A comprehensive bioinformatic analysis revealed novel MicroRNA biomarkers of Parkinson's disease

Identifying Genetic Profiles in Peripheral Blood Mononuclear Cells in Women with Polycystic Ovary Syndrome: An Observational Case-Control Study

BACKGROUND

Polycystic ovary syndrome (PCOS) is an endocrine and reproductive condition affecting women of reproductive age, although its expression profiles and molecular pathways are not fully understood.

AIMS

To identify the transcriptome expression profiles of peripheral blood mononuclear cells (PBMCs) in women with PCOS and controls. To investigate noninvasive diagnostic biomarkers and potential treatment targets to improve women's fertility.

METHODS

RNA sequencing (RNA-Seq) was conducted on PBMC samples from six patients with PCOS and six healthy controls. qRT-PCR validation was carried out in 68 subjects. Multivariate logistic regression was performed to assess the combined impact of biomarkers.

RESULTS

A total of 186 differentially expressed genes (DEG) were found between patients and controls (log2FC >1, p <0.05). Enrichment analysis revealed cytokine-mediated signaling pathways, cytokine activity, and cytokine-cytokine receptor interaction. RNA sequencing showed consistency with qRT-PCR. Women with PCOS had significantly higher levels of AQP9 (p <0.001), PROK2 (p = 0.001), and S100A12 (p <0.001) expression compared to controls. AQP9 (AUC = 0.77), PROK2 (AUC = 0.71), and S100A12 (AUC = 0.82) adequately discriminated women with PCOS from healthy controls. In addition, multiple logistic regression on biomarkers resulted in a significant diagnostic power with an AUC = 0.89, 95% CI: 0.81-0.97, p <0.0001. Further associations were analyzed between relative gene expression and clinical, anthropometric, hormonal, and ultrasonographic data.

CONCLUSIONS

Dysregulated RNA expression in PBMCs may contribute to an increased risk of PCOS and serve as a potential diagnostic biomarker. The involvement of inflammatory and cytokine-related pathways supports the notion that PCOS is a chronic inflammatory condition.

Identification and Validation of Biomarkers for Alzheimer's Disease Based on Akt and Wnt Signaling Pathways in Mouse Models

Alzheimer's disease (AD) is a neurodegenerative disease that remains challenging to treat. Akt and Wnt play a role in complex cellular signaling, which is crucial for examining the onset of AD. In this study, we aimed to identify and analyze Akt pathway-related genes (ARGs) and Wnt pathway-related genes (WRGs) as AD biomarkers, determine the effects of ARGs and WRGs on AD, and verify these effects in AD mouse models. We searched for differentially expressed genes in the Gene Expression Omnibus database, constructed candidate gene protein-protein interaction networks, and used least absolute shrinkage and selection operator regression analysis and the support vector machine-recursive feature elimination algorithm to screen key genes. Correlation and functional similarity analyses of key genes, immune infiltration analysis, competing endogenous RNA network construction, and drug prediction of key genes were performed. Expression of key genes in streptozotocin-treated (STZ)-treated AD mice was validated using quantitative reverse transcription polymerase chain reaction (RT-qPCR). Bioinformatics analysis identified five key genes in AD: PRKACA, CDH3, ATP6V0C, DLL1, and CELSR2. Step-down tests, immunohistochemistry, and silver plate staining confirmed successful treatment of STZ-induced AD in mice. According to RT-qPCR analysis, the relative expression of DLL1 mRNA in AD mice was higher than that in control mice, whereas the relative expression of ATP6V0C and PRKACA mRNA in AD mice was lower than that in control mice; this was consistent with the results of bioinformatics analysis (p < 0.05). This study screened and validated AD biomarkers associated with the Akt and Wnt pathways in mouse models.

CircRNA-mediated ceRNA regulatory networks: transcriptomic insights into obesity type 2 diabetes progression and treatment strategies

The aim of this study was to deeply explore the pathogenesis of obesity type 2 diabetes mellitus (O-T2DM) and search for potential biomarkers through high-throughput RNA sequencing technology. The study included 15 patients with O-T2DM and 15 healthy controls, and peripheral blood samples were collected for transcriptome analysis. The results showed that compared with the control group, there were 442 circRNAs and 2756 mRNAs with significant differential expression in the O-T2DM group. Through weighted gene co-expression network analysis (WGCNA) and pathway enrichment analysis, it was found that the differentially expressed mRNAs were mainly enriched in signaling pathways such as T cell receptor, cell senescence, cytotoxicity mediated by NK cells, IL-17, lipids and atherosclerosis, and the oxidative phosphorylation pathway was activated, and apoptosis was inhibited. Based on the ceRNA theory, a regulatory network was constructed, and key circRNAs such as hsa_circ_0060614 were screened out, which may regulate the expression of the MT2A gene by adsorbing hsa-mir-4668-3p, and the expression levels of the three were significantly increased in O-T2DM patients. This study provides a new perspective for the research on the molecular mechanism of O-T2DM and an important theoretical basis for the development of personalized treatment and precision medicine for it.

Upregulated PCAT-1 predicts poor prognosis and reduced immune cell infiltration in head and neck squamous cell carcinoma through the miR-145-5p / FSCN-1 axis

BACKGROUND

LncRNA PCAT-1 is known to promote cancer proliferation, invasion, and metastasis. However, its significance in HNSCC is not fully understood. This research investigates how the PCAT-1 / miR-145-5p / FSCN-1 axis promote HNSCC.

METHODS AND RESULTS

We analyzed the gene expression patterns on 238 fresh-frozen samples, comparing tumors with their normal adjacent tissues (NATs). HNSCC samples showed higher PCAT-1 and FSCN-1 expression compared to NATs (p < 0.001 and p < 0.001, respectively). In contrast, miR-145-5p expression was markedly downregulated compared to NATs (p < 0.001). Notably, ROC curve analysis revealed exceptional diagnostic power, with an AUC of 0.83 for PCAT-1, 0.95 for miR-145-5p, and 0.91 for FSCN-1. Pearson correlation analysis unveiled a significant positive correlation between PCAT-1 and FSCN-1 expression levels (r = 0.084, p < 0.001) and negative correlations between FSCN-1 and miR-145-5p (r = -0.710, p < 0.001) as well as between PCAT-1 and miR-145-5p (r = -0.759, p < 0.001). Distinct molecular profiles were observed in the levels of PCAT-1, miR-145-5p, and FSCN-1 between HPV (-) and HPV ( +) 16 and 18 genotypes (p = 0.007, p = 0.027, and p = 0.002). MiR-145-5p expression showed significant differences between HPV (-) and HPV ( +) other genotypes (p = 0.035). FSCN-1 expression showed notable distinctions between HPV ( +) 18 & 16 and HPV ( +) other genotypes (p = 0.031).

CONCLUSIONS

Elevated levels of lncRNA PCAT-1 promote HNSCC through the miR-145-5p/FSCN-1 axis and are associated with poor prognosis and reduced immune cell infiltration levels.

Biomarker potential of competing endogenous RNA networks in Polycystic Ovary Syndrome (PCOS)

Polycystic ovary syndrome (PCOS) is the most common condition affecting women of reproductive age globally. PCOS continues to be the largest contributing factor to female infertility despite significant progress in our knowledge of the molecular underpinnings and treatment of the condition. The fact that PCOS is a very diverse condition makes it one of the key reasons why we haven't been able to overcome it. Non-coding RNAs (ncRNAs) are implicated in the development of PCOS, according to growing evidence. However, it is unclear how the complex regulatory relationships between the many ncRNA types contribute to the growth of this malignancy. Competing endogenous RNA (ceRNA), a recently identified mechanism in the RNA world, suggests regulatory interactions between various RNAs, including long non-coding RNAs (lncRNAs), microRNAs (miRNAs), transcribed pseudogenes, and circular RNAs (circRNAs). Recent studies on PCOS have shown that dysregulation of multiple ceRNA networks (ceRNETs) between these ncRNAs plays crucial roles in developing the defining characteristics of PCOS development. And it is believed that such a finding may open a new door for a deeper comprehension of PCOS's unexplored facets. In addition, it may be able to provide fresh biomarkers and effective therapy targets for PCOS. This review will go over the body of information that exists about the primary roles of ceRNETs before highlighting the developing involvement of several newly found ceRNETs in a number of PCOS characteristics.

Investigating the role of mitochondrial DNA D-loop variants, haplotypes, and copy number in polycystic ovary syndrome: implications for clinical phenotypes in the Chinese population

Background

The presence of genetic variations in mitochondrial DNA (mtDNA) has been associated with a diverse array of diseases. The objective of this study was to examine the correlations between mtDNA D-loop, its haplotypes, and polycystic ovary syndrome (PCOS) in the Chinese population, and the associations between mtDNA D-loop and symptoms of PCOS. The study also sought to determine whether the mtDNA copy number in Chinese patients with PCOS differed from that of individuals in the control group.

Methods

Infertile individuals who only had tubal or male factor treatment were the focus of research by The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). mtDNA haplotypes were categorized using polymorphic D-loop sites. mtDNA D-loop, PCOS features, and mtDNA haplotypes were analyzed using R software to determine the strength of the association between the three. There are certain DNA haplotypes linked to PCOS. Microdroplet digital polymerase chain reaction (PCR) was used to determine the mtDNA copy number in a convenience sample of 168 PCOS patients and 83 controls.

Results

Among the research group, the majority of D-loop mutations were infrequent (frequency< 1%), with only 45 variants displaying a minimum allele frequency (MAF) of 5% or higher. No association was found between polymorphism loci in PCOS patients and body mass index (BMI). Noteworthy, C194T, 1A200G, 523delAC, and C16234T showed positive correlations with elevated LH/FSH levels. Additionally, specific polymorphic loci G207A, 16036GGins, and 16049Gins within the D-loop region of mtDNA potentially exerted a protective role in PCOS development. Conversely, no statistical significance was observed in the expression levels of C16291T and T489C. Chinese women with mtDNA haplotype A15 exhibited a decreased risk of developing PCOS. Moreover, a significant difference in mtDNA copy number was detected, with controls averaging 25.87 (21.84, 34.81), while PCOS patients had a mean of 129.91 (99.38, 168.63).

Conclusion

Certain mtDNA D-loop mutations and haplotypes appear to confer protection against PCOS in Chinese women. In addition, elevated mtDNA copy number may serve as an indicator during early stages of PCOS.

Weighted Gene Co-Expression Network Analysis (WGCNA) Discovered Novel Long Non-Coding RNAs for Polycystic Ovary Syndrome

Polycystic ovary syndrome (PCOS) affects reproductive-age women. This condition causes infertility, insulin resistance, obesity, and heart difficulties. The molecular basis and mechanism of PCOS might potentially generate effective treatments. Long non-coding RNAs (lncRNAs) show control over multifactorial disorders' growth and incidence. Numerous studies have emphasized its significance and alterations in PCOS. We used bioinformatic methods to find novel dysregulated lncRNAs in PCOS. To achieve this objective, the gene expression profile of GSE48301, comprising PCOS patients and normal control tissue samples, was evaluated using the R limma package with the following cut-off criterion: p-value < 0.05. Firstly, weighted gene co-expression network analysis (WGCNA) was used to determine the co-expression genes of lncRNAs; subsequently, hub gene identification and pathway enrichment analysis were used. With the defined criteria, nine novel dysregulated lncRNAs were identified. In WGCNA, different colors represent different modules. In the current study, WGCNA resulted in turquoise, gray, blue, and black co-expression modules with dysregulated lncRNAs. The pathway enrichment analysis of these co-expressed modules revealed enrichment in PCOS-associated pathways, including gene expression, signal transduction, metabolism, and apoptosis. In addition, CCT7, EFTUD2, ESR1, JUN, NDUFAB1, CTTNB1, GRB2, and CTNNB1 were identified as hub genes, and some of them have been investigated in PCOS. This study uncovered nine novel PCOS-related lncRNAs. To confirm how these lncRNAs control translational modification in PCOS, functional studies are required.