The role of circular RNAs in porcine antral follicular degeneration
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ABSTRACT:
PROVIDER: PRJNA562775 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10034586_1.fastq.gz | Fastqsanger.gz | |||
| SRR10034586_2.fastq.gz | Fastqsanger.gz | |||
| SRR10034587_1.fastq.gz | Fastqsanger.gz | |||
| SRR10034587_2.fastq.gz | Fastqsanger.gz | |||
| SRR10034588_1.fastq.gz | Fastqsanger.gz |
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Project description:Goal:Circular RNAs (circRNAs) are thought to play important roles in multiple biological processes including apoptosis. In the ovary granulosa cell apoptosis plays an essential role in the follicular phase of the estrous cycle as it determines if the selected follicles will degenerate or escape this fate and ovulate. Whether circRNAs play a role in granulosa cell apoptosis is at present unknown. By investigating the potential role of circRNAs in the granulosa cell apoptotic cascade we hope to gain novel information regarding the regulation of antral follicular apoptosis using the porcine ovary as a model. Method: Ribosomal-depleted RNA-sequencing was performed to generate circRNA expression profiles from isolated mural porcine granulosa cells of healthy antral (HA) and atretic antral (AA) follicles, respectively. Results:In total, more than 9,632 circRNAs were identified, of which 62 circRNAs were differentially expressed (DE-circRNAs). GO and KEGG analysis of DE-circRNAs showed that apoptosis, cellular responses to stress and cell cycle pathways, were significantly enriched. Next the characteristics of DE-circRNAs, including back-splicing, RNase R resistance and stability were validated, and miRNA binding sites of DE-circRNAs were predicted. Conclusion: Based on these observations, we conclude that aberrantly expressed circRNAs and their targeted genes seem to be associated with granulosa cell apoptosis and thus antral follicular atresia.
2020-08-31 | GSE136589 | GEO
Project description:The antral follicle stage plays a crucial role in mammalian oocyte maturation, signifying the final stages of oocyte development and ovulation. This complex process relies on synchronized interactions between oocyte maturation and the proliferation of neighboring granulosa cells. Previous studies have identified two subtypes of granulosa cells in antral follicles: cumulus granulosa cells, located in the inner region, which surround and support the oocyte, and mural granulosa cells, present in the outer layers, which provide mechanical support to the follicular wall and possess steroidogenic functions. Despite the wealth of molecular data generated by these studies, many fundamental questions regarding key developmental events, granulosa cell heterogeneity, functional annotation, and the intricate relationship between somatic cells and oocytes still lack detailed, single-cell resolution-level investigations. In this study, we isolated follicular cells from porcine antral follicles and conducted scRNA-seq to analyze the single-cell transcriptomes of these cells. By identifying and sub-clustering ovarian cells, such as mural granulosa cells and cumulus granulosa cells, we elucidated the heterogeneity of granulosa cells in pigs.
2023-10-24 | GSE237134 | GEO
Project description:Exosomes and microvesicles (i.e., extracellular vesicles; EVs) have been identified within ovarian follicular fluid, and recent evidence suggests that EVs are able to elicit profound effects on ovarian cell function. While existence of miRNA within EVs has been reported, it remains unknown if EV size and concentration as well as their cargos (i.e., proteins and RNA) change during antral follicle growth. Extracellular vesicles isolated from follicular fluid of small, medium and large bovine follicles were similar in size, while concentration of EVs decreased progressively as follicle size increased. Electron microscopy indicated a highly purified population of the lipid bilayer enclosed vesicles that were enriched in exosome biomarkers including CD81 and Alix. Small RNA sequencing identified a large number of known and novel miRNAs that changed in the EVs of different size follicles. Ingenuity Pathway Analysis (IPA) indicated that miRNA abundant in small follicle EV preparations were associated with cell proliferation pathways, while those miRNA abundant in large follicle preparations were related to inflammatory response pathways. These studies are the first to demonstrate that EVs change in their levels and makeup during antral follicle development and point to the potential for a unique vesicle-mediated cell-to-cell communication network within the ovarian follicle. Examination of small RNA population in bovine follicular fluid extracellular vesicles isolated from antral follicles
2016-02-09 | E-GEOD-74879 | biostudies-arrayexpress
Project description:Proteomic Analysis of Healthy and Atretic Porcine Follicular Granulosa Cells
2020-08-25 | PXD021092 |
Project description:Antral follicle size might be a valuable additive predictive marker for IVF outcome. However, while some studies show positive relations between follicle size and reproductive outcome, others have not been successful in establishing this relation. To better understand consequences of antral follicle size for reproductive outcome, we aimed to obtain insight in follicle size-related granulosa cell processes, as granulosa cells play an essential role in follicular development via the production of growth factors, steroids and metabolic intermediates, needed for follicular growth and oocyte development. Using pigs as a model, we compared gene and protein expression in granulosa cells of smaller and larger follicles in the healthy antral follicle pool at the start of the follicular phase of the estrous cycle. In sows, the early antral follicle pool is very heterogeneous when e.g. size and steroid content of the follicular fluid are considered. To which extent this variety contributes to the developmental competence of the follicles is not clear. Therefore, sows with high variation in antral follicle size (HighVAR) as well as sows with low variation in antral follicle size (LowVAR) were used. Granulosa cells of smaller antral follicles in the healthy antral follicle pool show increased cell proliferation, which was accompanied by a metabolic shift towards aerobic glycolysis (i.e. the Warburg effect), similar to other highly proliferating cells. High granulosa cell proliferation rates in smaller follicles might be regulated via increased granulosa cell expression of AR and EGFR which are activated in response to locally produced mitogens. While granulosa cells of smaller follicles in the pool were more proliferative, indicative of higher follicular growth, granulosa cells of larger follicles in the pool showed less proliferation and were more differentiated, as they showed a higher expression of follicular maturation marker IGF1 and ANGPT1. Our results imply that the inclusion of strict criteria of antral follicle size in IVF protocols might improve reproductive outcome. In addition, we have granulosa cell gene expression of healthy follicles to unravel underlying mechanisms of differences in COC morphology. We compared gene expression in sows with low vs. high-COC-health and found a decreased expression of genes involved in ovarian steroidogenesis (e.g. CYP19A1, ADM, SPP1) and higher expression of genes involved in follicular atresia (e.g. GADD45A, INHBB) in sows with low-COC-health. Thereby we have identified several genes which may serve as markers for follicle developmental competence.
2019-08-15 | GSE125189 | GEO
Project description:Follicles of polycystic ovaries (PCO) often become arrested in early antral stages at around 3 to 11 mm in diameter. The condition disturbs dominant follicle selection and may result in altered ovulation and anovulation. During the growth and development of human follicles, the follicular fluid (FF) constitutes the avascular microenvironment in which the oocyte develops and acts as a vehicle for hormone signaling between cues from circulation and follicular cells. Previous proteomics studies performed on FF from women with polycystic ovarian syndrome (PCOS) have revealed information on the protein changes associated with the pathophysiology of this disorder. However, these studies have been conducted on FF samples obtained in connection with oocyte pick-up during ovarian stimulation right at the time of ovulation and are limited to follicular conditions during the follicular phase of the menstrual cycle. This study aimed to detect proteomic alterations in FF from human small antral follicles (hSAF) obtained from women with PCO as compared to normal women.
2022-04-07 | PXD031485 | Pride
Project description:Exosomes and microvesicles (i.e., extracellular vesicles; EVs) have been identified within ovarian follicular fluid, and recent evidence suggests that EVs are able to elicit profound effects on ovarian cell function. While existence of miRNA within EVs has been reported, it remains unknown if EV size and concentration as well as their cargos (i.e., proteins and RNA) change during antral follicle growth. Extracellular vesicles isolated from follicular fluid of small, medium and large bovine follicles were similar in size, while concentration of EVs decreased progressively as follicle size increased. Electron microscopy indicated a highly purified population of the lipid bilayer enclosed vesicles that were enriched in exosome biomarkers including CD81 and Alix. Small RNA sequencing identified a large number of known and novel miRNAs that changed in the EVs of different size follicles. Ingenuity Pathway Analysis (IPA) indicated that miRNA abundant in small follicle EV preparations were associated with cell proliferation pathways, while those miRNA abundant in large follicle preparations were related to inflammatory response pathways. These studies are the first to demonstrate that EVs change in their levels and makeup during antral follicle development and point to the potential for a unique vesicle-mediated cell-to-cell communication network within the ovarian follicle.
2016-02-09 | GSE74879 | GEO
Project description:The objective of this study was to identify miRNA expression profiles of extracellular vesicles (EVs) from porcine follicular fluids (FFs) in association with oocyte quality. Antral follicles were aspirated individually and oocytes were stained with 0.5% Lissamine Green B stain (LB), a vital stain for oocyte quality. Each oocyte was classified separately according to the stain into high-quality (unstained; HQ) and low-quality (stained; LQ). Oocyte corresponding FFs were pooled together into HQ and LQ groups and their EV-miRNAs were isolated and sequenced. Sequencing analysis revealed that a total of 295 known miRNAs were commonly detected in both groups. MiR-27b-3p, miR-140-3p, miR-29a-3p, miR-202-5p, and miR-16 were the top highly abundant miRNAs in both groups. Differentially expression (DE) analysis exhibited that 19 miRNAs (including miR-193a-5p, miR-125b, and miR-320) were up- while 22 (including miR-9, miR-6516, and miR-206) were down-regulated in the HQ compared to the LQ group.
2022-06-29 | GSE181182 | GEO
Project description:In mammals, female fertility is determined by the outcome of follicular development (ovulation or atresia). Follicular atresia is a complex physiological process that results in the degeneration of oocytes from the ovary. However, the molecular mechanisms of oocyte degeneration and key protein markers of follicular atresia remain unclear. In this study, we explored the complex transcriptional regulatory mechanisms and protein profiles in oocytes and follicular fluid in atretic follicle stages using single-cell RNA sequencing and tandem mass tag proteomics.
2024-05-30 | PXD052738 |
Project description:Sma- and Mad-related protein 4 (SMAD4) is closely associated with the development of ovarian follicular. However, current knowledge of the genome-wide view on the role of SMAD4 gene in mammalian follicular granulosa cells (GCs) is still largely unknown. In the present study, RNA-Seq was performed to investigate the effects of SMAD4 knockdown by RNA interference (SMAD4-siRNA) in porcine follicular GCs. A total of 1025 differentially expressed genes (DEGs), including 530 upregulated genes and 495 downregulated genes, were identified in SMAD4-siRNA treated GCs compared with that treated with NC-siRNA. Furthermore, functional enrichment analysis indicated that upregulated DEGs in SMAD4-siRNA treated cells were mainly enriched in cell-cycle related processes, interferon signaling pathway, and immune system process, while downregulated DEGs were mainly involved in extracellular matrix organization/disassembly, pathogenesis, and cell adhesion. In particular, cell cycle and TGF-β signaling pathway were discovered as the canonical pathways changed under the SMAD4 silencing. Taken together, our data reveals SMAD4 knockdown alters the expression of numerous genes involved in key biological processes of the development of follicular GCs and provides a novel global clue of the role of SMAD4 gene in porcine follicular GCs. mRNA profiles of NC-siRNA treated and SMAD4-siRNA treated porcine GCs were generated by RNA sequencing using Ion Torren Proton
2016-07-25 | E-GEOD-76833 | biostudies-arrayexpress