Identification of a microRNA signature associated with survivability in cervical squamous cell carcinoma

LINC-PINT suppresses breast cancer cell proliferation and migration via MEIS2/PPP3CC/NF-κB pathway by sponging miR-576-5p

BACKGROUND

Breast cancer (BCa) is the most frequent malignant tumor in women. Long non-coding RNAs (lncRNAs) have been acknowledged to exert critical regulating functions in various cancers. Long intergenic non-protein coding RNA, p53 induced transcript (LINC-PINT) has been reported to be a chemosensitizer and a tumor suppressor in BCa. However, its downstream molecular mechanism contributing to its tumor-suppressing role remains to be explored in BCa.

METHODS

LINC-PINT expression in BCa tissues and cells was measured using quantitative real-time polymerase chain reaction (RT-qPCR). The proliferation of transfected BCa cells was examined by counting kit-8 (CCK-8) and EdU assay. The migrating ability of indicate BCa cells was assessed by wound healing assays. Bioinformatics analysis and mechanism experiments such as RNA immunoprecipitation (RIP), RNA pull down assay, and luciferase reporter assay, were applied to demonstrate the downstream targets of LINC-PINT.

RESULTS

LINC-PINT was downregulated in BCa tissues and cell lines. Overexpression of LINC-PINT suppressed BCa cell proliferation and migration. LINC-PINT could interact with miR-576-5p to upregulate Meis homeobox 2 (MEIS2) that positively regulated protein phosphatase 3 catalytic subunit gamma (PPP3CC) by inactivating the nuclear factor-κB (NF-κB) pathway.

CONCLUSIONS

These findings elucidated the anti-tumor role of LINC-PINT in BCa via the miR-576-5p/MEIS2/PPP3CC/NF-κB axis, which suggested that LINC-PINT might serve as a potential therapeutic target for BCa.

LUM as a novel prognostic marker and its correlation with immune infiltration in gastric cancer: a study based on immunohistochemical analysis and bioinformatics

BACKGROUND

Gastric cancer (GC) is considered the sixth highly prevailing malignant neoplasm and is ranked third in terms of cancer mortality rates. To enable an early and efficient diagnosis of GC, it is important to detect the fundamental processes involved in the oncogenesis and progression of gastric malignancy. The understanding of molecular signaling pathways can facilitate the development of more effective therapeutic strategies for GC patients.

METHODS

The screening of genes that exhibited differential expression in early and advanced GC was performed utilizing the Gene Expression Omnibus databases (GSE3438). Based on this, the protein and protein interaction network was constructed to screen for hub genes. The resulting list of hub genes was evaluated with bioinformatic analysis and selected genes were validated the protein expression by immunohistochemistry (IHC). Finally, a competing endogenous RNA network of GC was constructed.

RESULTS

The three genes (ITGB1, LUM, and COL5A2) overexpressed in both early and advanced GC were identified for the first time. Their upregulation has been linked with worse overall survival (OS) time in patients with GC. Only LUM was identified as an independent risk factor for OS among GC patients by means of additional analysis. IHC results demonstrated that the expression of LUM protein was increased in GC tissue, and was positively associated with the pathological T stage. LUM expression can effectively differentiate tumorous tissue from normal tissue (area under the curve = 0.743). The area under 1-, 3-, and 5-year survival relative operating characteristics were greater than 0.6. Biological function enrichment analyses suggested that the genes related to LUM expression were involved in extracellular matrix development-related pathways and enriched in several cancer-related pathways. LUM affects the infiltration degree of cells linked to the immune system in the tumor microenvironment. In GC progression, the AC117386.2/hsa-miR-378c/LUM regulatory axis was also identified.

CONCLUSION

Collectively, a thorough bioinformatics analysis was carried out and an AC117386.2/hsa-miR-378c/LUM regulatory axis in the stomach adenocarcinoma dataset was detected. These findings should serve as a guide for future experimental investigations and warrant confirmation from larger studies.

Functional Screen for microRNAs Suppressing Anchorage-Independent Growth in Human Cervical Cancer Cells

The progression of anchorage-dependent epithelial cells to anchorage-independent growth represents a critical hallmark of malignant transformation. Using an in vitro model of human papillomavirus (HPV)-induced transformation, we previously showed that acquisition of anchorage-independent growth is associated with marked (epi)genetic changes, including altered expression of microRNAs. However, the laborious nature of the conventional growth method in soft agar to measure this phenotype hampers a high-throughput analysis. We developed alternative functional screening methods using 96- and 384-well ultra-low attachment plates to systematically investigate microRNAs regulating anchorage-independent growth. SiHa cervical cancer cells were transfected with a microRNA mimic library (n = 2019) and evaluated for cell viability. We identified 84 microRNAs that consistently suppressed growth in three independent experiments. Further validation in three cell lines and comparison of growth in adherent and ultra-low attachment plates yielded 40 microRNAs that specifically reduced anchorage-independent growth. In conclusion, ultra-low attachment plates are a promising alternative for soft-agar assays to study anchorage-independent growth and are suitable for high-throughput functional screening. Anchorage independence suppressing microRNAs identified through our screen were successfully validated in three cell lines. These microRNAs may provide specific biomarkers for detecting and treating HPV-induced precancerous lesions progressing to invasive cancer, the most critical stage during cervical cancer development.

An immune-associated ten-long noncoding RNA signature for predicting overall survival in cervical cancer

BACKGROUND

Several immune-associated long non-coding RNA (lncRNA) signatures have been reported as prognostic models in different types of cancers; however, the immune-associated lncRNA signature for predicting overall survival (OS) in cervical cancer is unknown.

METHODS

The lncRNA expression profiles and clinical data of cervical cancer were acquired from The Cancer Genome Atlas (TCGA) dataset. Immune-associated genes were extracted from the Molecular Signatures Database (MSigDB), and the immune-associated lncRNAs were extracted for Cox regression analysis. Principal component analysis (PCA) was used to distinguish the high and low risk status of cervical cancer patients. Gene Set Enrichment Analysis (GSEA) was used for functional analyses.

RESULTS

Cox regression analyses and the least absolute shrinkage and selection operator (LASSO) Cox regression model were used to construct an immune-associated ten-lncRNA signature (containing AL021807.1, AL109976.1, LINC02446, MIR4458HG, AC004540.2, AC009065.8, AC083809.1, AC055822.1, AP000904.1, and FBXL19-AS1) for predicting OS in cervical cancer. The signature segregated the cervical cancer patients into 2 groups (high-risk group and low-risk group). The Kaplan-Meier survival curves of AL021807.1, AL109976.1, LINC02446, and MIR4458HG were statistically significant (P<0.05) and the others (including AC004540.2, AC009065.8, AC083809.1, AC055822.1, AP000904.1, and FBXL19-AS1) were not statistically significant (P>0.05). The Kaplan-Meier survival curves of the signature were statistically significant (P=1.134e-10), and the 5-year survival rate was 0.444 in the high-risk group [95% confidence interval (CI): 0.334 to 0.590] and 0.884 in the low-risk group (95% CI: 0.807 to 0.969). The area under curve (AUC) of the receiver operating characteristic (ROC) curve of the signature was 0.833. The concordance index (C-index) of the signature was 0.788 (95% CI: 0.730 to 0.846, P=1.884778e-22). The PCA successfully distinguished the high-risk group and low-risk group based on the signature. The GSEA showed that the signature-related protein coding genes (PCGs) may participate in immunologic biological processes and pathways.

CONCLUSIONS

This study revealed that the immune-associated ten-lncRNA signature is an independent factor for cervical cancer prognosis prediction, providing a bright future for immunotherapy of cervical cancer patients.

miR-378c suppresses Wilms tumor development via negatively regulating CAMKK2

Wilms tumor is a rare kidney malignancy primarily developed in children. Treatment for Wilms tumor includes surgery, radiotherapy, and chemotherapy. Recent studies have demonstrated that microRNAs (miRNAs) play important roles in regulating Wilms tumor development. In this study, we aimed to elucidate the expression and function of miR-378c in Wilms tumor. Quantitative real-time PCR (qRT-PCR) results showed that miR-378c was downregulated in Wilms tumor tissues and cell lines. Functionally, further CCK-8, would healing, and transwell assays revealed that overexpression of miR-378c impaired Wilms tumor cell growth and metastasis in vitro. In addition, xenograft assay showed that miR-378c overexpression inhibited Wilms tumor development in vivo. Mechanistically, luciferase reporter assay confirmed that miR-378c directly targets CAMKK2 in Wilms tumor. qRT-PCR and western blot assays demonstrated that CAMKK2 was highly expressed in Wilms tumor tissues and cell lines. Rescue experiments were performed to further evaluate the functional relationship between miR-378c and CAMKK2. Overexpression of miR-378c suppressed Wilms tumor cell metastasis via negatively regulating CAMKK2 expression. Consistently, inhibition of miR-378c enhanced Wilms tumor cell malignancy behavior via augmenting CAMKK2 expression, which could be abrogated by CAMKK2 knockdown. In summary, our findings suggest that miR-378c inhibits the development and metastasis of Wilms tumor via negatively regulating CAMKK2 expression, which could be utilized to develop new therapy strategy.

Identification of a Six-Gene Signature for Predicting the Overall Survival of Cervical Cancer Patients

Background

Although the incidence of cervical cancer has decreased in recent decades with the development of human papillomavirus vaccines and cancer screening, cervical cancer remains one of the leading causes of cancer-related death worldwide. Identifying potential biomarkers for cervical cancer treatment and prognosis prediction is necessary.

Methods

Samples with mRNA sequencing, copy number variant, single nucleotide polymorphism and clinical follow-up data were downloaded from The Cancer Genome Atlas database and randomly divided into a training dataset (N=146) and a test dataset (N=147). We selected and identified a prognostic gene set and mutated gene set and then integrated the two gene sets with the random survival forest algorithm and constructed a prognostic signature. External validation and immunohistochemical staining were also performed.

Results

We obtained 1416 differentially expressed prognosis-related genes, 624 genes with copy number amplification, 1038 genes with copy number deletion, and 163 significantly mutated genes. A total of 75 candidate genes were obtained after overlapping the differentially expressed genes and the genes with genomic variations. Subsequently, we obtained six characteristic genes through the random survival forest algorithm. The results showed that high expression of SLC19A3, FURIN, SLC22A3, and DPAGT1 and low expression of CCL17 and DES were associated with a poor prognosis in cervical cancer patients. We constructed a six-gene signature that can separate cervical cancer patients according to their different overall survival rates, and it showed robust performance for predicting survival (training set: p ˂ 0.001, AUC = 0.82; testing set: p ˂ 0.01, AUC = 0.59).

Conclusion

Our study identified a novel six-gene signature and nomogram for predicting the overall survival of cervical cancer patients, which may be beneficial for clinical decision-making for individualized treatment.

miR-642a-5p partially mediates the effects of lipopolysaccharide on human pulmonary microvascular endothelial cells via eEF2

Inhalation or systemic administration of lipopolysaccharide (LPS) can induce acute pulmonary inflammation and lung injury. The pulmonary vasculature is composed of pulmonary microvascular endothelial cells (PMVECs), which form a semiselective membrane for gas exchange. The miRNA miR‐642a‐5p has previously been reported to be up‐regulated in patients with acute respiratory distress syndrome; thus, here, we examined whether this miRNA is involved in the effects of LPS on PMVECs. The levels of miR‐642a‐5p and mRNA encoding eukaryotic elongation factor 2 (eEF2) were detected by quantitative RT‐PCR. Moesin and eEF2 protein levels were tested by western blot assay. Dual‐luciferase reporter assay was used to examine the relationship between miR‐642a‐5p and eEF2. Cell viability was assessed using the 3‐(4,5‐dimethylthiazol‐2‐yl)‐2,5‐diphenyltetrazolium bromide assay, and cell permeability was analyzed using the transendothelial electrical resistance assay. We report that miR‐642a‐5p levels are significantly up‐regulated in LPS‐stimulated PMVECs, and miR‐642a‐5p contributes to LPS‐induced hyperpermeability and apoptosis of PMVECs. LPS treatment results in down‐regulation of eEF2 in PMVECs. Overexpression of eEF2, a direct target of miR‐642a‐5p, inhibited the effect of LPS on PMVECs. miR‐642a‐5p promoted LPS‐induced hyperpermeability and apoptosis by targeting eEF2. Thus, miR‐642a‐5p and eEF2 may serve as potential targets for acute lung injury/acute respiratory distress syndrome diagnosis or treatment.

Inhibition of miR-378a-3p by Inflammation Enhances IL-33 Levels: A Novel Mechanism of Alarmin Modulation in Ulcerative Colitis

Ulcerative colitis (UC) is an inflammatory bowel disease (IBD) characterized by mucosa damage associated with an uncontrolled inflammatory response. This immunological impairment leads to altered inflammatory mediators such as IL-33, which is shown to increase in the mucosa of active UC (aUC) patients. MicroRNAs present a distorted feature in inflamed colonic mucosa and are potential IL-33 regulating candidates in UC. Therefore, we studied the microRNA and mRNA profiles in inflamed colonic samples of UC patients, evaluating the effect of a microRNA (selected by in silico analysis and its expression in UC patients), on IL-33 under inflammatory conditions. We found that inflamed mucosa (n = 8) showed increased expression of 40 microRNAs and 2,120 mRNAs, while 49 microRNAs and 1,734 mRNAs were decreased, as determined by microarrays. In particular, IL-33 mRNA showed a 3.8-fold increase and eight members of a microRNA family (miR-378), which targets IL-33 mRNA in the 3'UTR, were decreased (-3.9 to -3.0 times). We selected three members of the miR-378 family (miR-378a-3p, miR-422a, and miR-378c) according to background information and interaction energy analysis, for further correlation analyses with IL-33 expression through qPCR and ELISA, respectively. We determined that aUC (n = 24) showed high IL-33 levels, and decreased expression of miR-378a-3p and miR-422a compared to inactive UC (n = 10) and controls (n = 6). Moreover, both microRNAs were inversely correlated with IL-33 expression, while miR-378c does not show a significant difference. To evaluate the effect of TNFα on the studied microRNAs, aUC patients with anti-TNF therapy were compared to aUC receiving other treatments. The levels of miR-378a-3p and miR-378c were higher in aUC patients with anti-TNF. Based on these findings, we selected miR-378a-3p to exploring the molecular mechanism involved by in vitro assays, showing that over-expression of miR-378a-3p decreased the levels of an IL-33 target sequence β-gal-reporter gene in HEK293 cells. Stable miR-378a-3p over-expression/inhibition inversely modulated IL-33 content and altered viability of HT-29 cells. Additionally, in an inflammatory context, TNFα decreased miR-378a-3p levels in HT-29 cells enhancing IL-33 expression. Together, our results propose a regulatory mechanism of IL-33 expression exerted by miR-378a-3p in an inflammatory environment, contributing to the understanding of UC pathogenesis.

The microRNApolymorphisms inmiR-150 and miR-1179 are associated with risk of idiopathic recurrent pregnancy loss

RESEARCH QUESTION

Are single nucleotide polymorphisms of microRNAs (miRNAs) and risk of idiopathic recurrent pregnancy loss (RPL) associated?

DESIGN

A total 375 patients with idiopathic RPL (age, mean ± standard deviation [SD] 33.02 ± 4.24 years; body mass index [BMI], mean ± SD, 21.57 ± 3.70 kg/m²) and 276 control participants (age, mean ± SD, 33.01 ± 5.27 years; BMI, mean ± SD, 21.58 ± 3.20) were recruited. Pregnancy loss was diagnosed using human chorionic gonadotrophin concentrations, ultrasonography and/or physical examination prior to 20 weeks of gestation. The genotype of the participants was determined by polymerase chain reaction restriction fragment length polymorphism analysis. Statistical analysis was performed to investigate the differences in frequencies between the control and RPL genotypes RESULTS: The miR-150G>A heterozygous genotype was significantly associated with increased risk of RPL (adjusted odds ratio 2.502, 95% confidence interval 1.555-4.025; P = 0.0002). The miR-1179A>T heterozygous genotype was significantly associated with decreased risk of RPL (adjusted odds ratio 0.633, 95% confidence interval 0.454-0.884; P = 0.007). Some allele combinations that included miR-150A or miRNA-1179T resulted in an increase or decrease in risk of RPL, respectively.

CONCLUSIONS

The miR-150G>A and miR-1179A>T polymorphisms were more frequently associated with RPL compared with controls.

A Comprehensive RNA Expression Signature for Cervical Squamous Cell Carcinoma Prognosis

Clinicopathological characteristics alone are not enough to predict the survival of patients with cervical squamous cell carcinoma (CESC) due to clinical heterogeneity. In recent years, many genes and non-coding RNAs have been shown to be oncogenes or tumor-suppressors in CESC cells. This study aimed to develop a comprehensive transcriptomic signature for CESC patient prognosis. Univariate, multivariate, and Least Absolute Shrinkage and Selection Operator penalized Cox regression were used to identify prognostic signatures for CESC patients from transcriptomic data of The Cancer Genome Atlas. A normalized prognostic index (NPI) was formulated as a synthetical index for CESC prognosis. Time-dependent receiver operating characteristic curve analysis was used to compare prognostic signatures. A prognostic transcriptomic signature was identified, including 1 microRNA, 1 long non-coding RNA, and 6 messenger RNAs. Decreased survival was associated with CESC patients being in the high-risk group stratified by NPI. The NPI was an independent predictor for CESC patient prognosis and it outperformed the known clinicopathological characteristics, microRNA-only signature, gene-only signature, and previously identified microRNA and gene signatures. Function and pathway enrichment analysis revealed that the identified prognostic RNAs were mainly involved in angiogenesis. In conclusion, we proposed a transcriptomic signature for CESC prognosis and it may be useful for effective clinical risk management of CESC patients. Moreover, RNAs in the transcriptomic signature provided clues for downstream experimental validation and mechanism exploration.