Genetic variants in regulatory regions of microRNAs are associated with lung cancer risk

A novel prognostic signature for clear cell renal cell carcinoma constructed using necroptosis-related miRNAs

Background

This work aims to analyze the relationship between necroptosis-related microRNAs (miRNAs) and the prognosis of clear cell renal cell carcinoma (ccRCC).

Methods

The miRNAs expression profiles of ccRCC and normal renal tissues from The Cancer Genome Atlas (TCGA) database were used to construct a matrix of the 13 necroptosis-related miRNAs. Cox regression analysis was used to construct a signature to predict the overall survival of ccRCC patients. The genes targeted by the necroptosis-related miRNAs in the prognostic signature were predicted using miRNA databases. Gene Ontology (Go) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were used to investigate the genes targeted by the necroptosis-related miRNAs. The expression levels of selected miRNAs in 15 paired samples (of ccRCC tissues and adjacent normal renal tissues) were investigated using reverse transcriptase quantitative polymerase chain reaction (RT-qPCR).

Results

Six necroptosis-related miRNAs were found to differentially expressed between ccRCC and normal renal tissues. A prognostic signature consisting of miR-223-3p, miR-200a-5p, and miR-500a-3p was constructed using Cox regression analysis and risk scores were calculated. Multivariate Cox regression analysis showed that the hazard ratio was 2.0315 (1.2627–3.2685, P = 0.0035), indicating that the risk score of the signature was an independent risk factor. The receiver operating characteristic (ROC) curve showed that the signature has a favorable predictive capacity and the Kaplan-Meier survival analysis indicated that ccRCC patients with higher risk scores had worse prognoses (P < 0.001). The results of the RT-qPCR verified that all three miRNAs used in the signature were differentially expressed between ccRCC and normal tissues (P < 0.05).

Conclusion

The three necroptosis-related-miRNAs used in this study could be a valuable signature for the prognosis of ccRCC patients. Necroptosis-related miRNAs should be further explored as prognostic indicators for ccRCC.

The association between polymorphisms in miRNA and the cholinesterase activity of workers in an omethoate-exposed environment

To explore the association between polymorphisms in microRNAs (miRNAs) and the cholinesterase (ChE) activity in omethoate-exposed workers, we recruited 180 omethoate-exposed workers and 115 controls to measure their ChE activity using acetylcholine and dithio-bis-(nitrobenzoic acid) and genotype susceptible SNPs in their miRNA by time-of-flight mass spectrometry. ChE activity in the exposure group was lower than that in the control group (P < 0.001). The analysis of covariance result showed that ChE activity was lower in the (- -/- T) genotype in miR-30a rs111456995 (1.97 ± 0.47) than in the TT genotype (2.23 ± 0.59) of the exposure group (P = 0.004). Multivariate linear regression was performed to find influencing factors on ChE activity, and variables kept in the model included omethoate exposure (b = -1.094, P < 0.001), gender (b = -0.381, P < 0.001), miR-30a rs111456995 (- -/- T)(b = -0.248, P < 0.001), and drinking (b = 0.258, P =0.019). The results suggest that individuals carrying a (- -/- T) genotype in miR-30a rs111456995 were more susceptible to damage in their cholinesterase induced by omethoate exposure.

Regulatory functions of miR‑200b‑3p in tumor development (Review)

MicroRNAs (miRNAs/miRs), non‑coding single‑stranded RNAs of length 18‑24 nucleotides, can modulate gene expression through post‑transcriptional control. As such, they can influence tumor proliferation, apoptosis, invasion, metastasis as well as chemotherapy resistance by regulating certain downstream genes. In this context, miR‑200b‑3p, one particular member of the miR‑200 family, possesses the ability to suppress tumor progression. However, many studies have suggested that, in certain cases, this miRNA may also promote the development of some tumors due to differences in the microenvironments and molecular backgrounds of different cancers. This review summarizes previous studies on the involvement of miR‑200b‑3p in tumors, including the underlying mechanism.

miR-200a-3p promoted cell proliferation and metastasis by downregulating SOX17 in non-small cell lung cancer cells

Lung cancer has high mortality and incidence rates in which non-small cell lung cancer (NSCLC) is the primary type of lung cancer that accounts for about 80%-85% of total patients. It has been demonstrated that microRNAs (miRNAs) are critical in the incidence and progression of tumors, while the role and inner mechanism of miR-200a-3p, one type of essential miRNAs, in NSCLC have yet to be revealed. Herein, we investigated the in vitro and vivo pro-/antiproliferative influence of miR-200a-3p on NSCLC cells and utilized bioinformatic programs to further predict the SOX17 gene as miR-200a-3p's potential target. A double luciferase reporter gene experiment was performed to confirm that miR-200a-3p interacts with the SOX17 3'-UTR region specifically. On the basis of the results of Western blot and quantitative reverse-transcription polymerase chain reaction (qRT-PCR), miR-200a-3p impacted the posttranscriptional levels of SOX17 rather than influencing its mRNA expression. In the end, we found that overexpressed SOX17 can reverse miR-200a-3p's impact on NSCLC cell proliferation and metastasis. Therefore, this study demonstrated that miR-200a-3p influences NSCLC cell proliferation and metastasis by modulating the levels of SOX17.

MicroRNA‑200a‑3p and GATA6 are abnormally expressed in patients with non‑small cell lung cancer and exhibit high clinical diagnostic efficacy

Lung cancer is one of the main threats to human health. Survival of patients with lung cancer depends on timely detection and diagnosis. Among the genetic irregularities that control cancer development and progression, there are microRNAs (miRNAs/miRs). The present study aimed to investigate the expression patterns of miR-200a-3p and transcription factor GATA-6 (GATA6) in peripheral blood of patients with non-small cell lung cancer (NSCLC) and their clinical significance. The expression patterns of miR-200a-3p and GATA6 in the peripheral blood of patients with NSCLC and healthy subjects were measured via reverse transcription-quantitative PCR. The correlation between GATA6/miR-200a-3p expression and their diagnostic efficacy were analyzed by receiver operating characteristic curve analysis. The association between miR-200a-3p/GATA6 expression with the patient clinicopathological characteristics, and their correlation with carcinoembryonic antigen (CEA), neuron specific enolase (NSE) and squamous cell carcinoma antigen (SCCAg) were evaluated. The cumulative survival rate was examined, and whether miR-200a-3p and GATA6 expression levels were independently correlated with the prognosis of NSCLC was analyzed using multivariate logistic regression model. The results demonstrated that the expression of miR-200a-3p was high and that of GATA6 was low in the peripheral blood of patients with NSCLC, and both exhibited high clinical diagnostic efficacy. miR-200a-3p was revealed to target GATA6 by dual-luciferase assay. miR-200a-3p in the peripheral blood was correlated with TNM stage, lymph node metastasis and distal metastasis, while GATA6 in the peripheral blood was correlated with TNM stage and lymph node metastasis. miR-200a-3p and GATA6 were positively correlated with CEA and SCCAg, but not with NSE. High expression of miR-200a-3p and low expression of GATA6 predicted poor prognosis in patients with NSCLC. After adjusting for TNM stage, lymph node metastasis, distance metastasis, GATA6, CEA, NSE and SCCAg in the logistic regression model, it was indicated that the high expression of miR-200a-3p increased the risk of death in patients with NSCLC. Collectively, it was revealed that miR-200a-3p and GATA6 were abnormally expressed in the peripheral blood of patients with NSCLC. Serum levels of miR-200a-3p >1.475 and GATA6 <1.195 may assist the early diagnosis of NSCLC. GATA6 may function in NSCLC as a miR-200a-3p target, which may provide a future reference for NSCLC early diagnosis and treatment.

The Impact of Air Pollution Exposure on the MicroRNA Machinery and Lung Cancer Development

Small non-coding RNA molecules (miRNAs) play an important role in the epigenetic regulation of gene expression. As these molecules have been repeatedly implicated in human cancers, they have been suggested as biomarkers of the disease. Additionally, miRNA levels have been shown to be affected by environmental pollutants, including airborne contaminants. In this review, we searched the current literature for miRNAs involved in lung cancer, as well as miRNAs deregulated as a result of exposure to air pollutants. We then performed a synthesis of the data and identified those molecules commonly deregulated under both conditions. We detected a total of 25 miRNAs meeting the criteria, among them, miR-222, miR-21, miR-126-3p, miR-155 and miR-425 being the most prominent. We propose these miRNAs as biomarkers of choice for the identification of human populations exposed to air pollution with a significant risk of developing lung cancer.

Relationship between miR-143/145 cluster variations and cancer risk: proof from a Meta-analysis

Recent studies have suggested that single-nucleotide polymorphisms (SNPs) located in the miR-143/145 cluster might be linked to cancer risk. In this meta-analysis association study, we sought to quantitatively measure the strength of this association with cancer susceptibility in the overall analysis. Relevant publications were retrieved through a literature search in Web of Science, Medline, PubMed, Scopus, and Google scholar databases (updated January 22, 2020). Pooled odds ratios (ORs) with 95% confidence intervals (CIs) were estimated under different genetic contrasted models. Our findings showed that rs4705341 (under allelic, codominant AA, dominant, and recessive), rs4705342 (under allelic, codominant TC, codominant CC, dominant, and recessive), and rs353292 (under allelic, codominant CT, and dominant) significantly decreased cancer risk. However, we did not find any association between the rs4705343, rs353293, rs3733845, and rs3733846 variants and cancer risk under any genetic models. The stratified analysis by cancer type showed that the rs41291957 and rs4705342 variants showed protective effects against colorectal- and prostate cancers, respectively. Our findings support the association between some miR-143/145 cluster variants and cancer risk. Replication large-scale studies on different races are encouraged to precisely delineate such associations.

Identification of miR-200a-5p targeting the peptide transporter TAP1 and its association with the clinical outcome of melanoma patients

Tumor escape is often associated with abnormalities in the surface expression of the human leukocyte antigen class I (HLA-I) antigens thereby limiting CD8+ cytotoxic T cell responses. This impaired HLA-I surface expression can be mediated by deficient expression of components of the antigen processing and presentation machinery (APM) due to epigenetic, transcriptional and/or post-transcriptional processes. Since a discordant mRNA and protein expression pattern of APM components including the peptide transporter associated with antigen processing 1 (TAP1) has been frequently described in tumors of distinct origin, a post-transcriptional control of APM components caused by microRNAs (miR) was suggested. Using an in silico approach, miR-200a-5p has been identified as a candidate miR binding to the 3' untranslated region (UTR) of TAP1. Luciferase reporter assays demonstrated a specific binding of miR-200a-5p to the TAP1 3'-UTR. Furthermore, the miR-200a-5p expression is inversely correlated with the TAP1 protein expression in HEK293T cells and in a panel of melanoma cell lines as well as in primary melanoma lesions. High levels of miR-200a-5p expression were associated with a shorter overall survival of melanoma patients. Overexpression of miR-200a-5p reduced TAP1 levels, which was accompanied by a decreased HLA-I surface expression and an enhanced NK cell sensitivity of melanoma cells. These data show for the first time a miR-mediated control of the peptide transporter subunit TAP1 in melanoma thereby leading to a reduced HLA-I surface expression accompanied by an altered immune recognition and reduced patients' survival.

Abbreviations

Ab: antibody; ACTB: β-actin; APM: antigen processing and presentation machinery; ATCC: American tissue culture collection; β2-m: β2-microglobulin; BSA: bovine serum albumin; CTL: cytotoxic T lymphocyte; FCS: fetal calf serum; FFL: firefly luciferase; FFPE: formalin-fixed paraffin-embedded; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; HC: heavy chain; HLA: human leukocyte antigen; HLA-I: HLA class I; HRP: horseradish peroxidase; IFN: interferon; im-miR: immune modulatory miRNA; LMP: low molecular weight protein; luc: luciferase; MFI: mean fluorescence intensity; MHC: major histocompatibility complex; miR: microRNA; NC: negative control; NK: natural killer; NSCLC: non-small cell lung carcinoma; OS: overall survival; PBMC: peripheral blood mononuclear cells; RBP: RNA-binding proteins; RL: Renilla; RLU: relative light units; TAP: transporter associated with antigen processing; tpn: tapasin; UTR: untranslated region.

Genetic Variations in miR-30 Family Member Regulatory Regions Are Associated with Breast Cancer Risk in a Chinese Population

MicroRNAs (miRNAs) of the miR-30 family are closely linked with tumor metastasis and play key roles in the complex malignant phenotypes of cancers by targeting many tumor-related genes. Deregulated expression of miR-30 family members has been commonly observed in breast cancer. However, associations between the genetic variants in the regulatory region of miR-30 family and the risk of breast cancer are still limited, especially in the Chinese Han population. In the present study, we conducted a case-control analysis wherein 1064 breast cancer patients and 1073 healthy controls underwent genotyping of 10 SNPs in the regulatory region of miR-30 family members. Multivariate logistic regression analyses illustrated that the rs763354 variant in the miR-30a regulatory region was linked with a significant decrease in breast cancer risk in an additive model (adjusted OR = 0.86, 95% CI: 0.75-0.98, P = 0.022). Further, eQTL analyses also indicated that this SNP was associated with miR-30a expression levels in breast cancer samples compiled in the TCGA database (P = 0.020). The Kaplan-Meier plotter showed that breast cancer patients with higher miR-30a expression have significantly better outcomes than do patients expressing low levels of this miRNA (HR = 0.75, 95% CI: 0.61-0.91, P = 0.0041). Together, these findings suggest that the miR-30a rs763354 SNP is an important regulator of breast cancer risk, thus making it a potentially viable prognostic biomarker and one that can be used to guide therapeutic treatment in affected patients.

Effects of microRNAs polymorphism in cancer progression

MicroRNAs (miRNAs) are known as a new class of small RNAs (18-25 nucleotides) that regulate gene expression at multiple levels from transcription to translation. Considering the important role of miRNAs in cell proliferation, differentiation, and apoptosis, any variations in their expression can contribute to various anomalies, such as tumorigenesis. Single-nucleotide polymorphisms (SNPs) have received much attention as potential genetic markers for diseases due to their advantage of being present at a high frequency in the human genome. SNPs can occur in different parts of the miRNA genes (primary, precursor, and mature) which result in pathological conditions. In this study, recent findings related to the effects of SNPs in miRNAs on their biogenesis and functions and their role in cancer development and progression are discussed. This review was performed using PubMed to search for related reports. The identified effects may be useful for clinical decision-making and providing important new information about the pathophysiology of miRNAs.

Effects of polycyclic aromatic hydrocarbon exposure and miRNA variations on peripheral blood leukocyte DNA telomere length: A cross-sectional study in Henan Province, China

Telomeres play a major role in human aging and disease, especially in most cancers. Telomere length was shortened in workers exposed to polycyclic aromatic hydrocarbons (PAHs) and influenced by individual genetic variations in telomere-binding proteins. MicroRNAs (miRNAs) can affect the progress of messenger RNA (mRNA) transcription; however, whether polymorphisms in miRNA can act on the telomere length is still unknown. Therefore, we aimed to explore the relationships between telomere damage and genetic polymorphisms in miRNA or environmental exposure. A total of 544 coke oven workers and 238 healthy controls were recruited. After collecting peripheral blood and extracting the genomic DNA of the study subjects, the telomere length (TL) in their leucocytes was detected by a real-time quantitative polymerase chain reaction (PCR), and polymorphisms in miRNAs were genotyped using the flight mass spectrometry technique. The concentrations of the four urine OH-PAHs were determined by high performance liquid chromatography (HPLC), and the Soxhlet extraction method was used to detect the concentration of coke oven emissions (COEs) in the air. We found that the peripheral blood leucocyte DNA TL was significantly shorter in the exposure group (0.75; 0.51, 1.08) than that in the control group (1.05; 0.76, 1.44) (Z = 7.692, P < 0.001). The total cumulative exposure dose (CED), 1-hydroxypyrene, 2-hydroxynaphthalene, and 3-hydroxyphenanthrene were significantly negatively correlated with TL (r = -0.307, P < 0.001; r = -0.212, P < 0.001; r = -0.110, P = 0.025; r = -0.251, P < 0.001, respectively). MiR-145 rs353291 GG, miR-30a rs2222722 CT/CC, and miR-197 rs1889470 AA could protect the telomere end in the exposed workers (P < 0.05). The interaction between miR-197 rs1889470 and the CED had an effect on TL (β = 0.066, P = 0.034). This is the first study to evaluate gene-environmental interactions for miRNA polymorphisms and PAH exposure in coke oven workers.

MiR-182-5p and its target HOXA9 in non-small cell lung cancer: a clinical and in-silico exploration with the combination of RT-qPCR, miRNA-seq and miRNA-chip

BACKGROUND

MiR-182-5p, a cancer-related microRNA (miRNA), modulates tumorigenesis and patient outcomes in various human malignances. This study interroted the clinicopathological significance and molecular mechanisms of miR-182-5p in non-small cell lung cancer (NSCLC).

METHODS

The clinical significance of miR-182-5p in NSCLC subtypes was determined based on an analysis of 124 samples (lung adenocarcinomas [LUADs], n = 101; lung squamous cell carcinomas [LUSCs], n = 23) obtained from NSCLC patients and paired noncancer tissues and an analysis of data obtained from public miRNA-seq database, miRNA-chip database, and the scientific literature. The NSCLC samples (n = 124) were analyzed using the real-time quantitative polymerase chain reaction (RT-qPCR). Potential targets of miR-182-5p were identified using lists generated by miRWalk v.2.0, a comprehensive atlas of predicted and validated targets of miRNA-target interactions. Molecular events of miR-182-5p in NSCLC were unveiled based on a functional analysis of candidate targets. The association of miR-182-5p with one of the candidate target genes, homeobox A9 (HOXA9), was validated using in-house RT-qPCR and dual-luciferase reporter assays.

RESULTS

The results of the in-house RT-qPCR assays analysis of data obtained from public miRNA-seq databases, miRNA-chip databases, and the scientific literature all supported upregulation of the expression level of miR-182-5p level in NSCLC. Moreover, the in-house RT-qPCR data supported the influence of upregulated miR-182-5p on malignant progression of NSCLC. In total, 774 prospective targets of miR-182-5p were identified. These targets were mainly clustered in pathways associated with biological processes, such as axonogenesis, axonal development, and Ras protein signal transduction, as well as pathways involved in axonal guidance, melanogenesis, and longevity regulation, in multiple species. Correlation analysis of the in-house RT-qPCR data and dual-luciferase reporter assays confirmed that HOXA9 was a direct target of miR-182-5p in NSCLC.

CONCLUSIONS

The miR-182-5p expression level was upregulated in NSCLC tissues. MiR-182-5p may exert oncogenic influence on NSCLC through regulating target genes such as HOXA9.

LncRNA MALAT1 contributes to non-small cell lung cancer progression via modulating miR-200a-3p/programmed death-ligand 1 axis

This study was to investigate the expression correlation between long non-coding RNA metastasis-associated lung adenocarcinoma transcript 1 (lncRNA MALAT1), miR-200a-3p and programmed death-ligand 1 (PD-L1) in non-small cell lung cancer (NSCLC), and their roles in NSCLC. Real-time polymerase chain reaction (PCR) was performed to detect the expressions of MALAT1, miR-200a-3p and PD-L1 in NSCLC tissues and cells for the correlation analysis. The starBase and Targetscan databases were used to predict the binding sites between MALAT1 and miR-200a-3p, and miR-200a-3p and PD-L1, respectively. The targeting relationship between MALAT1 and miR-200a-3p, and miR-200a-3p and PD-L1 were further verified by real-time PCR and dual luciferase reporter gene assay. Cell proliferation was monitored by CCK8 and colony formation assays. The apoptosis was detected using flow cytometry. Wound healing assay and transwell assay were conducted to determine cell migration and invasion. In this study, we demonstrated that in NSCLC tissues, the expression level of MALAT1 was negatively correlated with that of miR-200a-3p, while positively correlated with PD-L1. Besides, MALAT1 promoted proliferation, mobility, migration, and invasion of NSCLC cells via sponging miR-200a-3p. PD-L1 was validated as a target of miR-200a-3p, and indirectly modulated by MALAT1. In conclusion, LncRNA MALAT1 facilitates the progression of NSCLC by modulating miR-200a-3p/PDL1 axis.

Association of Hsa-miR-23a rs3745453 variation with prostate cancer risk among Chinese Han population: A case-control study

Prostate cancer (PCa) is a frequently diagnosed malignant solid tumor in men. The etiology of PCa has been attributed to both environmental and genetic factors. In recent years, many studies have reported that miRNA gene single-nucleotide polymorphisms (SNPs) influence the susceptibility to several diseases such as cancer. To date, the mechanisms of PCa have remained unknown. The main aim of this study was to evaluate the association between PCa susceptibility and miRNA gene SNPs. A total of 156 PCa cases and 188 control subjects were included in this case-control study. The data were collected from hospitalized cases. We collected the demographic characteristic information, which included age, body mass index, tobacco smoking, alcohol consumption, and family history of cancer. Polymorphisms were analyzed by the ligase detection reaction. Unconditional logistic and stratified analyses were used to analyze the association between these SNPs and PCa susceptibility and to calculate the adjusted odds ratios (ORs) and the 95% confidence intervals (CIs). Cox regression model and the log-rank test were used to test the association between genetic variants and the overall survival. We found that miR-23a gene polymorphism rs3745453 carrying CC homozygotes had a 4.16-fold increased risk (95% CI = 1.30-13.25) than those carrying the TT/CT genotypes (P = .02), and the C allele displayed a higher prevalence of PCa than the T allele (OR = 1.68, 95% CI = 1.16-2.45, P = .01). Moreover, miR-23a showed that the homozygous carriers of the C-variant significantly increased the risk of survival rate as compared to the carriers of the TT/CT genotype (OR = 9.67, 95% CI = 2.83-33.09, P = .001). The rs3745453 polymorphism was potentially associated with PCa in the Chinese Han population and had an interactive relationship with the environmental factors.

Association Between Two Polymorphisms in the Promoter Region of miR-143/miR-145 and the Susceptibility of Lung Cancer in Northeast Chinese Nonsmoking Females

Lung cancer is known to cause high mortality and morbidity. The study aimed to explore the association between rs3733845 and rs3733846 polymorphisms in the promoter region of miR-143/145 and the risk of lung cancer among 575 nonsmoking cases and 575 cancer-free controls in a Chinese female population. We genotyped two single nucleotide polymorphisms (SNPs) in the promoter region of miR-143/145 in 575 cases and 575 controls using TaqMan allelic discrimination method. Logistic regression analysis was conducted to assess the association between polymorphisms in the promoter of miR-143/miR-145 and risk of lung cancer females. Crossover analysis was used to explore the interaction between the two SNPs and environmental risk factors (cooking oil fume exposure and passive smoking exposure). The results showed that both rs3733845 and rs3733846 polymorphisms were associated with an increased lung adenocarcinoma risk in dominant model (adjusted odds ratio [OR] = 1.329, 95% confidence intervals [CIs] = 1.026-1.723, p = 0.031 and adjusted OR = 1.450, 95% CI = 1.112-1.890, p = 0.006, respectively). The results of crossover analysis revealed that rs3733845 and rs3733846 risk genotypes along with cooking oil exposure increased lung cancer risk by 1.862-fold and 2.260-fold, respectively (adjusted OR = 1.862, 95% CI = 1.105-3.138, p = 0.020 for rs3733845; adjusted OR = 2.260, 95% CI = 1.354-3.769, p = 0.002 for rs3733846). There was positive multiplicative interaction between the two SNPs and cooking oil fume exposure (adjusted OR = 1.362, 95% CI = 1.078-1.719, p = 0.009 for oil × rs3733845; adjusted OR = 1.399, 95% CI = 1.122-1.745, p = 0.003 for oil × rs3733846). In nonsmoking females, rs3733845 and rs3733846 polymorphisms might be associated with lung adenocarcinoma risk. Moreover, the interactions between the two SNPs and cooking oil fume exposure were statistically significant on a multiplicative scale rather than an addictive scale.

Association of genetic polymorphisms of miR-145 gene with telomere length in omethoate-exposed workers

Omethoate, an organophosphorous pesticide, causes a variety of health effects, especially the damage of chromosome DNA. The aim of the study was to assess the correlation between polymorphisms of encoding miRNA genes and telomere length in omethoate-exposure workers. 180 workers with more than 8 years omethoate-exposure and 115 healthy controls were recruited in the study. Genotyping for the selected single nucleotide polymorphisms loci were performed using the flight mass spectrometry. Real-time fluorescent quantitative polymerase chain reaction(PCR) method was applied to determine the relative telomere length(RTL) in human peripheral blood leukocytes DNA. After adjusting the covariate of affecting RTL, covariance analysis showed that the female was significantly longer than that of the male in control group(P < 0.046). For the miR-145 rs353291 locus, this study showed that RTL of mutation homozygous AG+GG individuals was longer than that of wild homozygous AA in the exposure group (P = 0.039). In the control group, RTL with wild homozygous TT genotype in miR-30a rs2222722 polymorphism locus was longer than that of the mutation homozygous CC genotype (P = 0.038). After multiple linear regression analysis, the independent variables of entering into the model were omethoate-exposure (b = 0.562, P < 0.001), miR-145 rs353291 (AG+GG) (b = 0.205, P = 0.010). The prolongation of relative telomere length in omethoate exposed workers was associated with AG+GG genotypes in rs353291 polymorphism of encoding miR-145 gene.

miR‑146a‑5p targets TCSF and influences cell growth and apoptosis to repress NSCLC progression

Several studies have indicated that microRNAs (miRs) mediate multiple pathways associated with tumorigenesis and progression. Our preliminary study experimentally verified that miR-146a-5p has a role in the biological behavior of non-small cell lung cancer (NSCLC) cells. To perform further investigation of miR-146a-5p, the present study evaluated miR-146a-5p by targeting its downstream gene tumor collagenase stimulatory factor (TCSF) to influence cell viability, proliferation and apoptosis in NSCLC. Online sequence prediction, a thorough search of the open source database The Cancer Genome Atlas (TCGA), immunohistochemistry (IHC) of TCSF in clinical lung cancer tissues, and a dual-luciferase assay, as well as assays to test viability, proliferation and apoptosis in vitro, were conducted to explain the targeted regulation association between miR-146a-5p and TCSF in NSCLC. The miRanda and TargetScanHuman database revealed that TCSF and miR-146a-5p had target binding sites. A luciferase reporter assay demonstrated that miR-146a-5p and TCSF did have complementary sequences (P<0.05). From the TCGA database, TCSF was highly expressed in lung adenocarcinoma and lung squamous cell carcinoma tissues when compared with normal lung tissues (P<0.05). Furthermore, the protein level of TCSF in cancerous lung tissues was determined by IHC, and it was concluded that TCSF protein was also upregulated in NSCLC tissues (P<0.001). A significant difference was identified following in vitro experiments for the NSCLC cell line A549, which revealed that miR-146a-5p and TCSF regulated cell viability, proliferation and apoptosis. In conclusion, the present study verified the target action association between TCSF and miR-146a-5p with high throughput data analysis and experimental results in NSCLC.

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.

Candidate diagnostic miRNAs that can detect cancer in prostate biopsy

BACKGROUND

While histopathological evaluation remains the gold standard for diagnosis of prostate cancer (PCa), sampling errors remain a frequent problem; therefore, use of tissue biomarkers that can distinguish between benign and malignant prostate disease is a potentially beneficial diagnostic strategy.

METHODS

Deep sequencing of the miRNA transcriptome of 14 benign prostatic hyperplasia (BPH) and 60 cancerous and non-cancerous prostate samples extracted from 34 cancer-bearing prostates removed by prostatectomy was performed; of the latter 60 samples, 16, 21, and 23 samples contained <10%, >30%, and no dysplastic cells, respectively. The predictive value of selected miRNAs was then tested by quantitative reverse-transcribed PCR (qRT-PCR), using two separate chemistries, Exiqon and Taqman, to evaluate the tissue samples obtained by prostatectomy. Validation experiments were also performed for a subset of miRNAs by qRT-PCR of 87 prostate core biopsies.

RESULTS

We identified 123 miRNAs significantly dysregulated in PCa (adjusted P-values <0.05); 110 and 13 miRNAs were dysregulated only in cancerous samples and non-cancerous samples extracted from cancer-bearing prostates, respectively, while 31 were dysregulated regardless of the dysplastic cell content of the studied specimens. The clinical utility of eight selected miRNAs was analyzed using the same sample set with two qRT-PCR chemistries. Measurable qRT-PCR signals were obtained for seven and six miRNAs using the Exiqon and Taqman chemistries, respectively, and expression levels of six and four of these miRNAs differed significantly between BPH and PCa samples, regardless of dysplastic cell content. Validation experiments on core biopsies using qRT-PCR confirmed differential expression between BPH and PCa of four miRNAs (miR-187-3p, miR-183-5p, miR-32-5p, and miR-141-5p) using the Exiqon and one miRNA (miR-187-3p) with the Taqman chemistry.

CONCLUSIONS

Our sequencing analyses identified several candidate diagnostic miRNAs and confirmed some which have previously been reported as diagnostic in prostate malignancy. The results of this study suggest also that some of selected miRNAs can differentiate between non-malignant and malignant prostates even when neoplastic cells are missing from the studied specimen.

Down-regulation of miR-30a-3p/5p promotes esophageal squamous cell carcinoma cell proliferation by activating the Wnt signaling pathway

AIM

To investigate the potential role of microRNA-30a (miR-30a) in esophageal squamous cell carcinoma (ESCC).

METHODS

Expression of miR-30a-3p/5p was analyzed using microarray data and fresh ESCC tissue samples. Both in vitro and in vivo assays were used to investigate the effects of miR-30a-3p/5p on ESCC cell proliferation. Furthermore, Kyoto Encyclopedia of Genes and Genomes analysis was performed to explore underlying mechanisms involved in ESCC, and then, assays were carried out to verify the potential molecular mechanism of miR-30a in ESCC.

RESULTS

Low expression of miR-30a-3p/5p was closely associated with advanced ESCC progression and poor prognosis of patients with ESCC. Knock-down of miR-30a-3p/5p promoted ESCC cell proliferation. Increased miR-30a-3p/5p expression inhibited the Wnt signaling pathway by targeting Wnt2 and Fzd2.

CONCLUSION

Down-regulation of miR-30a-3p/5p promotes ESCC cell proliferation by activating the Wnt signaling pathway through inhibition of Wnt2 and Fzd2.

Comprehensive analysis of aberrantly expressed microRNA profiles reveals potential biomarkers of human lung adenocarcinoma progression

Lung adenocarcinoma (LUAD) is a complex disease that poses challenges for diagnosis and treatment. The aim of the present study is to investigate LUAD-specific key microRNAs (miRNAs) from large-scale samples in The Cancer Genome Atlas (TCGA) database. We used an integrative computational method to identify LUAD-specific key miRNAs related to TNM stage and lymphatic metastasis from the TCGA database. Twenty-five LUAD-specific key miRNAs (fold change >2, p<0.05) from the TCGA database were investigated, and 15 were found to be aberrantly expressed with respect to clinical features. Three miRNAs were correlated with overall survival (log-rank p<0.05). Then, 5 miRNAs were randomly selected for verification of expression in 53 LUAD patient tissues using qRT-PCR. Diagnostic value of these above 5 miRNAs was determined by areas under receiver operating characteristic curves (ROC). Finally, the LUAD-related miRNA miR-30a-3p was selected for verification of biologic function in A549 cells. The results of tests for cell proliferation, apoptosis, and target genes suggested that miR-30a-3p decreases cell proliferation and promotes apoptosis through targeting AKT3. Therefore, miR-30a-3p may be a promising biomarker for the early screening of high-risk populations and early diagnosis of LUAD. Our studies provide insights into identifying novel potential biomarkers for diagnosis and prognosis of LUAD.

MicroRNA-30a-5p suppresses epithelial-mesenchymal transition by targeting profilin-2 in high invasive non-small cell lung cancer cell lines

PFN2 is an invasion promoter in several cancers including lung cancer. However, the probable effects and underlying mechanisms of PFN2 in tumor cell epithelial-mesenchymal-transition (EMT) of non-small cell lung cancer (NSCLC) remain poorly understood. The protein and mRNA levels of PFN2 in human bronchial epithelial cell line 16HBE and three NSCLC cell lines A549, NCI-H520 and 95D were assessed. The gain-of-function (overexpression) and loss‑of-function (siRNA) experiments of PFN2 were performed in 95D cells. A dual-luciferase reporter assay, western blotting and real-time PCR were used to investigate the relationship between PFN2 and miR‑30a‑5p. PFN2 was upregulated in three NSCLC cell lines, and the highest in 95D cell line. Furthermore, the upregulation of PFN2 promoted, whereas the downregulation of PFN2 suppressed invasion and EMT in 95D. Dual-luciferase reporter assay showed that miR‑30a‑5p directly interacts with the 3'-untranslated region (3'-UTR) of PFN2 mRNA. Interestingly, miR‑30a‑5p negatively regulates the expression of PFN2 and suppresses EMT and invasion in 95D. In summary, the present study demonstrated that miR‑30a‑5p inhibits EMT and invasion in high invasive NSCLC cell lines via targeting PFN2. Suggesting the association of miR‑30a‑5p and PFN2 may play an essential role in the development of NSCLC by modulating EMT and cell invasion.

miR-30a radiosensitizes non-small cell lung cancer by targeting ATF1 that is involved in the phosphorylation of ATM

Increasing number of studies report that microRNAs play important roles in radiosensitization. miR-30a has been proved to perform many functions in the development and treatment of cancer, and it is downregulated in non-small cell lung cancer (NSCLC) tissues and cells. This study was conducted to understand if miR-30a plays a role in the radiosensitivity of NSCLC cells. Radiosensitivity was examed by colony survival assay and tumor volume changing in vitro and in vivo, respectively. Bioinformatic analysis and luciferase reporter assays were used to distinguish the candidate target of miR-30a. qRT-PCR and western blotting were carried out to detect the relative expression of mRNAs and proteins. Cell cycle and cell apoptosis were determined by flow cytometry. Our results illustrated miR-30a could increase the radiosensitivity of NSCLC, especially in A549 cell line. In vivo experiment also showed the potential radiosensitizing possibility of miR-30a. Further exploration validated that miR-30a was directly targeting activating transcription factor 1 (ATF1). In studying the ataxia-telangiectasia mutated (ATM) associated effects on cell radiosensitivity, we found that miR-30a could reduce radiation induced G2/M cell cycle arrest and may also affect radiation induced apoptosis. Together, our results demonstrated that miR-30a may modulate the radiosensitivity of NSCLC through reducing the function of ATF1 in phosphorylation of ATM and have potential therapeutic value.

Exome-Wide Association Study Identifies Low-Frequency Coding Variants in 2p23.2 and 7p11.2 Associated with Survival of Non-Small Cell Lung Cancer Patients

INTRODUCTION

A growing body of evidence has suggested that low-frequency or rare coding variants might have strong effects on the development and prognosis of cancer. Here, we aim to assess the role of low-frequency and rare coding variants in the survival of NSCLC in Chinese populations.

METHODS

We performed an exome-wide scan of 247,870 variants in 1008 patients with NSCLC and replicated the promising variants by using imputed genotype data of The Cancer Genome Atlas (TCGA) with a Cox regression model. Gene-based and pathway-based analysis were also performed for nonsynonymous or splice site variants. Additionally, analysis of gene expression data in the TCGA was used to increase the reliability of candidate loci and genes.

RESULTS

A low-frequency missense variant in chaperonin containing TCP1 subunit 6A gene (CCT6A) (rs33922584: adjusted hazard ratio [HR_adjusted] = 1.75, p = 6.06 × 10^-4) was significantly related to the survival of patients with NSCLC, which was further replicated by the TCGA samples (HR_adjusted = 4.19, p = 0.015). Interestingly, the G allele of rs33922584 was significantly associated with high expression of CCT6A (p = 0.019) that might induce the worse survival in the TCGA samples (HR_adjusted = 1.15, p = 0.047). Besides, rs117512489 in gene phospholipase B1 gene (PLB1) (HR = 2.02, p = 7.28 × 10^-4) was also associated with survival of the patients with NSCLC in our samples, but it was supported only by gene expression analysis in the TCGA (HR_adjusted = 1.15, p = 0.023). Gene-based and pathway-based analysis revealed a total of 32 genes, including CCT6A and 34 potential pathways might account for the survival of NSCLC, respectively.

CONCLUSION

These results provided more evidence for the important role of low-frequency or rare variants in the survival of patients with NSCLC.