Differential expression profiles of microRNAs as potential biomarkers for the early diagnosis of lung cancer

Differential gene expression analysis and machine learning identified structural, TFs, cytokine and glycoproteins, including SOX2, TOP2A, SPP1, COL1A1, and TIMP1 as potential drivers of lung cancer

BACKGROUND

Lung cancer is a primary global health concern, responsible for a considerable portion of cancer-related fatalities worldwide. Understanding its molecular complexities is crucial for identifying potential targets for treatment. The goal is to slow disease progression and intervene early to prevent the development of advanced lung cancer cases. Hence, there's an urgent need for new biomarkers that can detect lung cancer in its early stages.

METHODS

The study conducted RNA-Seq analysis of lung cancer samples from the publicly available SRA database (NCBI SRP009408), including both control and tumour samples. The genes with differential expression between tumour and healthy tissues were identified using R and Bioconductor. Machine learning (ML) techniques, Random Forest, Lasso, XGBoost, Gradient Boosting and Elastic Net were employed to pinpoint significant genes followed by classifiers, Multilayer Perceptron (MLP), Support Vector Machines (SVM) and k-Nearest Neighbours (k-NN). Gene ontology and pathway analyses were performed on the significant differentially expressed genes (DEGs). The top genes from DEG and machine learning analyses were combined for protein-protein interaction (PPI) analysis, identifying 10 hub genes essential for lung cancer progression.

RESULTS

The integrated analysis of ML and DEGs revealed the significance of specific genes in lung cancer samples, identified the top 5 upregulated genes (COL11A1, TOP2A, SULF1, DIO2, MIR196A2) and the top 5 downregulated genes (PDK4, FOSB, FLYWCH1, CYB5D2, MIR328), along with their associated genes implicated in pathways or co-expression networks were identified. Among the various algorithms employed, Random Forest and XGBoost proved effective in identifying common genes, underscoring their potential significance in lung cancer pathogenesis. The MLP exhibited the highest accuracy in classifying samples using all genes. Additionally, the protein-protein interaction (PPI) analysis identified 10 hub genes that are pivotal in lung cancer pathogenesis: COL1A1, SOX2, SPP1, THBS2, POSTN, COL5A1, COL11A1, TIMP1, TOP2A and PKP1.

CONCLUSION

The study contributes to the early prediction of lung cancer by identifying potential biomarkers that could enhance early diagnosis and pave the way for practical clinical applications in the future. Integrating DEGs and machine learning-derived significant genes for PPI analysis offers a robust approach to uncovering critical molecular targets for lung cancer treatment.

Production of novel theranostic nano-vector based on superparamagnetic iron oxide nanoparticles/miR-497 targeting colorectal cancer

Colorectal cancer (CRC) is a serious public health concern worldwide. Immune checkpoint inhibition medication is likely to remain a crucial part of CRC clinical management. This study aims to create new super paramagnetic iron oxide nano-carrier (SPION) that can effectively transport miRNA to specific CRC cell lines. In addition, evaluate the efficiency of this nano-formulation as a therapeutic candidate for CRC. Bioinformatics tools were used to select a promising tumor suppressor miRNA (mir-497-5p). Green route, using Fusarium oxyporium fungal species, manipulated for the synthesis of SPION@Ag@Cs nanocomposite as a carrier of miR-497-5p. That specifically targets the suppression of PD1/PDL1 and CTLA4pathways for colorectal therapy. UV/visible and FTIR spectroscopy, Zeta potential and MTT were used to confirm the allocation of the miR-497 on SPION@Ag@Cs and its cytotoxicity against CRC cell lines. Immunofluorescence was employed to confirm transfection of cells with miR-497@NPs, and the down- regulation of CTLA4 in HT29, and Caco2 cell lines. On the other hand, PDL1 showed a significant increase in colorectal cell lines (HT-29 and Caco-2) in response to mir497-5p@Nano treatment. The data suggest that the mir-497 -loaded SPION@Ag@Cs nano-formulation could be a good candidate for the suppression of CTLA4in CRC human cell lines. Consequently, the targeting miR-497/CTLA4 axis is a potential immunotherapy treatment strategy for CRC.

MicroRNAs as Potential Biomarkers of Environmental Exposure to Polycyclic Aromatic Hydrocarbons and Their Link with Inflammation and Lung Cancer

Exposure to atmospheric air pollution containing volatile organic compounds such as polycyclic aromatic hydrocarbons (PAHs) has been shown to be a risk factor in the induction of lung inflammation and the initiation and progression of lung cancer. MicroRNAs (miRNAs) are small single-stranded non-coding RNA molecules of ~20-22 nucleotides that regulate different physiological processes, and their altered expression is implicated in various pathophysiological conditions. Recent studies have shown that the regulation of gene expression of miRNAs can be affected in diseases associated with outdoor air pollution, meaning they could also be useful as biomarkers of exposure to environmental pollution. In this article, we review the published evidence on miRNAs in relation to exposure to PAH pollution and discuss the possible mechanisms that may link these compounds with the expression of miRNAs.

Aberrant Methylation of the Imprinted C19MC and MIR371-3 Clusters in Patients with Non-Small Cell Lung Cancer

Epigenetic mechanisms have emerged as an important contributor to tumor development through the modulation of gene expression. Our objective was to identify the methylation profile of the imprinted C19MC and MIR371-3 clusters in patients with non-small cell lung cancer (NSCLC) and to find their potential target genes, as well as to study their prognostic role. DNA methylation status was analyzed in a NSCLC patient cohort (n = 47) and compared with a control cohort including COPD patients and non-COPD subjects (n = 23) using the Illumina Infinium Human Methylation 450 BeadChip. Hypomethylation of miRNAs located on chromosome 19q13.42 was found to be specific for tumor tissue. We then identified the target mRNA-miRNA regulatory network for the components of the C19MC and MIR371-3 clusters using the miRTargetLink 2.0 Human tool. The correlations of miRNA-target mRNA expression from primary lung tumors were analyzed using the CancerMIRNome tool. From those negative correlations identified, we found that a lower expression of 5 of the target genes (FOXF2, KLF13, MICA, TCEAL1 and TGFBR2) was significantly associated with poor overall survival. Taken together, this study demonstrates that the imprinted C19MC and MIR371-3 miRNA clusters undergo polycistronic epigenetic regulation leading to deregulation of important and common target genes with potential prognostic value in lung cancer.

M2 macrophages-derived exosomal miR-3917 promotes the progression of lung cancer via targeting GRK6

Macrophages in the tumor microenvironment (TME) can serve as potential targets for therapeutic intervention. The aim of this study was to investigate the molecular mechanism by which M2 macrophage-derived exosomes (M2-Ex) affect lung cancer progression through miRNA transport. The THP-1 cells were differentiated into M0 and M2 macrophages. M2-Ex were isolated and identified by transmission electron microscopy (TEM) and nanoparticle tracking analysis (NTA). Cancer tissues and adjacent tissues of non-small-cell lung cancer (NSCLC) patients were collected. H1299 and A549 cells were co-cultured with M2-Ex. Subcutaneous xenograft mouse model was established. miR-3917 is highly expressed in lung cancer tissues and M2-Ex. Interference of miR-3917 in M2-Ex inhibits H1299 cell proliferation, migration and invasion, while overexpression of miR-3917 had the opposite effect in A549 cells. M2-Ex promote tumor growth by delivering miR-3917 in vivo. miR-3917 could target G protein-coupled receptor kinase 6 (GRK6), and interference of miR-3917 in M2-Ex inhibits H1299 cells proliferation, migration and invasion by up-regulating GRK6 level, while overexpression of miR-3917 had the opposite effect in A549 cells. M2-Ex can transfer miR-3917 into lung cancer cells and promote lung cancer progression, providing theoretical basis for the diagnosis and effective treatment of lung cancer.

A feature selection-based framework to identify biomarkers for cancer diagnosis: A focus on lung adenocarcinoma

Lung cancer (LC) represents most of the cancer incidences in the world. There are many types of LC, but Lung Adenocarcinoma (LUAD) is the most common type. Although RNA-seq and microarray data provide a vast amount of gene expression data, most of the genes are insignificant to clinical diagnosis. Feature selection (FS) techniques overcome the high dimensionality and sparsity issues of the large-scale data. We propose a framework that applies an ensemble of feature selection techniques to identify genes highly correlated to LUAD. Utilizing LUAD RNA-seq data from the Cancer Genome Atlas (TCGA), we employed mutual information (MI) and recursive feature elimination (RFE) feature selection techniques along with support vector machine (SVM) classification model. We have also utilized Random Forest (RF) as an embedded FS technique. The results were integrated and candidate biomarker genes across all techniques were identified. The proposed framework has identified 12 potential biomarkers that are highly correlated with different LC types, especially LUAD. A predictive model has been trained utilizing the identified biomarker expression profiling and performance of 97.99% was achieved. In addition, upon performing differential gene expression analysis, we could find that all 12 genes were significantly differentially expressed between normal and LUAD tissues, and strongly correlated with LUAD according to previous reports. We here propose that using multiple feature selection methods effectively reduces the number of identified biomarkers and directly affects their biological relevance.

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.

Serum miR-27a is a biomarker for the prognosis of non-small cell lung cancer patients receiving chemotherapy

BACKGROUND

Lung cancer has a high incidence and a 5-year survival rate of less than 15%. Non-small cell lung cancer (NSCLC) accounts for approximately 85% of lung cancer cases. Chemotherapy and immunotherapy are the most frequently used alternative treatments for patients with advanced-stage NSCLC in whom surgery failed. Previous studies have suggested that miR-27a is involved in cancer development and progression. The purpose of this study was to investigate the clinical value of miR-27a in the prognosis of NSCLC patients after chemotherapy.

METHODS

Flow cytometry was used to detect the apoptosis rate of SPC-A1 cells treated with optical cisplatin at different times. Simultaneously, the expression of miR-27a in supernatants and cells was detected. Fifty-two newly diagnosed NSCLC patients were recruited. All patients received gemcitabine and cisplatin as first-line chemotherapy and docetaxel as second-line chemotherapy. At the end of every chemotherapy cycle, a therapeutic evaluation was performed according to the RECIST criteria. The expression of serum miR-27a was detected in each cycle.

RESULTS

After treatment with 2.5 µg/mL cisplatin, the apoptosis rates of SPC-A1 cells were significantly greater than those of the paired untreated control groups at 12, 24, 48 and 72 h. The expression of miR-27a in supernatants and cells was also consistent with the apoptosis rate and changed a time-dependent manner. The chi-square test showed that an increase in miR-27a after chemotherapy was more common in patients who achieved partial response (PR) than in those who achieved no response (NR) (61.5% vs. 30.8%, P=0.026). Kaplan-Meier survival analysis indicated that patients with decreased miR-27a levels had poorer outcomes than those with increased miR-27a levels (P<0.05). Furthermore, dynamic changes in serum miR-27a with a gradual increasing trend during chemotherapy predicted a good prognosis.

CONCLUSIONS

Collectively, our results suggest that miR-27a is involved in the apoptosis of lung cancer cells and that serum miR-27a levels are related to the prognosis of NSCLC patients. The expression levels of miR-27a in the serum may be an independent predictor for the prognosis of NSCLC.

miR-30d-5p: A Non-Coding RNA With Potential Diagnostic, Prognostic and Therapeutic Applications

Cancer is a great challenge facing global public health. Scholars have made plentiful efforts in the research of cancer therapy, but the results are still not satisfactory. In relevant literature, the role of miRNA in cancer has been widely concerned. MicroRNAs (miRNAs) are a non-coding, endogenous, single-stranded RNAs that regulate a variety of biological functions. The abnormal level of miR-30d-5p, a type of miRNAs, has been associated with various human tumor types, including lung cancer, colorectal cancer, esophageal cancer, prostate cancer, liver cancer, cervical cancer, breast cancer and other types of human tumors. This reflects the vital function of miR-30d-5p in tumor prognosis. miR-30d-5p can be identified either as an inhibitor hindering the development of, or a promoter accelerating the occurrence of tumors. In addition, the role of miR-30d-5p in cell proliferation, motility, apoptosis, autophagy, tumorigenesis, and chemoresistance are also noteworthy. The multiple roles of miR-30d-5p in human cancer suggest that it has broad feasibility as a biomarker and therapeutic target. This review describes the connection between miR-30d-5p and the clinical indications of tumors, and summarizes the mechanisms by which miR-30d-5p mediates cancer progression.

MiR-205-5p promotes lung cancer progression and is valuable for the diagnosis of lung cancer

BACKGROUND

MicroRNAs (miRNAs) function as potential diagnostic biomarkers in various cancers. This study aimed to evaluate the roles of miR-205-5p in lung cancer progression and diagnosis.

MATERIALS AND METHODS

MiR-205-5p was detected by quantitative real-time PCR. The effect of miR-205-5p on cell proliferation and metastasis was estimated by MTT and flow cytometry. The expression of TP53INP1 and related genes was analyzed by immunoblotting. The diagnostic value of miR-205-5p was analyzed using receiver operating characteristic (ROC) curve analysis, sensitivity, and specificity.

RESULTS

The miR-205-5p was increased in lung cancer tissues. MiR-205-5p mimics were promoted but its inhibitor suppressed cell proliferation and metastasis compared with control treatment in vitro and in vivo. By regulating the 3' untranslated region, miR-205-5p could negatively regulate TP53INP1 expression, which further inhibited the expression of RB1 and P21, but increased that of cyclinD1. Moreover, the serum miR-205-5p levels of patients with lung cancer were significantly higher than those of normal controls, and they were correlated with patients' gender, drinking status, and clinical stage. The area under the ROC curve of serum miR-205-5p in the diagnosis of non-small-cell lung cancer was 0.8250, respectively. The finding supported its possession of high diagnostic efficiency for lung cancer.

CONCLUSIONS

MiR-205-5p promoted lung cancer cell proliferation and metastasis by negatively regulating the novel target TP53INP1, which further affected the expression of P21, RB1, and cyclin D1. Serum miR-205-5p is a novel and valuable biomarker for lung cancer diagnosis.

MicroRNA-326 impairs chemotherapy resistance in non small cell lung cancer by suppressing histone deacetylase SIRT1-mediated HIF1α and elevating VEGFA

Compelling evidence has implicated the role of microRNAs (miRs or miRNAs) in lung cancer. Sirtuin-1 (SIRT1) is key contributor to the progression of non small cell lung cancer (NSCLC). This study was intended to investigate whether miR-326 affected NSCLC associated with SIRT1. miR-326 and SIRT1 expression in H460 cells and chemoresistant cells H460-R was measured by RT-qPCR. Dual luciferase reporter gene assay and RIP assay were used to identify and validate the relationship between miR-326 and SIRT1. Using gain- and loss-of-function approaches, we evaluated their effects on the chemoresistance of NSCLC cells. ChIP assay was used to detect binding of SIRT1 to the promoter of HIF1α gene, and the binding H3K9Ac to HIF1α, binding of H3K9Ac and HIF1α after silencing SIRT1, and binding HIF1α to VEGFA promoter. In vivo experiments were performed to validate the in vitro findings. MiR-326 expression was decreased while SIRT1 expression was increased in NSCLC cells. SIRT1 was a target of miR-326. MiR-326 inhibited the proliferation of chemotherapy-resistant NSCLC cells and promoted their apoptosis by suppressing SIRT1. In addition, SIRT1 promoted chemoresistance of NSCLC cell by elevating VEGFA expression. Through this mechanism, miR-326 reduced the chemoresistance, which was validated in vivo. Taken together, miR-326 represses SIRT1 through impeding HIF1α expression, thus hindering chemotherapy resistance in lung cancer. These findings provide an exquisite therapeutic target for NSCLC.

Prognostic value of microRNA-4521 in non-small cell lung cancer and its regulatory effect on tumor progression

Background

Non-small cell lung cancer (NSCLC) is a malignant tumor with the highest mortality rate in our country. It has been found in many studies that microRNA-4521 (miR-4521) is abnormally expressed and plays a role in clear cell renal cell carcinoma and other cancers.

Objective

The purpose of this study was to explore the relationship between miR-4521 expression and clinical prognosis, as well as its influence on cell biological behavior.

Methods

The expression differences of miR-4521 in NSCLC tissues and cells were examined by qRT-PCR technology. Kaplan–Meier survival analysis and Cox regression analysis were used to analyze the clinical information and survival status of patients to explore the relationship. Using the vitro cell MTT assay, Transwell assay, and western-blot analysis, the effects of miR-4521 on cell proliferation, migration, and invasion were analyzed.

Results

The expression of miR-4521 in NSCLC tissues and cells was significantly downregulated. miR-4521 can be used as an independent prognostic factor. The survival rate of the miR-4521 low expression group was lower, which was significantly related to poor prognosis. In addition, the low expression of miR-4521 significantly promoted cell proliferation, migration, and invasion with highly expressed related protein levels. FOXM1 might be a direct target of miR-4521.

Conclusion

The results of this study showed that the low expression of miR-4521 indicated the poor prognosis of NSCLC and promoted cell proliferation, migration, and invasion by targeting FOXM1.

Peptide Nucleic Acid-Functionalized Nanochannel Biosensor for the Highly Sensitive Detection of Tumor Exosomal MicroRNA

Compared with free miRNAs in blood, miRNAs in exosomes have higher abundance and stability. Therefore, miRNAs in exosomes can be regarded as an ideal tumor marker for early cancer diagnosis. Here, a peptide nucleic acid (PNA)-functionalized nanochannel biosensor for the ultrasensitive and specific detection of tumor exosomal miRNAs is proposed. After PNA was covalently bound to the inner surface of the nanochannels, the detection of tumor exosomal miRNAs was achieved by the charge changes on the surface of nanochannels before and after hybridization (PNA-miRNA). Due to the neutral characteristics of PNA, the efficiency of PNA-miRNA hybridization was improved by significantly reducing the background signal. This biosensor could not only specifically distinguish target miRNA-10b from single-base mismatched miRNA but also achieve a detection limit as low as 75 aM. Moreover, the biosensor was further used to detect exosomal miRNA-10b derived from pancreatic cancer cells and normal pancreatic cells. The results indicate that this biosensor could effectively distinguish pancreatic cancer tumor-derived exosomes from the normal control group, and the detection results show good consistency with those of the quantitative reverse-transcription polymerase chain reaction method. In addition, the biosensor was used to detect exosomal miRNA-10b in clinical plasma samples, and it was found that the content of exosomal miRNA-10b in cancer patients was generally higher than that of healthy individuals, proving that the method is expected to be applied for the early diagnosis of cancer.

miR-934 promotes breast cancer metastasis by regulation of PTEN and epithelial-mesenchymal transition

Breast cancer (BC) is the most commonly diagnosed malignancy and the leading cause of cancer-related mortality among females. Over 90 % of the cases of death in BC patients are attributed to tumor cell metastasis. Therefore, it is urgently needed to investigate the molecular mechanisms of BC metastasis. The expression of miRNA in BC was evaluated by qRT-PCR and bioinformatics analysis. Clone formation, EdU assays, and subcutaneous xenograft model were used to test the growth of BC cells. Wound healing, transwell assays, and lung-metastasis model were used to explore the effect of miR-934 knockdown on cell metastasis. The miR-934 targets in BC were identified through bioinformatics analysis and luciferase reporter assays. The expression of protein was tested by western blot. The binding of mRNA and RNA-binding-protein was verified using RIP assays. miR-934 expression was significantly elevated in BC tissues, especially in those with lymph node metastasis and associated with poor patient prognosis. Experiments in vitro and in vivo showed that that upregulated miR-934 was not necessarily required for the growth of BC cells. However, miR-934 knockdown significantly inhibited the migration and invasion abilities of BC cells. Moreover, PTEN as identified as the direct target of miR-934 in BC, and miR-934 could promote BC cell metastasis by regulation of PTEN and epithelial-mesenchymal transition (EMT). Our results suggested that targeting miR-934 may be a practical treatment for BC cell metastasis.

The Role of MicroRNAs in Lung Cancer: Implications for Diagnosis and Therapy

Lung cancer is the first cause of cancer death in the world due to its high prevalence, aggressiveness, late diagnosis, lack of effective treatment and poor prognosis. It also shows high rate of recurrence, metastasis and drug resistance. All these problems highlight the urgent needs for developing new strategies using noninvasive biomarkers for early detection, metastasis and recurrence of disease. MicroRNAs (miRNAs) are a class of small noncoding RNAs that regulate gene expression post-transcriptionally. These molecules found to be abnormally expressed in increasing number of human disease conditions including cancer. miRNAs could be detected in body fluids such as blood, serum, urine and sputum, which leads us towards the idea of using them as non-invasive biomarker for cancer detection and monitoring cancer treatment and recurrence. miRNAs are found to be deregulated in lung cancer initiation and progression and could regulate lung cancer cell proliferation and invasion. In this review, we summarized recent progress and discoveries in microRNAs regulatory role in lung cancer initiation and progression. In addition, the role of microRNAs in EGFR signaling pathway regulation is discussed briefly.

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.

Recognizing lung cancer and stages using a self-developed electronic nose system

Exhaled breath contains thousands of gaseous volatile organic compounds (VOCs) that could be used as non-invasive biomarkers of lung cancer. Breath-based lung cancer screening has attracted wide attention on account of its convenience, low cost and easy popularization. In this paper, the research of lung cancer detection and staging is conducted by the self-developed electronic nose (e-nose) system. In order to investigate the performance of the device in distinguishing lung cancer patients from healthy controls, two feature extraction methods and two different classification models were adopted. Among all the models, kernel principal component analysis (KPCA) combined with extreme gradient boosting (XGBoost) achieved the best results among 235 breath samples. The accuracy, sensitivity and specificity of e-nose system were 93.59%, 95.60% and 91.09%, respectively. Meanwhile, the device could innovatively classify stages of 90 lung cancer patients (i.e., 44 stage III and 46 stage IV). Experimental results indicated that the recognition accuracy of lung cancer stages was more than 80%. Further experiments of this research also showed that the combination of sensor array and pattern recognition algorithms could identify and distinguish the expiratory characteristics of lung cancer, smoking and other respiratory diseases.

High heterogeneity undermines generalization of differential expression results in RNA-Seq analysis

BACKGROUND

RNA sequencing (RNA-Seq) has been widely applied in oncology for monitoring transcriptome changes. However, the emerging problem that high variation of gene expression levels caused by tumor heterogeneity may affect the reproducibility of differential expression (DE) results has rarely been studied. Here, we investigated the reproducibility of DE results for any given number of biological replicates between 3 and 24 and explored why a great many differentially expressed genes (DEGs) were not reproducible.

RESULTS

Our findings demonstrate that poor reproducibility of DE results exists not only for small sample sizes, but also for relatively large sample sizes. Quite a few of the DEGs detected are specific to the samples in use, rather than genuinely differentially expressed under different conditions. Poor reproducibility of DE results is mainly caused by high variation of gene expression levels for the same gene in different samples. Even though biological variation may account for much of the high variation of gene expression levels, the effect of outlier count data also needs to be treated seriously, as outlier data severely interfere with DE analysis.

CONCLUSIONS

High heterogeneity exists not only in tumor tissue samples of each cancer type studied, but also in normal samples. High heterogeneity leads to poor reproducibility of DEGs, undermining generalization of differential expression results. Therefore, it is necessary to use large sample sizes (at least 10 if possible) in RNA-Seq experimental designs to reduce the impact of biological variability and DE results should be interpreted cautiously unless soundly validated.

Measurements Methods for the Development of MicroRNA-Based Tests for Cancer Diagnosis

Studies investigating microRNAs as potential biomarkers for cancer, immune-related diseases, or cardiac pathogenic diseases, among others, have exponentially increased in the last years. In particular, altered expression of specific miRNAs correlates with the occurrence of several diseases, making these molecules potential molecular tools for non-invasive diagnosis, prognosis, and response to therapy. Nonetheless, microRNAs are not in clinical use yet, due to inconsistencies in the literature regarding the specific miRNAs identified as biomarkers for a specific disease, which in turn can be attributed to several reasons, including lack of assay standardization and reproducibility. Technological limitations in circulating microRNAs measurement have been, to date, the biggest challenge for using these molecules in clinical settings. In this review we will discuss pre-analytical, analytical, and post-analytical challenges to address the potential technical biases and patient-related parameters that can have an influence and should be improved to translate miRNA biomarkers to the clinical stage. Moreover, we will describe the currently available methods for circulating miRNA expression profiling and measurement, underlining their advantages and potential pitfalls.

Field Cancerization in NSCLC: A New Perspective on MicroRNAs in Macrophage Polarization

Lung cancer is currently the first cause of cancer-related death. The major lung cancer subtype is non-small cell lung cancers (NSCLC), which accounts for approximatively 85% of cases. The major carcinogenic associated with lung cancer is tobacco smoke, which produces long-lasting and progressive damage to the respiratory tract. The progressive and diffuse alterations that occur in the respiratory tract of patients with cancer and premalignant lesions have been described as field cancerization. At the level of tumor cells, adjacent tumor microenvironment (TME) and cancerized field are taking place dynamic interactions through direct cell-to-cell communication or through extracellular vesicles. These molecular messages exchanged between tumor and nontumor cells are represented by proteins, noncoding RNAs (ncRNAs) and microRNAs (miRNAs). In this paper, we analyze the miRNA roles in the macrophage polarization at the level of TME and cancerized field in NSCLC. Identifying molecular players that can influence the phenotypic states at the level of malignant cells, tumor microenvironment and cancerized field can provide us new insights into tumor regulatory mechanisms that can be further modulated to restore the immunogenic capacity of the TME. This approach could revert alterations in the cancerized field and could enhance currently available therapy approaches.

miR-1301-3p promotes the proliferation and migration of lung cancer cells via direct repression of polymerase I and transcript release factor

Aberrant expression of microRNAs (miRNAs or miRs) is associated with a number of human diseases, including lung cancer. Although numerous differentially expressed miRNAs have been identified in lung cancer via microarray and sequencing methods, to the best of our knowledge, only a small portion of these miRNAs have been experimentally verified. In the present study, miR-1301-3p expression levels in lung tumor tissues and lung cancer cells were measured by reverse transcription-quantitative PCR (RT-qPCR) and by analyzing previously published data. Cell Counting Kit-8 and Transwell assays were used to analyze the function of miR-1301-3p in lung cancer tissues and cells. Bioinformatics analysis, RT-qPCR, western blotting and a dual-luciferase reporter assay were performed to investigate the mechanism of miR-1301-3p in lung cancer cells. It was identified that miR-1301-3p is an upregulated miRNA in lung cancer via analyzing previously published microarray and The Cancer Genome Atlas-lung squamous cell carcinoma project data, and the upregulation of miR-1301-3p was confirmed in collected clinical samples and cells. Inhibition of miR-1301-3p suppressed lung cancer cell proliferation and migration. In addition, miR-1301-3p inhibition upregulated E-cadherin, an epithelial cell maker, and downregulated vimentin, a mesenchymal cell marker. Using bioinformatics analysis, it was revealed that polymerase I and transcript release factor (PTRF) is a target of miR-1301-3p. RT-qPCR, western blotting and dual-luciferase reporter assays demonstrated that PTRF is targeted by miR-1301-3p in lung cancer cells. The rescue experiments indicated that silencing PTRF could attenuate the inhibition of cell proliferation and migration induced by miR-1301-3p inhibitor in lung cancer cells. Furthermore, a strong negative correlation between miR-1301-3p and PTRF mRNA was identified in clinical samples. In summary, the present data highlight the involvement of miR-1301-3p in the proliferation and migration of lung cancer cells, indicating that miR-1301-3p may be a promising biomarker for lung cancer.

MYCT1 inhibits the EMT and migration of laryngeal cancer cells via the SP1/miR-629-3p/ESRP2 pathway

MYCT1 has an inhibitory effect on the migration of laryngeal cancer cells, although the underlying molecular mechanism remains unknown. In this study, we aimed to explore the mechanism of MYCT1 in the epithelial-mesenchymal transition (EMT) and migration of laryngeal cancer cells. We found that MYCT1 significantly decreased the expression of miR-629-3p but increased the expression of ESRP2 in laryngeal cancer cells. The expression of miR-629-3p and ESRP2 in laryngeal cancer tissues showed significantly positive and negative correlations with patient metastasis, respectively. miR-629-3p was confirmed to repress the expression of ESRP2 by targeting its 3'UTR. SP1 was verified to be a direct transcription factor for miR-629-3p and a downstream target of MYCT1. Moreover, MYCT1 inhibited the EMT and migration of laryngeal cancer cells through the SP1/miR-629-3p/ESRP2 pathway. Taken together, our results establish a novel MYCT1 signaling pathway in the EMT and migration of laryngeal cancer cells, thus providing important insights for further studying the pathway in the diagnosis and treatment of laryngeal cancer.

Clinical significance and functions of miR-203a-3p/AVL9 axis in human non-small-cell lung cancer

Aim: We aimed to investigate the clinical significance and biological function of miR-203a-3p in non-small-cell lung cancer (NSCLC). Methods: The association between miR-203a-3p expression and clinicopathological parameters in NSCLC was assessed by χ² test. Kaplan-Meier method and Cox regression model were applied to evaluate the prognosis value of miR-203a-3p. The biological function of miR-203-3p was explored using CCK-8 and transwell assays. Results: Significantly downregulated miR-203a-3p was associated with TNM stage, lymph node metastasis and poor prognosis. AVL9 was identified as a direct target of miR-203a-3p. Functionally, we found overexpression of miR-203a-3p inhibited cell proliferation, migration and invasion in NSCLC cells by targeting AVL9. Conclusion: Collectively, targeting the miR-203a-3p/AVL9 axis might help to develop useful therapeutic target for NSCLC.

β-elemene suppresses Warburg effect in NCI-H1650 non-small-cell lung cancer cells by regulating the miR-301a-3p/AMPKα axis

β-elemene has been evidenced to suppress the development of numerous cancers including lung cancer. Previous research has found that in A549 cells, β-elemene increased the expression of adenosine monophosphate-activated protein kinase (AMPK) α (AMPKα), which negatively regulates the Warburg effect. Bioinformatics predicted that binding sites exist between AMPKα and miR-301a-3p, an miRNA that has shown oncogenic function in many cancers. The aim of this work was to investigate the effect of β-elemene on the Warburg effect in non-small-cell lung cancer (NSCLC) cells and its mechanism. Herein, the expression of miR-301a-3p was evaluated in NSCLC cells. Then, miR-301a-3p was overexpressed or silenced by mimics or inhibitors, respectively, followed by treatment with AMPK agonists or antagonists. NSCLC cells subjected to miR-301a-3p overexpression or inhibition were further treated with β-elemene. The results demonstrated that AMPKα was targeted and negatively regulated by miR-301a-3p. AMPKα agonists attenuated the Warburg effect in NSCLC cells induced by miR-301a-3p, as evidenced by the decrease in glucose level, lactic acid level, and expression of metabolism-related enzymes (glucose transporter 1 (GLUT1), hexokinase 1 (HK1), and lactate dehydrogenase A (LDHA)). Additionally, β-elemene suppressed the expression of miR-301a-3p, enhanced that of AMPKα, and inhibited the Warburg effect in NSCLC cells. The results indicated that β-elemene attenuates the Warburg effect in NSCLC cells, possibly by mediating the miR-301a-3p/AMPKα axis.

Biomarkers in Early Diagnosis and Early Stage Lung Cancer: The Clinician's Point of View

Starting from the work of Ulivi and colleagues, we aim to summarize the research area of biomarkers for early diagnosis and early stage lung cancer.

Serum microRNA-592 serves as a novel potential biomarker for early diagnosis of colorectal cancer

Colorectal cancer (CRC) is the second leading cause of cancer-associated mortality worldwide. Currently, available diagnostic biomarkers are neither sensitive nor specific. Thus, the present study aimed to identify novel circulating microRNAs (miRNAs) as biomarkers for the early diagnosis of CRC. All samples were provided by The Second Affiliated Hospital of Nanjing Medical University (Nanjing, China). Analysis of the GSE108153 and GSE55139 datasets, downloaded from the Gene Expression Omnibus (GEO) database was performed using the online tool, GEO2R. Reverse transcription-quantitative PCR was performed to determine miR-592 expression in CRC tissues, cells and serums of patients. Subsequently, the diagnostic value of serum miR-592 was assessed via receiver operating characteristic (ROC) curve analysis. Both the assessment of clinical samples and bioinformatics analysis demonstrated that miR-592 expression levels were significantly upregulated in the tissues and serum of patients with CRC, suggesting that elevated serum miR-592 may be tumor-derived. ROC analysis indicated that serum miR-592 levels may differentiate patients with early stage CRC and advanced adenoma from healthy individuals, with area under the curve values of 0.801 and 0.747, respectively. Taken together, the results of the present study suggest that serum miR-592 may be implicated as a potential biomarker for the early diagnosis of CRC.

Plasma miR-30a-5p as an early novel noninvasive diagnostic and prognostic biomarker for lung cancer

Aim: Circulation miRNAs have become increasingly appreciated in the diagnosis and prognosis of lung cancer. This study aims to identify and evaluate plasma miRNA-30a-5p as an early noninvasive biomarker for the diagnosis and prognosis of lung cancer. Pateints & methods: Expression levels of plasma miRNA 30a-5p were measured by quantitative real-time PCR. Receiver operating characteristic analysis and area under the curve were used to differentiate malignant from benign tumors and from healthy controls. Kaplan-Meier curves and Cox regression were used to determine survival and prognosis. Results: Our results suggest that the level of miRNA-30a-5p in plasma might be a considerable early novel noninvasive diagnostic and prognostic biomarker for lung cancer. Conclusion: Prospective studies must be performed to confirm this new early novel noninvasive diagnostic and prognostic biomarker for lung cancer.

Genome-wide analysis to identify a novel microRNA signature that predicts survival in patients with stomach adenocarcinoma

Objective: Using genome-wide screening, this study was aimed at identifying prognostic microRNA (miRNA) in those patients suffering from stomach adenocarcinoma (STAD).

Methods: A genome-wide miRNA sequencing dataset and relevant STAD clinical information was obtained via The Cancer Genome Atlas (TCGA). Prognostic miRNA selection was carried out through a whole genome multivariate Cox regression model in order to establish a prognostic STAD signature.

Results: Eleven miRNAs (hsa-mir-509-2, hsa-mir-3917, hsa-mir-495, hsa-mir-653, hsa-mir-3605, hsa-mir-2115, hsa-mir-1292, hsa-mir-137, hsa-mir-6511b-1, hsa-mir-145, and hsa-mir-138-2) were recognized as prognostic and used for the construction of a STAD prognostic signature. This signature exhibited good performance in predicting prognosis (adjusted P<0.0001, adjusted hazard ratio= 3.047, and 95% confidence interval=2.148-4.323). The time-dependent receiver operating characteristic examination exhibited area under curve values of 0.711, 0.697, 0.716, 0.733, 0.805, and 0.805, for 1-, 2-, 3-, 4-, 5-, and 10-year overall survival (OS) estimation, respectively. Comprehensive survival analysis suggests that the 11-miRNA prognostic signature acts as an independent feature of STAD prognosis and exhibits superior performance in OS prediction when compared to traditional clinical parameters. Furthermore, fourteen miRNA target genes were linked to STAD OS. These included SERPINE1, MLEC, ANGPT2, C5orf38, FZD7, MARCKS, PDGFD, DUSP6, IRS1, PSAT1, TENM3, TMEM127, BLMH, and TIRAP. Functional and gene set enrichment analysis suggested that target genes and the 11-miRNA prognostic signature were both participate in various biological processes and pathways, including the growth factor beta, Wnt, and Notch signaling pathways.

Conclusions: By means of a genome-wide analysis, an 11-miRNA expression signature that may serve as an underlying prognostic indicator for those patients suffering from STAD has been identified and described here.

Effects of different doses of cisatracurium besilate on hemodynamics and postoperative cognitive function in patients undergoing radical resection of lung cancer

The effects of different doses of cisatracurium besilate on perioperative hemodynamics and early postoperative cognitive function in patients undergoing radical resection of lung cancer were investigated. One hundred and thirty-six patients who underwent radical resection of lung cancer from June 2013 to June 2016 in Dongying People's Hospital were retrospectively analyzed. Patients who were not given atracurium were selected as the control group (n=35). According to the different anesthetic doses, patients in the experimental group were separated into low dose (0.15 mg/kg cisatracurium besilate) group (LD group, n=34), medium dose (0.2 mg/kg cisatracurium besilate) group (MD group, n=36) and high dose (0.3 mg/kg cisatracurium besilate) group (HD group, n=31). The mean arterial pressure and heart rate (HR) were recorded before induction of anesthesia (T0), at the time of entering pleural cavity (T1), at the end of surgery (T2), and 1 day after surgery (T3). The Mini-Mental State Examination (MMSE) was used to evaluate the postoperative cognitive function scores of the 4 groups 1 day before operation and on the 1st, 3rd and 7th day after surgery. The agitation of patients at 6 and 12 h after operation was evaluated by Ramsay sedation score. There was no significant difference in arterial pressure among the four groups at T2 and T3 (P>0.05). There was no significant difference in terms of MMSE among the four groups 1 day before operation, 3 days after operation and 7 days after operation, but the MMSE score of the control group was significantly lower than that of the LD, MD and HD groups 1 day after surgery (P<0.05). Therefore, cisatracurium besilate can stabilize hemodynamics during radical operation of lung cancer and reduce the incidence of postoperative cognitive dysfunction, and it has no close association with the dose.

MicroRNA expression profiling provides novel insights into immune-related pathways involved in gastric cancer

Gastric cancer is one of the most common cancers, and an increasing number of studies have found that microRNAs (miRNAs) play essential roles in gastric cancer progression; however, the roles of specific miRNAs involved in the immune response to this disease remain unclear. We compared the miRNA expression in tissues from primary gastric cancer patients and healthy controls to find miRNAs dysregulated in gastric cancer and used bioinformatics tools to determine potential roles of these miRNAs in the immune system. We evaluated 25 primary gastric cancer tissues and five healthy gastric tissues. Quantitative real-time polymerase chain reaction was performed for a set of miRNAs, followed by the prediction of their target genes and functional enrichment analysis of these targets. Analysis of a microarray dataset showed that the miRNA miR-196a-5p was significantly upregulated, while miR-374a-5p and miR-375 were downregulated in gastric cancer patients. In addition, miR-374-5p was significantly downregulated in patients with metastasis compared with its expression levels in non-metastatic patients (p = 0.03). Bioinformatics analysis suggested that the pathways regulated by these differentially expressed miRNAs were related to the immune response, cell adhesion, and cell migration. Most importantly, this study provides a new insight into the potential use of multiple miRNAs to find distinct pathways of immune regulation in gastric cancer.

Are There New Biomarkers in Tissue and Liquid Biopsies for the Early Detection of Non-Small Cell Lung Cancer?

Lung cancer is one of the most lethal malignancies worldwide, mainly due to its late diagnoses. The detection of molecular markers on samples provided from routine bronchoscopy including several liquid-based cytology tests (e.g., bronchoaspirate, bronchoalveolar lavage) and/or on easily obtained specimens such as sputum could represent a new approach to improve the sensitivity in lung cancer diagnoses. Recently growing interest has been reported for "noninvasive" liquid biopsy as a valuable source for molecular profiling. Unfortunately, a biomarker and/or composition of biomarkers capable of detecting early-stage lung cancer has yet to be discovered even if in the last few years there has been, through the use of revolutionary new technologies, an explosion of lung cancer biomarkers. Assay sensitivity and specificity need to be improved particularly when new approaches and/or tools are used. We have focused on the most important markers detected in tissue, and on several cytological specimens and liquid biopsies overall.

Identification and imaging of miR-155 in the early screening of lung cancer by targeted delivery of octreotide-conjugated chitosan-molecular beacon nanoparticles

Lung cancer is still the most common cancer globally. Early screening remains the key to improve the prognosis of patients. There is currently a lack of specific and sensitive methods for early screening of lung cancer. In recent years, studies have found that microRNA plays an important role in the occurrence and development of lung cancer and become a biological target in the early diagnosis of lung cancer. In this study, lung cancer cells, subcutaneous xenografts of lung cancer in nude mice, and Lox-Stop-lox K-ras G12D transgenic mice were used as models. The transgenic mice displayed the dynamic processes from normal lung tissue to atypical hyperplasia, adenomas, carcinoma in situ and lung adenocarcinoma. It was found that miR-155 and somatostatin receptor 2 (SSTR2) were expressed in all the disease stages of transgenic mice. Through molecular beacon (MB) technology and nanotechnology, chitosan-molecular beacon (CS-MB) nanoparticles and targeted octreotide (OCT) were conjugated and synthesized. The octreotide-conjugated chitosan-molecular beacon nanoparticles (CS-MB-OCT) can specifically bind to SSTR2 expressed by the lung cancer cells to achieve the goal of identification of lung cancer cells and imaging miR-155 in vivo and in vitro. Fluorescence imaging at different disease stages of lung cancer in Lox-Stop-lox K-ras G12D transgenic mice was performed, and could dynamically monitor the occurrence and development of lung cancer by different fluorescence intensity ranges. The current research, in turn, provides new idea, new method, and new technology for the early screening of lung cancer.

Hypoxia-sensitive LINC01436 is regulated by E2F6 and acts as an oncogene by targeting miR-30a-3p in non-small cell lung cancer

Dysregulation of long noncoding RNA (lncRNA) is known to be involved in numerous human diseases, including lung cancer. However, the precise biological functions of most lncRNA remain to be elucidated. Here, we identified a novel up‐regulated lncRNA, LINC01436 (RefSeq: NR_110419.1), in non‐small cell lung cancer (NSCLC). High expression of LINC01436 was significantly associated with poor overall survival. Notably, LINC01436 expression was transcriptionally repressed by E2F6 under normoxia, and the inhibitory effect was relieved in a hypoxic microenvironment. Gain‐ and loss‐of‐function studies revealed that LINC01436 acted as a proto‐oncogene by promoting lung cancer cell growth, migration and invasion in vitro. Xenograft tumor assays in nude mice confirmed that LINC01436 promoted tumor growth and metastasis in vivo. Mechanistically, LINC01436 exerted biological functions by acting as a microRNA (miR)‐30a‐3p sponge to regulate the expression of its target gene EPAS1. Our findings characterize LINC01436 as a new hypoxia‐sensitive lncRNA with oncogenic function in NSCLC, suggesting that LINC01436 may be a potential biomarker for prognosis and a potential target for treatment.

Differences in microRNA expression between melanoma and healthy adjacent skin

Background

The tumor microenvironment is composed of cancer-associated fibroblasts, tumor-associated macrophages, endothelial cells, immune cells, signaling molecules and extracellular matrix structures, which closelycommunicate with the tumor via multiple mechanisms. MicroRNAs are paracrine regulators that provide a direct interaction between the microenvironment and cancer cells. In the presentstudy, we aimed to identify the microRNA expression profile in melanoma compared with thatin healthy adjacent skin, with a further assessment of altered microRNA signaling pathways and target genes.

Methods

Formalin-fixed paraffin-embedded (FFPE) melanoma tissue samples were separated by dissection into tumor and surrounding health tissue fragments. MicroRNA expression profiles were obtained by microarray using Gene Atlas Microarray System (Affymetrix, California, USA). To confirm microarray results real-time PCR was carried out. Bioinformatic analysis was performed using the DIANA-miRPath v.3.0 database. Target genes for miR-146a-5p were determined using three algorithms: TargetScan 7.0, miRWalk 2.0 and miRTarBase v.4.5.

Results

A microarray profiling revealed 143 microRNAs asdifferent in tumor versus adjacent tissues. Expression level of hsa-miR-146a-5p showedto be higher in melanoma cells as compared to thehealthy adjacent skin. The bioinformatic study has determined several signaling cascades associated with miR-146a-5p:Toll-like receptor pathway, NF-κB pathway, ErB pathway, and measles signaling pathway. The 38 target genes have been shown for miR-146a-5p of which NRAS gene is known asone of the most frequent mutated in melanoma.

Conclusions

Elucidation of the role of miR-146-a-5p in complex interactions between the tumor and the cells of healthy adjacent skin is necessary for our understanding of the mechanisms oftumor progression. Significant differences found between cancer cells and adjacent tissues in microRNA expression profile corresponding to divergent mRNA/protein levels in these structures should be taken into account when tumor samples characterization estimatedby high-throughput methods.

Electronic supplementary material

The online version of this article (10.1186/s12895-018-0081-1) contains supplementary material, which is available to authorized users.

Multidimensional communication of microRNAs and long non-coding RNAs in lung cancer

PURPOSE

Non-coding RNAs (ncRNAs) have been a hot topic for many years in the field of cancer research, especially miRNAs and lncRNAs. Because they play critical roles in regulating various cellular processes and are more often involved in tumorigenesis than protein-coding genes. But the cross talk between miRNAs and lncRNAs in cancer has been scarcely studied. This article aims to provide a retrospective review of the latest research on the link between miRNAs and lncRNAs in lung cancer and discusses their potential role as diagnostic biomarkers and therapeutic targets for lung cancer in clinical practice.

METHODS

We reviewed literatures about ncRNAs and lung cancer from PUBMED databases in this article.

RESULTS

As shown in our review, miRNAs and lncRNAs could represent underlying targets for diagnosis, therapy, prognosis, and drug resistence of lung cancer. By acting as ceRNAs, lncRNAs can competitively inhibit the expression levels of miRNAs, and the lncRNA/miRNA axis can contribute to tumorigenesis, metastasis, and mutidrug resistance in lung cancer via various classic signaling pathways or related proteins.

CONCLUSION

Based on present knowledge, ncRNAs may provide a novel perspective to understand the pathogenesis of lung cancer and could be candidates in screening of therapeutic targets for lung cancer.

Inhibition of microRNA‑939 suppresses the development of human non‑small cell lung cancer via the upregulation of tissue inhibitor of metalloproteinases 2

Numerous microRNAs (miRNA/miRs) have been reported to be associated with the initiation and progression of non‑small cell lung cancer (NSCLC). The aim of the present study was to examine the expression and biological role of miR‑939 in human NSCLC, in vitro. Reverse transcription‑quantitative polymerase chain reaction analysis was used to evaluate the expression of miR‑939 in NSCLC tissues. Cell Counting Kit‑8, 5‑ethynyl‑29‑deoxyuridine and Transwell assays were also used to determine the effects of miR‑939 on tumor cell proliferation and invasion in two human NSCLC cell lines (H1299 and SPCA1). Furthermore, tissue inhibitor of metalloproteinases 2 (TIMP2) was confirmed to be a target of miR‑939 by luciferase reporter assay, western blotting and bioinformatics analysis. Following downregulation of miR‑939 expression, cell proliferative and invasive abilities were significantly suppressed. Collectively, these findings indicated that the knockdown of miR‑939 may inhibit cell proliferation and invasion by regulating the expression of TIMP2 in NSCLC cells. Thus, miR‑939 may be a potential target in the treatment of NSCLC, although this requires further investigation.

[Progress of Liquid Biopsy in Early Diagnosis of Lung Cancer]

肺癌的早期诊断有利于提高患者的生存率。应用影像学方法对肺癌高风险人群进行筛查，可以起到早发现、早诊断的作用。越来越多的研究显示，液体活检（liquid biopsy）可以对该方法进行替代和补充。检测肺癌患者外周血中的循环肿瘤细胞（circulating tumor cells, CTCs）、循环肿瘤DNA（circulating tumor DNA, ctDNA）、微小核糖核酸（microRNA, miRNA）、外泌体（exosomes）、肿瘤血小板（tumor educated platelets, TEPs）可以用于肺癌的早期诊断，并且可能为影像学检查阴性的高风险人群提供相应的诊疗建议。全文就以上标志物的检测手段、在肺癌早期诊断中的价值以及存在优势与局限性进行综述，以期促进液体活检在肺癌早期诊断、与其他筛查手段相结合方面的应用。

MicroRNAs as biomarkers for the progression and prognosis of colon carcinoma

Early detection is critical for the treatment of colon carcinoma. However, current biomarkers for its diagnosis and prognosis are insufficient and improvement is required. Aberrantly expressed microRNAs (miRNAs/miRs) in colon carcinoma have been identified to function as potential diagnostic and prognostic biomarkers. In the present study, 245 differentially expressed miRNAs between colon carcinoma and normal tissues were identified by a bioinformatics analysis of a dataset from The Cancer Genome Atlas. A six-miRNA (miR-149, miR-3189, miR-3677, miR-3917, miR-4999 and miR-6854) prognostic prediction system was established, which is able to independently and effectively predict the prognosis of colon carcinoma patients [P<0.001, area under the receiver operating characteristic curve (AUC)=0.763]. Furthermore, the six miRNAs were highly correlated with the tumor-nodes-metastasis (TNM) stage and were able to distinguish between different stages (high vs. low TNM stage, P<0.001). Of note, combination of the six-miRNA signature and TNM stage provides an improved prediction of the patient's prognosis (AUC=0.797). Functional enrichment analysis revealed the possible mechanistic involvement of these predictive miRNAs in cancer-associated biological processes and pathways. Taken together, the present study demonstrated the promising potential of the novel six-miRNA model as an independent factor for the prediction of the progression and prognosis of colon carcinoma.

MicroRNA-21 promotes the proliferation, migration and invasion of non-small cell lung cancer A549 cells by regulating autophagy activity via AMPK/ULK1 signaling pathway

The present study investigated the expression of microRNA (miR)-21 in non-small cell lung cancer (NSCLC) tissues, its biological functions and mechanism of autophagy regulation. A total of 46 patients with NSCLC were enrolled in the present study. To measure the expression of miR-21, reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was employed. NSCLC A549 cells were transfected with miR-negative control (NC), miR-21 mimics or inhibitor. The CCK-8 assay was used to investigate the proliferation of A549 cells. To study migration and invasion abilities of A549 cells, The Transwell assay was performed. In addition, to determine the expression levels of ULK1, LC3B, AMPKα, p-AMPKα and p62 proteins, western blotting was conducted and laser confocal microscopy was performed to observe the formation of autophagosomes in A549 cells. To explore whether miR-21 regulates the biological functions of A549 cells via autophagy, an autophagy inhibitor, 3-MA, or agonist, rapamycin, were used in a rescue assay. Results indicated that miR-21 expression in NSCLC tissues was enhanced, and closely correlated with the occurrence and development of NSCLC. In vitro experiments showed that miR-21 mimics promoted the proliferation, migration and invasion of A549 cells, while miR-21 inhibitor inhibited these biological functions. Western blotting indicated that miR-21 upregulated autophagy marker LC3BII protein, but downregulated p62 protein. Laser confocal microscopy showed that miR-21 activated autophagy of A549. Rescue experiments indicated that autophagy reversed the effect of miR-21 on the proliferation, migration and invasion of A549 cells. Western blotting data suggested that autophagy-related AMPK/ULK1 signaling pathway was activated by miR-21, and interference or overexpression of ULK1 reversed the biological functions of miR-21. The present study demonstrated that miR-21 expression in NSCLC tissues was upregulated and positively correlated with lymphatic metastasis and clinical staging. In addition, miR-21 regulated autophagy activity of NSCLC A549 cells via AMPK/ULK1 signaling pathway, and promoted the proliferation, migration and invasion of NSCLC A549 cells.

miR‑378a‑3p exerts tumor suppressive function on the tumorigenesis of esophageal squamous cell carcinoma by targeting Rab10

Esophageal squamous cell carcinoma (ESCC) is a life-threatening cancer with increasing incidence worldwide. MicroRNAs (miRs) have been reported to be involved in the progression of various types of cancer. In previous studies, the expression of miR-378a-3p was shown to be reduced in ESCC tissues. However, the mechanism underlying the effect of miR-378a-3p in ESCC remains to be elucidated. By employing a reverse transcription-quantitative polymerase chain reaction, miR-378a-3p expression was tested in ESCC tissues and cell lines. In addition, the effects of miR-378a-3p on cell viability, proliferation, apoptosis, migration and invasion were studied using an MTT assay, an EdU assay, flow cytometry analysis, wound healing analysis and a Transwell assay. In the present study, the level of miR-378a-3p was significantly downregulated in ESCC clinical tissues and cell lines (EC109 and KYSE150). In addition, the overexpression of miR-378a-3p suppressed the viability, proliferation, migration and invasion of the ESCC cells. The upregulated expression of miR-378a-3p also increased the expression levels of B-cell lymphoma 2-associated X protein and caspase-3, and decreased the expression levels of matrix metalloproteinase (MMP)-2 and MMP-9, which attenuated ESCC tumorigenesis. Furthermore, Rab10 was confirmed to be a direct target gene of miR-378a-3p, and was negatively affected by miR-378a-3p. The silencing of Rab10 revealed antitumor effects in ESCC cell lines, and the expression of miR-378a-3p was negatively correlated with that of Rab10 in ESCC. Collectively, miR-378a-3p may act as a tumor-suppressor in ESCC cells through negatively regulating Rab10.

Identification of potential prognostic microRNA biomarkers for predicting survival in patients with hepatocellular carcinoma

Background

The aim of the present study was to identify potential prognostic microRNA (miRNA) biomarkers for hepatocellular carcinoma (HCC) prognosis prediction based on a dataset from The Cancer Genome Atlas (TCGA).

Materials and methods

A miRNA sequencing dataset and corresponding clinical parameters of HCC were obtained from TCGA. Genome-wide univariate Cox regression analysis was used to screen prognostic differentially expressed miRNAs (DEMs), and multivariable Cox regression analysis was used for prognostic signature construction. Comprehensive survival analysis was performed to evaluate the prognostic value of the prognostic signature.

Results

Five miRNAs were regarded as prognostic DEMs and used for prognostic signature construction. The five-DEM prognostic signature performed well in prognosis prediction (adjusted P < 0.0001, adjusted hazard ratio = 2.249, 95% confidence interval =1.491-3.394), and time-dependent receiver-operating characteristic (ROC) analysis showed an area under the curve (AUC) of 0.765, 0.745, 0.725, and 0.687 for 1-, 2-, 3-, and 5-year HCC overall survival (OS) prediction, respectively. Comprehensive survival analysis of the prognostic signature suggests that the risk score model could serve as an independent factor of HCC and perform better in prognosis prediction than other traditional clinical indicators. Functional assessment of the target genes of hsa-mir-139 and hsa-mir-5003 indicates that they were significantly enriched in multiple biological processes and pathways, including cell proliferation and cell migration regulation, pathways in cancer, and the cyclic adenosine monophosphate (cAMP) signaling pathway.

Conclusion

Our study indicates that the novel miRNA expression signature may be a potential prognostic biomarker for HCC patients.

Diagnosis value of aberrantly expressed microRNA profiles in lung squamous cell carcinoma: a study based on the Cancer Genome Atlas

Background

Lung cancer is considered as one of the most frequent and deadly cancers with high mortality all around the world. It is critical to find new biomarkers for early diagnosis of lung cancer, especially lung squamous cell carcinoma (LUSC). The Cancer Genome Atlas (TCGA) is a database which provides both cancer and clinical information. This study is a comprehensive analysis of a novel diagnostic biomarker for LUSC, based on TCGA.

Methods and Results

The present study investigated LUSC-specific key microRNAs (miRNAs) from large-scale samples in TCGA. According to exclusion criteria and inclusion criteria, the expression profiles of miRNAs with related clinical information of 332 LUSC patients were obtained. Most aberrantly expressed miRNAs were identified between tumor and normal samples. Forty-two LUSC-specific intersection miRNAs (fold change >2, p < 0.05) were obtained by an integrative computational method, among them six miRNAs were found to be aberrantly expressed concerning characteristics of patients (gender, lymphatic metastasis, patient outcome assessment) through Student t-test. Five miRNAs correlated with overall survival (log-rank p < 0.05) were obtained through the univariate Cox proportional hazards regression model and Mantel–Haenszel test. Then, five miRNAs were randomly selected to validate the expression in 47 LUSC patient tissues using quantitative real-time polymerase chain reaction. The results showed that the test findings were consistent with the TCGA findings. Also, the diagnostic value of the specific key miRNAs was determined by areas under receiver operating characteristic curves. Finally, 577 interaction mRNAs as the targets of 42 LUSC-specific intersection miRNAs were selected for further bioinformatics analysis.

Conclusion

This study indicates that this novel microRNA expression signature may be a useful biomarker of the diagnosis for LUSC patients, based on bioinformatics analysis.