Systematic Analysis to Identify the MIR99AHG-has-miR-21-5p-EHD1 CeRNA Regulatory Network as Potential Biomarkers in Lung Cancer.

Lung cancer (LC) remains an extremely lethal disease worldwide, and effective prognostic biomarkers are at top priority. With the rapid development of high-throughput sequencing and bioinformatic analysis methods, the quest to characterize cancer transcriptomes continues to move forward. However, the integrated systematic analysis of lncRNA-miRNA-mRNA regulatory network in LC is lacking. In this study, we collected samples of cancer tissues and adjacent normal tissues from patients with lung cancer and conducted transcriptome and small RNA sequencing to identify differentially expressed genes (DEGs), miRNAs (DEMs), and lncRNAs (DELs). The regulatory roles of miRNAs in LC were explained by functional analysis on DEM-targeted genes. The lncRNA-miRNA pairs, miRNA-mRNA pairs, and lncRNA-mRNA pairs were identified and combined to construct the interplay of lncRNA-miRNA-mRNA. We evaluated the prognostic value of selected lncRNA-miRNA-mRNA by Kaplan-Meier analysis. Finally, we analyzed the expression levels of selected DEM, DELs, and DEGs in lung cancer patients and healthy people to verify our findings. A total of 1492 DEGs, 12 DEMs, and 604 DELs were identified in LC patients. Based on the bioinformatic analysis and the regulatory mechanism of ceRNAs, 3 lncRNAs (GATA2-AS1, LINC00632, MIR99AHG), 1 miRNA (hsa-miR-21-5p) and 5 targeted genes (RECK, TIMP3, EHD1, RASGRP1 and ERG) were figured out first. Through further Kaplan-Meier analysis screening the prognostic value, we finally found the hub subnetwork (MIR99AHG-hsa-miR-21-5p-EHD1) by collating lncRNA-miRNA pairs, miRNA-mRNA pairs and lncRNA-mRNA pairs. As the key of ceRNA regulatory network, the expression of miRNA-21-5p in lung cancer patients was significantly higher than that in healthy people (P < 0.01), and its high expression was significantly associated with poor prognosis (P = 0.0025). Our study successfully constructed a MIR99AHG-hsa-miR-21-5p-EHD1 mutually regulatory network, suggesting the potential efficient biomarkers in LC.

Analysis of Methylome, Transcriptome, and Lipid Metabolites to Understand the Molecular Abnormalities in Polycystic Ovary Syndrome.

Purpose: This study aimed to identify differentially methylated genes (DMGs) and differentially expressed genes (DEGs) to investigate new biomarkers for the diagnosis and treatment of polycystic ovary syndrome (PCOS). Methods: To explore the potential biomarkers of PCOS diagnosis and treatment, we performed methyl-binding domain sequencing (MBD-seq) and RNA sequencing (RNA-seq) on ovarian granulosa cells (GCs) from PCOS patients and healthy controls. MBD-seq was also performed on the ovarian tissue of constructed prenatally androgenized (PNA) mice. Differential methylation and expression analysis were implemented to identify DMGs and DEGs, respectively. The identified gene was further verified by real-time quantitative PCR (RT-qPCR) and methylation-specific PCR (MSP) in clinical samples. Furthermore, ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) was carried out on PCOS patients and healthy controls to identify differential lipid metabolites. Results: Compared to the control group, 13,526 DMGs related to the promoter region and 2429 DEGs were found. The function analysis of DMGs and DEGs showed that they were mainly enriched in glycerophospholipid, ovarian steroidogenesis, and other lipid metabolic pathways. Moreover, 5753 genes in DMGs related to the promoter region were screened in the constructed PNA mice. Integrating the DMGs data from PCOS patients and PNA mice, we identified the following 8 genes: CDC42EP4, ERMN, EZR, PIK3R1, ARHGEF18, NECTIN2, TSC2, and TACSTD2. RT-qPCR and MSP verification results showed that the methylation and expression of TACSTD2 were consistent with sequencing data. Additionally, 15 differential lipid metabolites were shown in the serum of PCOS patients. The differential lipids were involved in glycerophospholipid and glycerolipid metabolism. Conclusion: Using integration of methylome and lipid metabolites profiling we identified 8 potential epigenetic markers and 15 potential lipid metabolite markers for PCOS. Our results suggest that aberrant DNA methylation and lipid metabolite disorders may provide novel insights into the diagnosis and etiology of PCOS.

MicroRNA biomarkers and their use in evaluating the prognosis of lung cancer.

OBJECTIVE: We aim to use the microRNA (miRNA, micro-ribonucleic acid) data of lung cancer tissues to establish a miRNA biomarker database for lung cancer that can be used for marker screening and analysis of lung cancer prognosis. METHODS: We obtained lung cancer-related data from The Cancer Genome Atlas (TCGA) and analyzed the miRNA expression profiles of lung cancer tissues and normal tissues using bioinformatics techniques to develop a new composite miRNA-based model for the prognostic assessment of lung cancer. The predictive power of this model was verified and evaluated based on grouping of data. We also performed RT-qPCR using lung cancer tissues from patients diagnosed with lung cancer. RESULTS: There was a significant difference between the miRNA expression profiles of lung cancer tissues and normal tissues adjacent to the cancerous lesions. The prognostic survival of patients with lung cancer was closely related to onset age and staging (p = 0.012) but was not related to gender (p = 0.39) and race (p = 0.51). Using three methods of survival model construction, we identified three miRNA composites, namely hsa-mir-21, hsa-mir-141, and has-mir-490, as markers for the prognosis of lung cancer. As confirmed by RT-qPCR, the expressions of hsa-miR-21-5p and hsa-miR-141-5p were upregulated, whereas hsa-miR-490-3p expression was downregulated in lung cancer lesion tissues. CONCLUSION: The three miRNA composites identified, namely hsa-mir-21, hsa-mir-141, and hsa-mir-490, have the potential to serve as novel prognostic biomarkers and therapeutic targets for lung cancer.