Dynamic and static circulating cancer microRNA biomarkers - a validation study

Automation and miniaturization of high-throughput qPCR for gene expression profiling

Quantitative PCR (qPCR) is a technique commonly employed in laboratories and core facilities. In our previous study, we had shown the possibility to automate steps in a panel-specific gene expression workflow by pairing Mosquito HV with BioMark HD. Here we aimed to automate the full workflow and explore miniaturization capabilities. Each step of the gene expression workflow was scripted on Mosquito HV genomics software. We performed three different automated runs: i. Replicates of a Reference RNA sample (obtained by pooling RNA isolated from 10 healthy individuals) were run on an immunology gene expression panel. We tested the full reaction (FR) and three miniaturization conditions, namely: 1.5x, 2.5x and 5x; the data obtained from the automated FR replicates was compared to the data obtained from the manual processing; ii. Biological RNA samples (isolated from n = 45 individuals) were run as FR and 1.5x on the immunology gene expression panel; iii. Biological RNA samples (isolated from n = 45 individuals) were run as FR and 1.5x on a pregnancy gene expression panel. The expression of each gene was calculated using the 2(-delta Ct) method. Successful amplification was observed for the reference samples when using FR and 1.5x conditions. The 2.5x condition exhibited suboptimal amplification with a lower success rate while the 5x condition retrieved no amplification. The 2.5x and 5x miniaturization conditions were excluded from further runs. A strong significant positive correlation was observed between the manual and automated workflows for the reference RNA sample, underscoring the robustness of the gene expression assay. The automation of the immunology and pregnancy gene expression panels on the 45 individual samples retrieved a success rate >70 % for both the FR and the 1.5x miniaturization conditions. A significant positive correlation was also observed between the FR and 1.5x miniaturization conditions for both panels. Our results show that the adoption and the 1.5x miniaturization capabilities of Mosquito HV system for automating the gene expression workflow did not interfere with data quality and reproducibility.

Research trend of lung cancer epigenetics research: Bibliometric and visual analysis of top-100 cited documents

Background

Lung cancer is a highly prevalent cancer on a global scale and its oncogenic process is driven by the accumulation of multiple pathological events. Epigenetics has gained significant recognition in recent years as a crucial contributor to the development of lung cancer. Epigenetics include processes such as DNA methylation, histone modification, chromatin remodeling, and RNA modification. These pathways lead to enduring alterations in genetic phenotypes, which are crucial in the advancement and growth of lung cancer. However, the specific mechanisms and roles of epigenetics in lung cancer still need to be further elucidated.

Methods

We obtained publications from the Web of Science databases and applied a rigorous search method to filter them. Ultimately, we gathered high-quality publications that had received the highest 100 number of citations. The data were processed and visualized by various bibliometric tools.

Results

The 100 papers had varying numbers of citations, with the lowest being 491 and the most being 6316. On average, each work received 1119 citations. A total of 1056 co-authors were involved in publishing these papers in 59 journals from 185 institutions in 27 countries. The majority of high-caliber research in the subject of lung cancer epigenetics is conducted in advanced countries, with the United States taking the lead in terms of both the quantity of articles produced and their academic influence. The study of DNA methylation has been a longstanding research priority in the discipline. With the development of next-generation sequencing technology in recent years, research related to non-coding RNA has become a research hotspot. Future research directions may focus more on exploring the mechanisms of action of messenger RNA and circular RNA and developing targeted treatment strategies based on non-coding RNA drugs.

Conclusion

We analyzed 100 top lung cancer and epigenetics documents through various bibliometric analysis tools. This study provides a concise overview of the findings from prior research, anticipates future research directions, and offers potential avenues for additional investigation.

Noncoding RNAs as a potential biomarker for the prognosis of bladder cancer: a systematic review and meta-analysis

OBJECTIVE

The relationship between noncoding RNAs and the prognosis of bladder cancer (BC) is still controversial. The purpose of this study is to evaluate the relationship between noncoding RNAs and prognosis by meta-analysis.

METHODS

Comprehensive retrieval of PubMed, Embase, the Cochrane Library, the Web of Science, CNKI, and WanFang databases is related to the correlation between noncoding RNAs and the prognosis of BC. Data were extracted, and the literature quality was evaluated. STATA16.0 served for the meta-analysis.

RESULTS

1. CircRNAs: High circ-ZFR expression led to poor overall survival (OS) of BC. 2. LncRNAs: Low lnc-GAS5 expression predicted poor OS of BC, high lnc-TUG1 expression predicted poor OS of BC. 3. MiRNAs: High miR-21 expression predicted poor OS of BC, high miR-222 expression led to poor OS of BC, high miR-155 expression predicted poor progression-free survival (PFS) of BC, high miR-143 expression caused poor PFS of BC, low miR-214 expression could result in poor recurrence-free survival (RFS) of BC.

CONCLUSIONS

High circ-ZFR, lnc-TUG1, miR-222, and miR-21 expressions were correlated with poor OS of BC; high miR-155 and miR-143 expression predicted poor PFS of BC; low lnc-GAS5 expression predicted poor OS of BC; low miR-214 expression predicted poor RFS of BC.

Expression of SPAG7 and its regulatory microRNAs in seminal plasma and seminal plasma-derived extracellular vesicles of patients with subfertility

Seminal plasma contains a variety of extracellular vesicles (EVs) that deliver RNAs including microRNAs (miRNAs) molecules. However, the roles of these EVs along with their delivered RNAs and their interactions with male infertility are not clear. Sperm-associated antigen 7 (SPAG 7) is expressed in male germ cells and plays a crucial role in several biological functions associated with sperm production and maturation. In this study, we aimed to identify the post-transcriptional regulation of SPAG7 in seminal plasma (SF-Native) and seminal plasma-derived extracellular vesicles (SF-EVs) collected from 87 men undergoing infertility treatment. Among the multiple binding sites for miRNAs within its 3'UTR of SPAG7, we identified the binding of four miRNAs (miR-15b-5p, miR-195-5p, miR-424-5p, and miR-497-5p) to the 3'UTR of SPAG7 by the dual luciferase assays. Analyzing sperm, we found reduced mRNA expression levels of SPAG7 in SF-EVs and SF-Native samples from oligoasthenozoospermic men. By contrast, two miRNAs (miR-424-5p and miR-497-5p) form the SF-Native samples, and four miRNAs (miR-195-5p, miR-424-5p, miR-497-5p, and miR-6838-5p) from the SF-EVs samples showed significantly higher expression levels in oligoasthenozoospermic men. The expression levels of miRNAs and SPAG7 were significantly correlated with basic semen parameters. These findings contribute significantly to our understanding of regulatory pathways in male fertility by showing a direct link between upregulated miRNA, notably miR-424, and downregulated SPAG7 both in seminal plasma and in plasma-derived EVs likely contributing to oligoasthenozoospermia.

Expression profiling analysis reveals key microRNA-mRNA interactions in patients with transposition of the great arteries and systemic left and right ventricles

Background

Patients with transposition of the great arteries (TGA) have different connected systemic chambers and this determines the long-term morbidities and survival. Limited findings have been reported to systematically identify miRNA and mRNA expression levels in such cohorts of patients. In this study, we aimed to characterize miRNAs, mRNAs, and miRNA-mRNA interaction networks in patients with TGA, with a systemic left (LV) and right ventricle (RV).

Materials and methods

Large panel of human miRNA and mRNA microarrays were conducted to determine the genome-wide expression profiles in the blood of 16 TGA-RV patients, 16 TGA-LV patients, and 16 age and gender-matched controls. Using real-time quantitative PCR (RT-qPCR), the differential expression level of a single miRNA was validated. Enrichment analyses of altered miRNA and mRNA expression levels were identified using bioinformatics tools.

Results

Altered miRNA and mRNA expression levels were observed between TGA-RV and TGA-LV patients, together or separated, compared to controls. Among the deregulated miRNAs and mRNAs, 39 and 101 miRNAs were identified as significantly differentially expressed in patients with TGA (both TGA-RV and TGA-LV) and TGA-RV, when compared to matched controls. Furthermore, 51 miRNAs were identified as significantly differentially expressed in patients with TGA-RV when compared to patients with TGA-LV. RT-qPCR relative expression level was highly consistent with microarray analysis results. Similarly, 36 and 164 mRNAs were identified as significantly differentially expressed in patients with TGA (both TGA-RV and TGA-LV) and TGA-RV, when compared to matched controls. Additionally, miR-140-3p showed a higher expression level in patients with overt heart failure (FC = 1.54; P = 0.001) and miR-502-3p showed a higher expression level in patients died due to cardiac death (FC = 1.41; P = 0.011). Integrative analysis resulted in 21 and 23 target genes with higher and lower expression levels, respectively (r ≥ 0.50 and P < 0.05). These target genes (i.e., 21 and 23 target genes) showed an inverse direction of regulation with miRNA and exhibited a miRNA binding site position within the 3'UTR of the target gene.

Conclusion

Our findings provide new insights into a potential molecular biomarker(s) for patients with TGA that may guide better risk stratification and the development of novel targeting therapies. Future studies are needed to investigate the potential significance of miRNAs and mRNAs in TGA-related cardiovascular diseases.