Exploring the molecular mechanism of Bushen Huoxue Fang on premature ovarian failure based on transcriptomics and systems biology
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE217193 | GEO | 2023/04/21
REPOSITORIES: GEO
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Project description:Exploring the molecular mechanism of Bushen Huoxue Fang on premature ovarian failure based on transcriptomics and systems biology
| PRJNA897894 | ENA
Project description:Background: Premature ovarian failure (POF) is a clinical condition characterized by the cessation of ovarian function, leading to infertility. The underlying molecular mechanisms remain unclear, and no predictable biomarkers have been identified. This study aimed to investigate the protein and metabolite contents of serum exosomes to identify underlying molecular mechanisms and explore potential biomarkers. Methods: This study was conducted on a cohort consisting of 14 POF patients and 16 healthy controls. The exosomes extracted from the serum of each group were subjected to label-free proteomic and unbiased metabolomic analysis. Differentially expressed proteins and metabolites were annotated. Pathway network clustering was conducted with further correlation analysis. The biomarkers were confirmed by ROC analysis and random forest machine learning. Results: The proteomic and metabolomic profiles of POF patients and healthy controls were compared. Two subgroups of POF patients, Pre-POF and Pro-POF, were identified based on the proteomic profile, while all patients displayed a distinguishable metabolomic profile. Signaling pathway clustering revealed progression of dysfunctional energy metabolism during the development of POF. The differentially expressed proteins and metabolites were highly correlated, with six of them selected as potential biomarkers. ROC curve analysis and random forest machine learning suggested that AFM combined with GE was a diagnostic biomarker for POF. Conclusion: Omic analysis revealed that inflammation and oxidative stress are factors that damage ovarian tissue, but progressive dysfunction of energy metabolism might be the critical pathogenetic pathway contributing to the development of POF. AFM combined with GE together serves as the best biomarker for clinical POF diagnosis.
2024-10-17 | PXD051569 | Pride
Project description:The biological function of human ovaries declines with increasing age. Moreover, disorders that cause reproductive failure, such as premature ovarian failure (POF), seriously affect the female health and may be related to abnormal gene expression in the ovaries. The objective of this study was to generate the gene expression profiles of ovaries in rhesus monkeys of different ages, so as to identify age-related changes in the ovaries and understand their significance in various human reproductive problems.
2014-08-31 | GSE44533 | GEO
Project description:Through comparing the global expression profiles of SSCTR, POF and WT using cDNA microarrays, the differences among the SSCTR, POF and WT will be revealed, especially about the molecular mechanisms induced transdifferentiation.
2022-06-21 | GSE39501 | GEO
Project description:The biological function of human ovaries declines with increasing age. Moreover, disorders that cause reproductive failure, such as premature ovarian failure (POF), seriously affect the female health and may be related to abnormal gene expression in the ovaries. The objective of this study was to generate the gene expression proM-oM-,M-^Ales of ovaries in rhesus monkeys of different ages, so as to identify age-related changes in the ovaries and understand their significance in various human reproductive problems. Ovaries were obtained from young (Y, 3 to 4 years), middle-age (M, 7 to 8 years) and old (O, 18 to 19 years) monkeys, and each group had 3 monkey replications. Half of ovary from each monkey was isolated mRNA for whole genome gene expression microarray analysis to detect differentially expressed genes, and followed by the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses by using a free web-based Molecular Annotation System 3.0 (MAS 3.0).
2014-08-31 | E-GEOD-44533 | biostudies-arrayexpress
Project description:Novel transcriptomic signatures associated with premature kidney allograft failure
| PRJNA923707 | ENA
Project description:Triplicate samples of oocyte and cumulus cells were isolated from follicles of 2-8 mm, containing oocytes with several layers of cumulus cells were collected from ovaries. Proteins were extracted using DDF and digested using trypsin. The peptides were desalted, separated using in-line SCX-RPLC and analyzed using ion trap MS/MS. Proteins were identified using TurboSEQUEST 3.2
2011-04-15 | PRD000082 | Pride
Project description:Premature progesterone (P) rise during GnRH antagonist cycles for IVF is a frequent phenomenon and has been associated with lower pregnancy and implantation rates. Different thresholds of progesterone have been used so far to define its premature rise during the follicular phase of an IVF stimulated cycle. In this study, we evaluated endometrial gene expression on the day of oocyte retrieval according to the level of serum progesterone on the day of hCG administration in GnRH antagonist cycles.Endometrial biopsies from eleven patients were taken with a Pipelle de Cornier (Prodimed, Neuilly-en-Thelle, France) on the day of oocyte retrieval in a GnRH antagonist/rec-FSH stimulated IVF cycle with fresh embryo transfer. Biopsies were analysed for gene expression with Affymetrix Human Genome (HG) U133 Plus 2.0 Arrays and GCOS software (Affymetrix, Santa Clara, CA, USA). Patients were divided into three different groups according to their progesterone serum concentration on the day of hCG administration (A) P <= 0.9 ng/mL, (B) 1 < P < 1.5 ng/mL, and (C) P > 1.5 ng/mL. Serum P was measured with the automated Elecsys immunoanalyser (Roche Diagnostics, Mannheim, Germany). Selected differentially expressed genes were validated with quantitative real-time PCR (QPCR) with TaqMan Gene Expression Assays (Applied Biosystems, Foster City, CA, USA). Keywords: gene expression analysis, premature progesterone rise Endometrial biopsies from fourteen patients were taken on the day of oocyte retrieval in a GnRH/rec-FSH stimulated IVF cycle with fresh embryo transfer and analyzed with microarrays. Patients were divided into three groups according to their progesterone serum concentration on day of hCG: A <=0.9ng/ml; B 1-1.5 ng/ml; C > 1.5ng/ml
2010-12-21 | E-GEOD-19959 | biostudies-arrayexpress
Project description:Heart failure (HF) is a complex disease entity with high clinical impact, poorly understood pathophysiology and scantly known miRNA-mediated epigenetic regulation. We have analysed miRNA patterns in patients with chronic HF (cHF) and a sex- and age-matched reference group and pursued an in silico system biology analysis to discern pathways involved in cHF pathophysiology. Twenty-eight miRNAs were identified in cHF that were up-regulated in the reference group, and eight of them were validated by RT-qPCR. In silico analysis of predicted targets by STRING protein-protein interaction networks revealed eight cluster networks (involving seven of the identified miRNAs) enriched in pathways related to cell cycle, Ras, chemokine, PI3K-AKT and TGF-β signaling. By ROC curve analysis, combined probabilities of these seven miRNAs (let-7a-5p, miR-107, miR-125a-5p, miR-139-5p, miR-150-5p, miR-30b-5p and miR-342-3p; clusters 1-4 [C:1-4]), discriminated between HF with preserved ejection fraction (HFpEF) and HF with reduced ejection fraction (HFrEF), and ischaemic and non-ischaemic aetiology. A combination of miR-107, miR-139-5p and miR-150-5p, involved in clusters 5 and 7 (C:5+7), discriminated HFpEF from HFrEF. Pathway enrichment analysis of miRNAs present in C:1-4 (let-7a-5p, miR-125a-5p, miR-30b-5p and miR-342-3p) revealed pathways related to HF pathogenesis. In conclusion, we have identified a differential signature of down-regulated miRNAs in the plasma of HF patients and propose novel cellular mechanisms involved in cHF pathogenesis.
| S-EPMC9740605 | biostudies-literature
Project description:Mixtures risk assessment needs an efficient integration of in vivo, in vitro, and in silico data with epidemiology and human studies data. This involves several approaches, some in current use and others under development. This work extends the Agency for Toxic Substances and Disease Registry physiologically based pharmacokinetic (PBPK) toolkit, available for risk assessors, to include a mixture PBPK model of benzene, toluene, ethylbenzene, and xylenes. The recoded model was evaluated and applied to exposure scenarios to evaluate the validity of dose additivity for mixtures. In the second part of this work, we studied toluene, ethylbenzene, and xylene (TEX)-gene-disease associations using Comparative Toxicogenomics Database, pathway analysis and published microarray data from human gene expression changes in blood samples after short- and long-term exposures. Collectively, this information was used to establish hypotheses on potential linkages between TEX exposures and human health. The results show that 236 genes expressed were common between the short- and long-term exposures. These genes could be central for the interconnecting biological pathways potentially stimulated by TEX exposure, likely related to respiratory and neuro diseases. Using publicly available data we propose a conceptual framework to study pathway perturbations leading to toxicity of chemical mixtures. This proposed methodology lends mechanistic insights of the toxicity of mixtures and when experimentally validated will allow data gaps filling for mixtures' toxicity assessment. This work proposes an approach using current knowledge, available multiple stream data and applying computational methods to advance mixtures risk assessment.
| S-EPMC8215597 | biostudies-literature