The complex and multiway nature of the problem, nonetheless, suggests that user interaction feedback is a key element to boost the cognitive process of analysis, and must be both broad and fluid.

RESULTS

In this article, we present a technique for biomedical data analytics, based on blending meaningful views in an efficient manner, allowing to provide a natural smooth way to transition among different but complementary representations of data and knowledge. Our hypothesis is that the confluence of diverse complementary information from different domains on a highly interactive interface allows the user to discover relevant relationships or generate new hypotheses to be investigated by other means. We illustrate the potential of this approach with three case studies involving gene expression data and clinical metadata, as representative examples of high dimensional, multidomain, biomedical data.

AVAILABILITY AND IMPLEMENTATION

Code and demo app to reproduce the results available at https://gitlab.com/idiazblanco/morphing-projections-demo-and-dataset-preparation.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Clinical Significance of miR-183-3p and miR-182-5p in NSCLC and Their Correlation

Purpose

Accumulating evidence has indicated that dysregulated microRNAs (miRNAs) are involved in cancer progression. In this study, we evaluated the clinicopathologic significance of miR-183-3p and miR-182-5p, and the role of miR-183-3p in non-small-cell lung cancer (NSCLC) progression.

Patients and Methods

Seventy-six NSCLC patients from Beijing Chest Hospital were included. The expression of miR-183-3p and miR-182-5p was evaluated by real-time quantitative polymerase chain reaction (RT-qPCR). Then, cell growth curve assays and colony formation assays were performed. Bioinformatics analysis of TCGA database was performed to explore the clinicopathological significance and prognostic value.

Results

miR-183-3p and miR-182-5p were significantly increased in NSCLC tumor tissues (both P < 0.0001) and were positively correlated (r = 0.8519, P < 0.0001). miR-183-3p (P = 0.0444) and miR-182-5p (P = 0.0132) were correlated with tumor size. In addition, miR-183-3p (P = 0.0135) and miR-182-5p (P = 0.0009) were upregulated in normal lung tissues from smokers. In vitro, miR-183-3p was correlated with cell proliferation. In addition, bioinformatics analysis indicated that miR-183-3p was correlated with poor prognosis (P = 0.0466) and tumor size (P = 0.0017). In addition, miR-183-3p was higher in lung squamous carcinoma (LUSC) tissue (P < 0.0001) than in lung adenocarcinoma (LUAD) tissue, and miR-183-3p was higher in the tumor tissue of smokers (P = 0.0053) than in that of nonsmokers.

Conclusion

Upregulation of miR-183-3p and miR-182-5p may play an oncogenic role in NSCLC. miR-183-3p could be used as a potential prognostic biomarker and therapeutic target to manage lung cancer.

miRNAs in lung cancer. A systematic review identifies predictive and prognostic miRNA candidates for precision medicine in lung cancer

Lung cancer (LC) is the leading cause of cancer-related death worldwide and miRNAs play a key role in LC development. To better diagnose LC and to predict drug treatment responses we evaluated 228 articles encompassing 16,697 patients and 12,582 healthy controls. Based on the criteria of ≥3 independent studies and a sensitivity and specificity of >0.8 we found blood-borne miR-20a, miR-10b, miR-150, and miR-223 to be excellent diagnostic biomarkers for non-small cell LC whereas miR-205 is specific for squamous cell carcinoma. The systematic review also revealed 38 commonly regulated miRNAs in tumor tissue and the circulation, thus enabling the prediction of histological subtypes of LC. Moreover, theranostic biomarker candidates with proven responsiveness to checkpoint inhibitor treatments were identified, notably miR-34a, miR-93, miR-106b, miR-181a, miR-193a-3p, and miR-375. Conversely, miR-103a-3p, miR-152, miR-152-3p, miR-15b, miR-16, miR-194, miR-34b, and miR-506 influence programmed cell death-ligand 1 and programmed cell death-1 receptor expression, therefore providing a rationale for the development of molecularly targeted therapies. Furthermore, miR-21, miR-25, miR-27b, miR-19b, miR-125b, miR-146a, and miR-210 predicted response to platinum-based treatments. We also highlight controversial reports on specific miRNAs. In conclusion, we report diagnostic miRNA biomarkers for in-depth clinical evaluation. Furthermore, in an effort to avoid unnecessary toxicity we propose predictive biomarkers. The biomarker candidates support personalized treatment decisions of LC patients and await their confirmation in randomized clinical trials.

EMT-associated microRNAs and their roles in cancer stemness and drug resistance

Epithelial‐to‐mesenchymal transition (EMT) is implicated in a wide array of malignant behaviors of cancers, including proliferation, invasion, and metastasis. Most notably, previou studies have indicated that both cancer stem‐like properties and drug resistance were associated with EMT. Furthermore, microRNAs (miRNAs) play a pivotal role in the regulation of EMT phenotype, as a result, some miRNAs impact cancer stemness and drug resistance. Therefore, understanding the relationship between EMT‐associated miRNAs and cancer stemness/drug resistance is beneficial to both basic research and clinical treatment. In this review, we preliminarily looked into the various roles that the EMT‐associated miRNAs play in the stem‐like nature of malignant cells. Then, we reviewed the interaction between EMT‐associated miRNAs and the drug‐resistant complex signaling pathways of multiple cancers including lung cancer, gastric cancer, gynecologic cancer, breast cancer, liver cancer, colorectal cancer, pancreatic cancer, esophageal cancer, and nasopharyngeal cancer. We finally discussed the relationship between EMT, cancer stemness, and drug resistance, as well as looked forward to the potential applications of miRNA therapy for malignant tumors.

MicroRNA-941 regulates the proliferation of breast cancer cells by altering histone H3 Ser 10 phosphorylation

Breast cancer including triple negative breast cancer (TNBC) represents an important clinical challenge, as these tumours often develop resistance to conventional chemotherapeutics. MicroRNAs play a crucial role in cell-cycle regulation, differentiation, apoptosis, and migration. Herein, we performed Affymetrix Gene Chip miRNA 4.0 microarray and observed differential regulation of miRNAs (75 upregulated and 199 downregulated) in metastatic MDA-MB-231 cells as compared to immortalized human non-tumorigenic breast epithelial (MCF-10A) cells. MicroRNA-941 was significantly upregulated in MDA-MB-231 cells (almost nine-fold increase) in comparison to MCF-10A cells. Transfection of MiRNA-941 inhibitor significantly decreased the proliferation and migration of MDA-MB-231 cells by altering the expressions of p21, Cyclin D1, PP2B-B1, E-cadherin and MMP-13. Interestingly, we provide first evidence that inhibiting miR-941 prevents cell proliferation and phosphorylation of histone H3 at Ser10 residue. Xenograft model of breast cancer was developed by subcutaneous injection of MDA-MB-231 cells into the mammary fat pad of female athymic nude mice (Crl:NU-Foxn1nu). The tumours were allowed to grow to around 60 mm³, thereafter which we divided the animals into seven groups (n = 5). Notably, intratumoral injection of miR-941 inhibitor significantly abolished the tumour growth in MDA-MB-231 xenograft model. 5-Fluorouracil (10 mg/kg, i.p.) was used as positive control in our study. To the best of our knowledge, we report for the first time that targeting miR-941 improves the sensitivity of MDA-MB-231 cells to 5-fluorouracil. This can be of profound clinical significance, as it provides novel therapeutic approach for treating variety of cancers (overexpressing miRNA-941) in general and breast cancers in particular.

Aberrant expression of miR-4728 in patients with non-small cell lung cancer and its regulatory effects on tumor progression in tumor cells

Non-small cell lung cancer (NSCLC) is a common malignant tumor with poor prognosis and an increasing number of cases. MicroRNA (miR)-4728 is related with the progression of various types of cancer, and is dysregulated in NSCLC, which indicates that miR-4728 may serve as a biomarker for NSCLC. The present study aimed to investigate the clinical significance of miR-4728 in NSCLC diagnosis and prognosis, and to explore the biological function of miR-4728 in NSCLC progression. Serum and tissue samples were collected from 122 patients with NSCLC. By conducting reverse transcription-quantitative PCR, the Cell Counting Kit-8 assay and Transwell assays, the expression of miR-4728 and its effect on NSCLC cell proliferation, migration and invasion were investigated. The diagnostic value of miR-4728 was evaluated by plotting a receiver operating characteristic curve, and Kaplan-Meier and Cox regression analyses were conducted to assess the prognostic value of miR-4728. miR-4728 was significantly downregulated in NSCLC serum and tissue samples compared with healthy controls, with a relatively high diagnostic accuracy and ability to predict poor overall survival time in patients with NSCLC. By conducting gain- and loss-of-function experiments, the results indicated that miR-4728 knockdown significantly promoted NSCLC cell proliferation, migration and invasion compared with the inhibitor negative control (NC) group. By contrast, miR-4728 overexpression displayed the opposite effect on NSCLC cell proliferation, migration and invasion. The present study indicated that miR-4728 was downregulated in NSCLC and may serve as a candidate diagnostic and prognostic biomarker. NSCLC cell proliferation, migration and invasion were inhibited by miR-4728 overexpression compared with the mimic NC group, which suggested that miR-4728 may serve as a therapeutic target for NSCLC.

MicroRNAs in Lung Cancer Oncogenesis and Tumor Suppression: How it Can Improve the Clinical Practice?

BACKGROUND

Lung cancer (LC) development is a process that depends on genetic mutations. The DNA methylation, an important epigenetic modification, is associated with the expression of non-coding RNAs, such as microRNAs. MicroRNAs are particularly essential for cell physiology, since they play a critical role in tumor suppressor gene activity. Furthermore, epigenetic disruptions are the primary event in cell modification, being related to tumorigenesis. In this context, microRNAs can be a useful tool in the LC suppression, consequently improving prognosis and predicting treatment.

CONCLUSION

This manuscript reviews the main microRNAs involved in LC and its potential clinical applications to improve outcomes, such as survival and better quality of life.

MicroRNA-374 is a potential diagnostic biomarker for atherosclerosis and regulates the proliferation and migration of vascular smooth muscle cells

Background

The occurrence and development of atherosclerosis (AS) are closely related to the abnormality of vascular smooth muscle cells (VSMCs), and multiple microRNAs (miRNAs) have been reported to participate in the pathogenesis of AS. This study explored the expression and clinical value of miR-374 in the serum of AS patients, and analyzed its effect on the proliferation and migration of VSMCs.

Methods

The expression levels of miR-374 in the serum of 102 asymptomatic patients with AS and 89 healthy patients were detected by fluorescence quantitative PCR. The diagnostic value of miR-374 was evaluated through the receiver operating characteristic (ROC) curve. What's more, CCK-8 and Transwell assays were used to analyze the effects of miR-374 on the proliferation and migration of VSMCs.

Results

The expression level of miR-374 in the serum of AS patients was significantly higher than that of the control group. At the same time, the expression of miR-374 in AS patients was positively correlated with carotid intima-media thickness (CIMT). The area under the ROC curve is 0.824. Furthermore, overexpression of miR-374 significantly promoted the proliferation and migration of VSMCs, whereas reducing miR-374 inhibited the proliferation and migration of VSMCs.

Conclusions

The high expression of miR-374 may be a potential diagnostic marker for AS, and overexpression of miR-374 may play a role in AS by promoting the proliferation and migration of VSMCs.

Identification of Novel microRNA Prognostic Markers Using Cascaded Wx, a Neural Network-Based Framework, in Lung Adenocarcinoma Patients

The evolution of next-generation sequencing technology has resulted in a generation of large amounts of cancer genomic data. Therefore, increasingly complex techniques are required to appropriately analyze this data in order to determine its clinical relevance. In this study, we applied a neural network-based technique to analyze data from The Cancer Genome Atlas and extract useful microRNA (miRNA) features for predicting the prognosis of patients with lung adenocarcinomas (LUAD). Using the Cascaded Wx platform, we identified and ranked miRNAs that affected LUAD patient survival and selected the two top-ranked miRNAs (miR-374a and miR-374b) for measurement of their expression levels in patient tumor tissues and in lung cancer cells exhibiting an altered epithelial-to-mesenchymal transition (EMT) status. Analysis of miRNA expression from tumor samples revealed that high miR-374a/b expression was associated with poor patient survival rates. In lung cancer cells, the EMT signal induced miR-374a/b expression, which, in turn, promoted EMT and invasiveness. These findings demonstrated that this approach enabled effective identification and validation of prognostic miRNA markers in LUAD, suggesting its potential efficacy for clinical use.

Integrating high-throughput microRNA and mRNA expression data to identify risk mRNA signature for pancreatic cancer prognosis

Pancreatic cancer is a malignancy of the digestive system characterized by poor prognosis. A number of prognostic messenger RNA (mRNA) signatures have been identified by using the high-throughput expression profiles. MicroRNAs (miRNA) play a critical role in regulating multiple cellular functions. However, no such integrated analysis of miRNAs and mRNAs for studying the prognostic mechanisms of pancreatic cancer has been reported. In this study, we first identified prognostic mRNAs and miRNAs based on The Cancer Genome Atlas datasets, and then performed an enrichment analysis to explore the underlying biological mechanisms involved in pancreatic cancer prognosis at the mRNA level. Furthermore, we performed an integrated analysis of mRNAs and miRNAs to identify prognostic subpathways, which were closely associated with pancreatic cancer genes and tumor hallmarks and involved in hypoxia, oxidative phosphyorylation and xenobiotic metabolisms. Meanwhile, we performed a random walk algorithm based on global network, prognostic mRNAs and miRNAs, and identified top risk mRNAs as the prognostic signature. Finally, an independent testing set was used to confirm the predictive power of the top mRNA signature, and most of these genes involved were known oncogenes. In conclusion, we performed a series of integrated analyses by comprehensively exploring pancreatic cancer prognosis and systematically optimized the prognostic signature for clinical use.

mmu_circ_0000790 Is Involved in Pulmonary Vascular Remodeling in Mice with HPH via MicroRNA-374c-Mediated FOXC1

Recently, the identification of several circular RNAs (circRNAs) as vital regulators of microRNAs (miRNAs) underlines the increasing complexity of non-coding RNA (ncRNA)-mediated regulatory networks. This study aimed to explore the effects of mmu_circ_0000790 on the biological behaviors of pulmonary artery smooth muscle cells (PASMCs) in hypoxic pulmonary hypertension (HPH). The HPH mouse model and hypoxia-induced PASMC model were initially established, and the expression of mmu_circ_0000790 in the pulmonary vascular tissues and hypoxic PASMCs was determined using quantitative reverse transcriptase polymerase chain reaction (qRT-PCR). A series of in vitro experiments such as dual-luciferase, RNA pull-down, and RNA-binding protein immunoprecipitation (RIP) assays were conducted to evaluate the interactions among mmu_circ_0000790, microRNA-374c (miR-374c), and forkhead transcription factor 1 (FOXC1). The potential physiological functions of mmu_circ_0000790, miR-374c, and FOXC1 in hypoxic PASMCs were investigated through gain- and loss-of function approaches. Upregulated mmu_circ_0000790 was found in both the HPH-pulmonary vascular tissues and hypoxic PASMCs. Additionally, mmu_circ_0000790 could competitively bind to miR-374c and consequently upregulate the target gene of miR-374c, FOXC1. It was also observed that mmu_circ_0000790 induced proliferation and inhibited apoptosis of hypoxic PASMCs, which further promoted the pulmonary vascular remodeling in mice with HPH. Therefore, we speculate that mmu_circ_0000790 may serve as a prospective target for the treatment of patients with HPH.

miR-552 promotes ovarian cancer progression by regulating PTEN pathway

Background

Increasing researches have demonstrated the critical functions of MicroRNAs (miRNAs) in the progression of malignant tumors, including ovarian cancer. It was reported that miR-552 was an important oncogene in both breast cancer and colorectal cancer. However, the role of miR-552 in ovarian cancer (OC) remains to be elucidated.

Methods

RT-PCR and western blot analysis were used to detect the expression of miR-552 and PTEN. The impact of miR-552 on ovarian cancer proliferation and metastasis was investigated in vitro. The prognostic value of miR-552 was evaluated using the online bioinformatics tool Kaplan-Meier plotter.

Results

In the present study, we for first found that miR-552 was upregulated in ovarian cancer, especially in metastatic and recurrence ovarian cancer. Forced miR-552 expression promotes the growth and metastasis of ovarian cancer cells. Consistently, miR-552 interference inhibits the proliferation and metastasis of ovarian cancer cells. Mechanically, bioinformatics and luciferase reporter analysis identified Phosphatase and tension homolog (PTEN) as a direct target of miR-552. miR-552 downregulated the PTEN mRNA and protein expression in ovarian cancer cells. Furthermore, the PTEN siRNA abolishes the discrepancy of growth and metastasis capacity between miR-552 mimic ovarian cells and control cells. More importantly, upregulation of miR-552 predicts the poor prognosis of ovarian cancer patients.

Conclusion

Our findings revealed that miR-552 could promote ovarian cancer cells progression by targeting PTEN signaling and might therefore be useful to predict patient prognosis.

miR-34a in serum is involved in mild-to-moderate COPD in women exposed to biomass smoke

Background

Chronic obstructive pulmonary disease (COPD) is characterized by persistent respiratory symptoms and airflow limitation that is due to airway and/or alveolar abnormalities. The main causes of COPD are Gene-environment interactions associated with tobacco smoking (COPD-TS) and biomass smoke (COPD-BS). It is well know that microRNAs (miRNAs) participate in the control of post-transcriptional regulation and are involved in COPD-TS; nevertheless, those miRNAS are participating in the COPD-BS are unidentified. Thus, we studied which miRNAs are involved in COPD-BS (GOLD stages I–II).

Methods

In the screening phase, the profile of the miRNAs was analyzed in serum samples (n = 3) by means of a PCR array. Subsequently, the miRNAs were validated with RT-qPCR (n = 25) in the corresponding study groups. Additionally, the serum concentration of Notch1 was measured comparing COPD-BS vs COPD-TS.

Results

miR-34a was down-regulated in COPD- BS vs COPD-TS. In the other study groups, three miRNAs were differentially expressed: miR-374a was down-regulated in COPD-BS vs C, miR-191-5p was up-regulated in COPD-BS vs H-BS, and miR-21-5p was down-regulated in COPD-TS compared to the C group. Moreover, the serum concentration of Notch1, one of the targets of miR-34a, was increased in COPD-BS compared to women with COPD-TS.

Conclusions

This is the first study in patients with COPD due to biomass that demonstrates miRNA expression differences between patients. The observations support the concept that COPD by biomass has a different phenotype than COPD due to tobacco smoking, which could have important implications for the treatment of these diseases.

Upregulated METTL3 promotes metastasis of colorectal Cancer via miR-1246/SPRED2/MAPK signaling pathway

BACKGROUND

m6A modification has been proved to play an important role in many biological processes. METTL3 as the main methyltransferase for methylation process has been found to be upregulated in many cancers, including CRC. Here, we investigate m6A modification and the underlying mechanism of METTL3 in the development of CRC.

METHODS

The expression of METTL3 was detected in large clinical patient samples. To evaluate the function of METTL3 in vitro and in vivo, colony formation, CCK-8, cell migration and invasion assays were performed. To find out the downstream target of METTL3, GEO dataset was re-mined. We analyzed expression and metastasis-related miRNA by Pearson correlation, and miR-1246 was selected. Here, to identify the downstream target of miR-1246, Targetscan and miRWalk were used. RIP and luciferase reporter assay further confirmed SPRED2 as the direct target of miR-1246.

RESULTS

We found that upregulated METTL3 is responsible for abnormal m6A modification in CRC and correlates positively with tumor metastasis. The gain- and loss-of-function indicates that METTL3 promotes cell migration and invasion in vitro and in vivo. Additionally, we confirmed that METTL3 can methylate pri-miR-1246, which further promotes the maturation of pri-miR-1246. By using bioinformatics tools, anti-oncogene SPRED2 was identified as the downstream target of miR-1246, wherein downregulated SPRED2 further reverses the inhibition of the MAPK pathway.

CONCLUSIONS

The present study demonstrates that the METTL3/miR-1246/SPRED2 axis plays an important role in tumor metastasis and provides a new m6A modification pattern in CRC development.

microRNA-374 inhibits proliferation and promotes apoptosis of mouse melanoma cells by inactivating the Wnt signalling pathway through its effect on tyrosinase

Melanoma is one of the most malignant skin tumours with constantly increasing incidence worldwide. Previous studies have demonstrated that microRNA‐374 (miR‐374) is a novel biomarker for cancer therapy. Therefore, this study explores whether miR‐374 targeting tyrosinase (TYR) affects melanoma and its underlying mechanism. We constructed subcutaneous melanoma models to carry out the following experiments. The cells were transfected with a series of miR‐374 mimics, miR‐374 inhibitors or siRNA against TYR. Dual luciferase reporter gene assay was used for the verification of the targeting relationship between miR‐374 and TYR. Reverse transcription quantitative polymerase chain reaction and western blot analysis were conducted to determine the expression of miR‐374, TYR, β‐catenin, B‐cell leukaemia 2 (Bcl‐2), Bcl‐2 associated X protein (Bax), Low‐density lipoprotein receptor‐related protein 6 (LRP6), Leucine‐rich repeat G protein‐coupled receptor 5 (LGR5) and CyclinD1. Cell proliferation, migration, invasion, cell cycle distribution and apoptosis were evaluated using cell counting kit‐8 assay, scratch test, transwell assay and flow cytometry respectively. TYR was proved as a putative target of miR‐374 as the evidenced by the result. It was observed that up‐regulated miR‐374 or down‐regulated TYR increased expression of Bax and decreased expressions of TYR, β‐catenin, LRP6, Bcl‐2, CyclinD1 and LGR5, along with diminished cell proliferation, migration, invasion and enhanced apoptosis. Meanwhile, cells with miR‐374 inhibitors showed an opposite trend. These findings indicated that up‐regulated miR‐374 could inhibit the expression of TYR to suppress cell proliferation, migration, invasion and promote cell apoptosis in melanoma cells by inhibiting the Wnt signalling pathway.

MiR-374a Activates Wnt/β-Catenin Signaling to Promote Osteosarcoma Cell Migration by Targeting WIF-1

MiR-374a was proved to take part in the initiation and development of several cancers. However, the molecular mechanism of miR-374a in osteosarcoma (OS) cells remains unclear. The aim of our research was to investigate the role of miR-374a in OS cells migration and clarify the potential mechanisms. Quantitative real-time PCR (qRT-PCR) and western blot analysis were applied to evaluate the expression of miR-374a and Wnt inhibitory factor-1 (WIF-1). Bioinformatical methods and luciferase reporter assay were carried out to predict and confirm the combination of miR-374a and WIF-1. Transwell and wound healing assays were performed to detect the migration capacity of OS cells. Lithium chloride (LiCl) was used to investigate the role of LiCl-activated Wnt/β-catenin signaling pathway in regulating cell migration. Our studies revealed that miR-374a was up-regulated whereas WIF-1 was down-regulated in OS cells. Besides, WIF-1 was the target of miR-374a by performing luciferase reporter assay. By transfection of miR-374a inhibitor and/or WIF-1 siRNA to OS cells, we found that miR-374a promoted the migration of OS cells. In addition, the inhibition of WIF-1 abolished the miR-374a inhibitor-induced migration suppression of OS cells. LiCl experiment revealed that miR-374a promoted OS cells migration by regulating Wnt/β-catenin signaling. In conclusion, miR-374a promotes OS cells migration by activating Wnt/β-catenin signaling pathway via targeting WIF-1.

Knockdown of arsenic resistance protein 2 inhibits human glioblastoma cell proliferation through the MAPK/ERK pathway

It is generally known that glioblastoma is the most common primary malignant brain tumor and that it is highly aggressive and deadly. Although surgical and pharmacological therapies have made long‑term progress, glioblastoma remains extremely lethal and has an uncommonly low survival rate. Therefore, further elucidation of the molecular mechanisms of glioblastoma initiation and its pathological processes are urgent. Arsenic resistance protein 2 (Ars2) is a highly conserved gene, and it has been found to play an important role in microRNA biosynthesis and cell proliferation in recent years. Furthermore, absence of Ars2 results in developmental death in Drosophila, zebrafish and mice. However, there are few studies on the role of Ars2 in regulating tumor development, and the mechanism of its action is mostly unknown. In the present study, we revealed that Ars2 is involved in glioblastoma proliferation and we identified a potential mechanistic role for it in cell cycle control. Our data demonstrated that Ars2 knockdown significantly repressed the proliferation and tumorigenesis abilities of glioblastoma cells in vitro and in vivo. Further investigation clarified that Ars2 deficiency inhibited the activation of the MAPK/ERK pathway, leading to cell cycle arrest in the G1 phase, resulting in suppression of cell proliferation. These findings support the conclusion that Ars2 is a key regulator of glioblastoma progression.

Prognostic value of microRNAs in lung cancer: A systematic review and meta-analysis

Lung cancer is one of the leading causes of cancer-associated mortality throughout the world. The prognosis of the disease depends on many factors including the stage and type of cancer. Many studies have identified various microRNAs (miRNAs) that affect the prognosis of lung cancer. In order to systemically analyze the available clinical data, the present study performed a meta-analysis to examine all evidence on the potential role of miRNAs as novel predictors of survival in lung cancer. Literature published in English prior to February 1st, 2018 was searched through PubMed to review all of the associations between individual miRNAs and groups of miRNAs with the prognosis of lung cancer. Data was extracted using standard forms and pooled odds ratios with 95% confidence intervals (CIs) were calculated. A total of 15 eligible studies were included in the meta-analysis. These represented 1,753 lung cancer patients and 20 miRNAs. A total of 8 downregulated miRNAs were associated with poorer overall survival (OS) [hazard ratio (HR)=0.59, 95% CI: 0.47–0.75, P<1×10⁻⁴], while 10 upregulated miRNAs were associated with poorer OS (HR=1.76, 95% CI: 1.31–2.35, P<1×10⁻⁴). Additionally, low miRNA expression was associated with lymph node metastasis [LNM; relative risk (RR)=0.53, 95% CI: 0.46–0.61, P<1×10⁻⁴]. The expression of miRNAs was not associated with lung cancer stage (RR=1.07, 95% CI: 0.94–1.22, P=0.23). Expression levels of different miRNAs were associated with the OS and LNM of patients with lung cancer. These miRNAs may be applied as potential prognostic markers in lung cancer.

Plasma small ncRNA pair panels as novel biomarkers for early-stage lung adenocarcinoma screening

Background

Lung cancer is a major cause of cancer-related mortality worldwide, and around two-thirds of patients have metastasis at diagnosis. Thus, detecting lung cancer at an early stage could reduce mortality. Aberrant levels of circulating small non-coding RNAs (small ncRNAs) are potential diagnostic or prognostic markers for lung cancer. We aimed to identify plasma small ncRNA pairs that could be used for early screening and detection of lung adenocarcinoma (LAC).

Results

A panel of seven small ncRNA pair ratios could differentiate patients with LAC or benign lung disease from high-risk controls with an area under the curve (AUC) of 100.0%, a sensitivity of 100.0% and a specificity of 100.0% at the training stage (which included 50 patients with early-stage LAC, 35 patients with benign diseases and 29 high-risk controls) and an AUC of 90.2%, a sensitivity of 91.5% and a specificity of 80.4% at the validation stage (which included 44 patients with early-stage LAC, 32 patients with benign diseases and 51 high-risk controls). The same panel could distinguish LAC from high-risk controls with an AUC of 100.0%, a sensitivity of 100.0% and a specificity of 100.0% at the training stage and an AUC of 89.5%, a sensitivity of 85.4% and a specificity of 83.3% at the validation stage. Another panel of five small ncRNA pair ratios (different from the first) was able to differentiate LAC from benign disease with an AUC of 82.0%, a sensitivity of 81.1% and a specificity of 78.1% in the training cohort and an AUC of 74.2%, a sensitivity of 70.4% and a specificity of 72.7% in the validation cohort.

Conclusions

Several small ncRNA pair ratios were identified as markers capable of discerning patients with LAC from those with benign lesions or high-risk control individuals.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4862-z) contains supplementary material, which is available to authorized users.

Lamins in Lung Cancer: Biomarkers and Key Factors for Disease Progression through miR-9 Regulation?

Lung cancer represents the primary cause of cancer death in the world. Malignant cells identification and characterization are crucial for the diagnosis and management of patients with primary or metastatic cancers. In this context, the identification of new biomarkers is essential to improve the differential diagnosis between cancer subtypes, to select the most appropriate therapy, and to establish prognostic correlations. Nuclear abnormalities are hallmarks of carcinoma cells and are used as cytological diagnostic criteria of malignancy. Lamins (divided into A- and B-types) are localized in the nuclear matrix comprising nuclear lamina, where they act as scaffolding protein, involved in many nuclear functions, with regulatory effects on the cell cycle and differentiation, senescence and apoptosis. Previous studies have suggested that lamins are involved in tumor development and progression with opposite results concerning their prognostic role. This review provides an overview of lamins expression in lung cancer and the relevance of these findings for disease diagnosis and prognosis. Furthermore, we discuss the link between A-type lamins expression in lung carcinoma cells and nuclear deformability, epithelial to mesenchymal transition, and metastatic potential, and which mechanisms could regulate A-type lamins expression in lung cancer, such as the microRNA miR-9.

Identification and verification of differentially expressed microRNAs and their target genes for the diagnosis of esophageal cancer

Bioinformatic tools were used to analyze GSE6188, GSE13937 and GSE43732 microarrays, and the top 10 upregulated and downregulated genes of each microarray were identified. It was determined that human microRNA (hsa-miR)-1 and hsa-miR-203 were two downregulated genes in common. Subsequently, it was identified that there were 145 and 335 genes in common targeted by hsa-miR-1 and hsa-miR-203, respectively. In order to narrow the number of target genes down further, the target genes were compared with GSE26886 microarray data. There were five upregulated genes in common with hsa-miR-1, i.e., MMD, BICD1, PTPRG, SDC2 and SEMA6D, and there were eight upregulated genes in common with hsa-miR-203, i.e., PXDN, NRCAM, FMNL2, EIF5A2, GLI3, FSL1, GREM1 and AHR. These genes may become promising biomarkers for the diagnosis of esophageal cancer.

Upregulation of miR-374a promotes tumor metastasis and progression by downregulating LACTB and predicts unfavorable prognosis in breast cancer

Breast cancer (BRCA) is the second leading cause of cancer-related death among female worldwide. Recent studies have revealed that LACTB was frequently repressed and functioned as a bona fide new tumor suppressor in a series of cancers, including BRCA. However, the molecular mechanisms underlying LACTB dysregulation in BRCA have not been reported. In the present study, we find that LACTB is repressed in BRCA and associated with poor prognosis by BRCA tissue microarray (TMA) analysis. Moreover, we confirm that LACTB is a direct target of miR-374a, which is significantly overexpressed and associated with malignancies in BRCA. Mechanistically, applying loss-of-function and gain-of-function approaches in a series of in vitro and in vivo experiments show that miR-374a knockdown suppresses the cell proliferative and colony formation activity, as well as migration and invasion capacity, but LACTB silencing in these cells reverses this change. Furthermore, we find that miR-374a silencing markedly reduces the tumor growth in xenograft mouse models. In summary, our findings suggest the miR-374a/LACTB axis plays a critical role in the tumorigenicity and progression of BRCA. miR-374a/LACTB axis may be a potential target in the development of therapeutic strategies for BRCA patients.

Validation of miRNA prognostic power in hepatocellular carcinoma using expression data of independent datasets

Multiple studies suggested using different miRNAs as biomarkers for prognosis of hepatocellular carcinoma (HCC). We aimed to assemble a miRNA expression database from independent datasets to enable an independent validation of previously published prognostic biomarkers of HCC. A miRNA expression database was established by searching the TCGA (RNA-seq) and GEO (microarray) repositories to identify miRNA datasets with available expression and clinical data. A PubMed search was performed to identify prognostic miRNAs for HCC. We performed a uni- and multivariate Cox regression analysis to validate the prognostic significance of these miRNAs. The Limma R package was applied to compare the expression of miRNAs between tumor and normal tissues. We uncovered 214 publications containing 223 miRNAs identified as potential prognostic biomarkers for HCC. In the survival analysis, the expression levels of 55 and 84 miRNAs were significantly correlated with overall survival in RNA-seq and gene chip datasets, respectively. The most significant miRNAs were hsa-miR-149, hsa-miR-139, and hsa-miR-3677 in the RNA-seq and hsa-miR-146b-3p, hsa-miR-584, and hsa-miR-31 in the microarray dataset. Of the 223 miRNAs studied, the expression was significantly altered in 102 miRNAs in tumors compared to normal liver tissues. In summary, we set up an integrated miRNA expression database and validated prognostic miRNAs in HCC.

miR-196b promotes lung cancer cell migration and invasion through the targeting of GATA6

MicroRNAs (miRNAs) have been proven to regulate gene expression at the protein translation level. miRNA abnormal expression has been associated with the development of lung cancer. In the present study, we aimed to investigate the mechanism of miR-196 in non-small cell lung cancer (NSCLC). The miR-196b and GATA-6 (GATA6) expression levels were examined in NSCLC by RT-qPCR and western blot analysis. Transwell assay was used to assess cell migration and invasion. Moreover, the specific target of miR-196b in NSCLC was verified by the luciferase reporter assay. The expression of miR-196b was higher in both NSCLC tissues and cells than the normal levels. Specifically, the miR-196b mimic group in NSCLC cells markedly promoted cell migration and invasion, while the miR-196b inhibitor group exhibited the opposite effect. Furthermore, GATA6 was verified as a specific target of miR-196b in NSCLC cells and GATA6 could attenuate the migratory and invasive ability of NSCLC cells regulated by miR-196b. In addition, the relationship between GATA6 and miR-196b expression was negatively correlated in NSCLC tissues. Thus, miR-196b enhanced NSCLC cell migration and invasion via the downregulation of GATA6, indicating its potential application in NSCLC diagnosis and therapy.

Long-Term Cigarette Smoke Exposure and Changes in MiRNA Expression and Proteome in Non-Small-Cell Lung Cancer

Chronic exposure to cigarette smoke markedly increases the risk for lung cancer. Regulation of gene expression at the post-transcriptional level by miRNAs influences a variety of cancer-related interactomes. Yet, relatively little is known on the effects of long-term cigarette smoke exposure on miRNA expression and gene regulation. NCI-H292 (H292) is a cell line sensitive to cigarette smoke with mucoepidermoid characteristics in culture. We report, in this study, original observations on long-term (12 months) cigarette smoke effects in the H292 cell line, using microarray-based miRNA expression profiling, and stable isotopic labeling with amino acids in cell culture-based quantitative proteomic analysis. We identified 112 upregulated and 147 downregulated miRNAs (by twofold) in cigarette smoke-treated H292 cells. The liquid chromatography-tandem mass spectrometry analysis identified 3,959 proteins, of which, 303 proteins were overexpressed and 112 proteins downregulated (by twofold). We observed 39 miRNA target pairs (proven targets) that were differentially expressed in response to chronic cigarette smoke exposure. Gene ontology analysis of the target proteins revealed enrichment of proteins in biological processes driving metabolism, cell communication, and nucleic acid metabolism. Pathway analysis revealed the enrichment of phagosome maturation, antigen presentation pathway, nuclear factor erythroid 2-related factor 2-mediated oxidative stress response, and cholesterol biosynthesis pathways in cigarette smoke-exposed cells. In conclusion, this report makes an important contribution to knowledge on molecular changes in a lung cell line in response to long term cigarette smoke exposure. The findings might inform future strategies for drug target, biomarker and diagnostics innovation in lung cancer, and clinical oncology. These observations also call for further research on the extent to which continuing or stopping cigarette smoking in patients diagnosed with lung cancer translates into molecular and clinical outcomes.

Non-small cell lung cancer associated microRNA expression signature: integrated bioinformatics analysis, validation and clinical significance

Recently, increasing studies of miRNA expression profiling has confirmed that miRNA plays an essential role in non-small cell lung cancer (NSCLC). However, inconsistent or discrepant results exist in these researches. In present study, we performed an integrative analysis of 32 miRNA profiling studies compared the differentially expressed miRNA between NSCLC tissue and non-cancerous lung tissue to identify candidate miRNAs associated with NSCLC. 7 upregulated and 10 downregulated miRNAs were identified as miRNA integrated-signature using Robust Rank Aggregation (RRA) method. qRT-PCR demonstrated that miR-21-5p, miR-210, miR-205-5p, miR-182-5p, miR-31-5p, miR-183-5p and miR-96-5p were up-regulated, whereas miR-126-3p, miR-30a-5p, miR-451a, miR-143-3p and miR-30d-5p were down-regulated more than 2 folds in the NSCLC, which was further validated in Tumor Cancer Genome Atlas (TCGA) database. Receiver operating characteristic (ROC) curve analysis confirmed that 9 miRNAs had good predictive performance (AUC > 0.9). Cox regression analysis revealed that miR-21-5p (hazard ratio [HR]: 1.616, 95% CI: 1.114–2.342, p = 0.011) and miR-30d-5p (HR: 0.578, 95% CI: 0.400–0.835, p = 0.003) were independent prognostic factors in NSCLC for overall survival. The accumulative effects of the two miRNAs on the prognosis of NSCLC were further estimated. The results showed that patients with two positive markers had a worse prognosis than those with one or none positive marker. In conclusion, this study contributes to the comprehension of the role of miRNAs in NSCLC and provides a basis for further clinical application.

Evaluation of Bioinformatics Approaches for Next-Generation Sequencing Analysis of microRNAs with a Toxicogenomics Study Design

MicroRNAs (miRNAs) are key post-transcriptional regulators that affect protein translation by targeting mRNAs. Their role in disease etiology and toxicity are well recognized. Given the rapid advancement of next-generation sequencing techniques, miRNA profiling has been increasingly conducted with RNA-seq, namely miRNA-seq. Analysis of miRNA-seq data requires several steps: (1) mapping the reads to miRBase, (2) considering mismatches during the hairpin alignment (windowing), and (3) counting the reads (quantification). The choice made in each step with respect to the parameter settings could affect miRNA quantification, differentially expressed miRNAs (DEMs) detection and novel miRNA identification. Furthermore, these parameters do not act in isolation and their joint effects impact miRNA-seq results and interpretation. In toxicogenomics, the variation associated with parameter setting should not overpower the treatment effect (such as the dose/time-dependent effect). In this study, four commonly used miRNA-seq analysis tools (i.e., miRDeep2, miRExpress, miRNAkey, sRNAbench) were comparatively evaluated with a standard toxicogenomics study design. We tested 30 different parameter settings on miRNA-seq data generated from thioacetamide-treated rat liver samples for three dose levels across four time points, followed by four normalization options. Because both miRExpress and miRNAkey yielded larger variation than that of the treatment effects across multiple parameter settings, our analyses mainly focused on the side-by-side comparison between miRDeep2 and sRNAbench. While the number of miRNAs detected by miRDeep2 was almost the subset of those detected by sRNAbench, the number of DEMs identified by both tools was comparable under the same parameter settings and normalization method. Change in the number of nucleotides out of the mature sequence in the hairpin alignment (window option) yielded the largest variation for miRNA quantification and DEMs detection. However, such a variation is relatively small compared to the treatment effect when the study focused on DEMs that are more critical to interpret the toxicological effect. While the normalization methods introduced a large variation in DEMs, toxic behavior of thioacetamide showed consistency in the trend of time-dose responses. Overall, miRDeep2 was found to be preferable over other choices when the window option allowed up to three nucleotides from both ends.

A 10‑microRNA prognosis scoring system in esophageal squamous cell carcinoma constructed using bioinformatic methods

MicroRNA (miR) signatures may aid the diagnosis and prediction of cancer; therefore, miRs associated with the prognosis of esophageal squamous cell carcinoma (ESCC) were screened. miR‑sequencing (seq) and mRNA‑seq data from early‑stage ESCC samples were downloaded from The Cancer Genome Atlas (TCGA) database, and samples from subjects with a >6‑month survival time were assessed with Cox regression analysis for prognosis‑associated miRs. A further two miR expression datasets of ESCC samples, GSE43732 and GSE13937, were downloaded from the Gene Expression Omnibus database. Common miRs between prognosis‑associated miRs, and miRs in the GSE43732 and GSE13937, datasets were used for risk score calculations for each sample, and median risk scores were applied for the stratification of low‑ and high‑risk samples. A prognostic scoring system of signature miRs was subsequently constructed and used for survival analysis for low‑ and high‑risk samples. Differentially‑expressed genes (DEGs) corresponding to all miRs were screened and functional annotation was performed. A total of 34 prognostic miRs were screened and a scoring system was created using 10 signature miRs (hsa‑miR‑140, ‑33b, ‑34b, ‑144, ‑486, ‑214, ‑129‑2, ‑374a and ‑412). Using this system, low‑risk samples were identified to be associated with longer survival compared with high‑risk samples in the TCGA and GSE43732 datasets. Age, alcohol and tobacco use, and radiotherapy were prognostic factors for samples with different risk scores and the same clinical features. There were 168 DEGs, and the top 20 risk scores positively‑correlated and the top 20 risk scores negatively‑correlated DEGs were significantly enriched for six and 10 functional terms, respectively. 'Tight junction' and 'melanogenesis' were two significantly enriched pathways of DEGs. miR‑214, miR‑129‑2, miR‑37a and miR‑486 may predict ESCC patient survival, although further studies to validate this hypothesis are required.

Dual roles of miR-374a by modulated c-Jun respectively targets CCND1-inducing PI3K/AKT signal and PTEN-suppressing Wnt/β-catenin signaling in non-small-cell lung cancer

MiR-374a appears to play a complex role in non-small-cell lung cancer (NSCLC). Here, we demonstrate a dual role for miR-374a in NSCLC pathogenesis. The effects and modulatory mechanisms of miR-374a on cell growth, migration, invasion, and in vivo tumorigenesis and metastasis in nude mice were also analyzed. The expression of miR-374a was examined in NSCLC and non-cancerous lung tissues by quantitative real-time reverse transcription-PCR (qRT-PCR), and in situ hybridization, respectively. miR-374a directly targets CCND1 and inactivates PI3K/AKT and Ras-mediated cell cycle signalings, as well as epithelial–mesenchymal transition (EMT). This not only dramatically suppressed cell growth, migration, invasion,and metastasis, but also elevated A549 and pc-9 NSCLC cell sensitivity to cisplatin (DDP) while increasing survival time of tumor-bearing mice. Interestingly, miR-374a serves an inverse function in SPCA-1 and H1975 NSCLC cells by directly targeting PTEN to activate Wnt/β-catenin and Ras signalings and its downstream cascade signals. Surprisingly, transcription factor c-Jun bound to the promoter region of human miR-374a and suppressed miR-374a in A549 and pc-9 cells while inducing it in SPCA-1 and H1975 cells. Increased levels of miR-374a appeared to serve a protective role by targeting CCND1 in early-stage NSCLC (Stages I and II). Inversely, increased miR-374a was an unfavorable factor when targeting PTEN in more advanced staged NSCLC patients. Our studies are the first to demonstrate that miR-374a plays divergent roles in NSCLC pathogenesis at different stages of the disease and implicate the potential application of miR-374a targeting for cancer therapy.

Protective Effect of miR-374a on Chemical Hypoxia-Induced Damage of PC12 Cells In Vitro via the GADD45α/JNK Signaling Pathway

To explore the effect of microRNA-374a (miR-374a) on chemical hypoxia-induced pheochromocytoma (PC12) cell damage by mediating growth arrest and the DNA damage-45 alpha (GADD45α)/c-Jun N-terminal kinase (JNK) signaling pathway. PC12 cells were divided into a Control group (no treatment), Model group (treated with CoCl₂ for 24 h), negative control (NC) group (transfected with miR-374a negative control sequence and treated with CoCl₂ for 24 h), and miR-374a mimic group (transfected with miR-374a mimics and treated with CoCl₂ for 24 h). The viability and apoptosis of PC12 cells were determined by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) assay and flow cytometry, while the mitochondrial membrane potential (MMP) and reactive oxygen species (ROS) content were assessed by Rh123 and dichloro-dihydro-fluorescein diacetate (DCFH-DA) methods. The expression of miR-374a and GADD45α/JNK proteins was detected using quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and Western blot. A significant decrease was found in the survival rate, MMP and miR-374a expression, while an increase was shown in the ROS content and GADD45α and p-JNK expression in hypoxic PC12 cells (all P < 0.05). A luciferase reporter gene assay demonstrated that GADD45α is the target gene of miR-374a. When transfected with miR-374a mimics, hypoxic PC12 cells showed an obvious elevation in survival rate and MMP but a great reduction in cell apoptosis and ROS content, as well as in the expression of GADD45α and p-JNK proteins (all P < 0.05). MiR-374a can protect PC12 cells against hypoxia-induced injury by inhibiting the GADD45α/JNK pathway, enhancing cell viability, suppressing oxidative stress, and inhibiting cell apoptosis, thereby becoming a potential therapeutic target for hypoxic damage.

TGF-β1-induced epithelial-mesenchymal transition in lung cancer cells involves upregulation of miR-9 and downregulation of its target, E-cadherin

Background

TGF-β1 plays an important role in the epithelial-mesenchymal transition (EMT) of epithelial cancers, including non-small cell lung cancer (NSCLC). While the full underlying mechanism remains unclear, miR-9 is known to play a critical role in the regulation of NSCLC cell invasion. We tested whether miR-9 targets E-cadherin and thus affects TGF-β1-induced EMT in NSCLC cells by assessing the expression levels of miR-9 and E-cadherin for NSCLC patients and then verifying the targeting of E-cadherin by miR-9 using the dual luciferase reporter system.

Results

MiR-9 was significantly upregulated in NSCLC tissues compared with its level in adjacent normal tissues. The expression of E-cadherin in NSCLC tissues was significantly decreased. In addition, we found that TGF-β1 significantly upregulated the expression of miR-9 and downregulated the expression of E-cadherin. E-cadherin was confirmed as a direct target gene of miR-9. Using an miR-9 inhibitor reversed the TGF-β1-mediated inhibition of E-cadherin expression and upregulation of the mesenchymal marker α-SMA. TGF-β1 significantly induced cell invasion, and this effect was significantly inhibited by miR-9 inhibitors.

Conclusions

TGF-β1 induced EMT in NSCLC cells by upregulating miR-9 and downregulating miR-9's target, E-cadherin.