Application of Omni-ATAC to Profile Chromatin Accessibility Before and After Ovarian Tissue Cryopreservation
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE165637 | GEO | 2022/05/27
REPOSITORIES: GEO
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Project description:Application of Omni-ATAC to Profile Chromatin Accessibility Before and After Ovarian Tissue Cryopreservation
| PRJNA695252 | ENA
Project description:Cryopreservation is an important technique for preserving fertility potential through ovarian tissue banking. Slow freezing has traditionally been the standard protocol used for ovarian tissue cryopreservation. However, vitrification, as an emerging method, is considered to be an alternative to slow freezing, thus generating some debate in the field. This study utilizes high-resolution spatial transcriptomics to comprehensively profile and compare the molecular impacts of two cryopreservation methods - slow freezing and vitrification - on human ovarian tissues at an unprecedented resolution. Over 135,000 spots were profiled from Fresh and cryopreserved ovarian tissue slices, identifying 8 major cell types and 25 subtypes through marker expression. Detailed spatial localization patterns revealed heterogeneous stromal cell subpopulations and ovarian structures. Transcriptional profiling showed that both cryopreservation methods significantly repressed gene expression, indicative of tissue damage. However, slow freezing induced a broader pro-survival inflammatory and tissue remodeling response compared to vitrification. Gene set enrichment analysis identified elevated ribosomal processes, inflammatory signaling pathways like TNF-?/NF-?B and IL-6/STAT3, as well as extracellular matrix (ECM) organization and collagen synthesis as dominant response themes in slow frozen tissue, which were observed to a lesser degree in vitrified tissue. Key response drivers included MYC, TIMP1, and DCN, with stromal cells located in the cortical regions showing the strongest pathway enrichment. Ribosomal gene expression displayed spatial gradients and supported stromal responses after freezing. We finally demonstrated signaling pathway differences between the two cryopreservation methods, noting TGF-? as a highly possible pathway responsible for coordinating with certain endothelial subgroups to enhance ECM deposition. In summary, this study provides a comprehensive atlas of cell types and their spatial structures in human ovary. It reveals that slow freezing elicits a strong but balanced inflammatory and tissue regenerative state compared to the vitrification. It also offers insights on cryoinjury to ovarian stroma, which may guide optimization of ovarian tissue cryopreservation protocols for clinical applications.
2024-05-18 | GSE267323 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE24753: Genome-wide analysis of the effect of cryopreservation on peripheral blood mononuclear cells GSE24755: Genome-wide analysis of the effect of long-term cryopreservation on peripheral blood mononuclear cells GSE24757: Genome-wide analysis of the effect of long-term freezing of PAXgene Blood RNA tubes Refer to individual Series
2011-07-21 | E-GEOD-24758 | biostudies-arrayexpress
Project description:We optimized a method previously developed to extract EVs from epithelial ovarian cancer (EOC) tissues and investigated whether cryopreservation of EOC tissues in clinical practice affects the phenotypes, contents, and biological functions of subsequently extracted EVs.
2023-05-10 | PXD039422 | Pride
Project description:Ovarian cancer is characterized by transcoelomic metastasis into the peritoneal cavity. The peritoneal malignant ascites is enriched with ovarian cancer cells and a small amount of tumor-associated immune cells which create a unique microenvironment actively contributing to progression of the disease. However, it is remain unclear how cancer cells communicate to its local environment under the influence of chemotherapy. To address this issue, we performed LC-MS/MS analyses of ovarian cancer ascites from the same patients before and after chemotherapy. We found that neoadjuvant chemotherapy causes a significant changes in the composition of ascites, and these changes are similar in samples obtained from all patients (n=10). Functional annotation of upregulated proteins with the use of KEGG and GO databases revealed that malignant ascites after chemotherapy were enriched with the cluster of spliceosomal proteins. These splicing factors were linked to induction of epithelial-to-mesenchymal transition leading to a more aggressive phenotype of cancer cells.
2024-05-29 | PXD019327 | Pride
Project description:Analysis of cryopreservation effects on peripheral blood mononuclear cells at gene expression level. The hypothesis tested in the present study was that cryopreservation has an influence on the transcriptome profile of peripheral blood mononuclear cells. Results indicated remarkable changes in expression patterns upon cryopreservation of PBMCs, with a strong loss of signal intensities to background levels for several transcripts. Total RNA obtained from isolated peripheral blood mononuclear cells of healthy human subjects eihter cryopreserved in liqiud nitrogen (frozen) or direclty lysed in Trizol after isolation (fresh).
2011-07-21 | E-GEOD-24753 | biostudies-arrayexpress
Project description:Human primary granulosa cells (GCs) derived from women, undergoing oocyte retrieval, can be cultured and are a cellular model for the study of human ovarian functions. In vitro they change rapidly, resembling initially cells of the preovulatory follicle and then cells of the corpus luteum. They are derived from individual patients and their different medical history, lifestyle and age lead to heterogeneity. Thus, cells can rarely be ideally matched for cellular experiments or, if available, only in small quantities. We reasoned that cryopreservation of human GCs may be helpful. Previous studies indicated feasibility of such an approach, but low survival of GCs was reported and consequences on GC functionality were only partially evaluated. We tested a slow freezing protocol (employing FCS and DMSO) of GCs upon isolation from follicular fluid. We compared cryopreserved and subsequently thawed cells with fresh, not cryopreserved ones, from the same patients. About 80 % of human GCs survived freezing/thawing. Neither morphology, nor levels of cell-cell contact, mitochondrial and steroidogenic genes were different between the two groups in cells cultured for 1-5 days. A proteomic analysis revealed no statistical significance in the abundance of a total of 5962 proteins. Both groups produced comparable basal levels of progesterone and responded similarly to hCG with elevation of progesterone. Taken together, we describe a rapid and readily available method for the cryopreservation of human GCs. We anticipate that it will allow future large-scale experiments and may thereby improve cellular studies with human ovarian cells.
2021-07-28 | PXD025632 | Pride
Project description:Analysis of effect of long-term cryopreservation on peripheral blood mononuclear cells at gene expression level. The hypothesis tested in the present study was that long-term cryopreservation has an influence on the transcriptome profile of peripheral blood mononuclear cells. Results indicated remarkable changes in expression patterns upon cryopreservation of PBMCs, with decreasing signal intensities over time. Total RNA obtained from isolated peripheral blood mononuclear cells of melanoma patients cryopreserved in liqiud nitrogen from 20 to 60 months.
2011-07-21 | E-GEOD-24755 | biostudies-arrayexpress
Project description:Analysis of cryopreservation effects on peripheral blood mononuclear cells at gene expression level. The hypothesis tested in the present study was that cryopreservation has an influence on the transcriptome profile of peripheral blood mononuclear cells. Results indicated remarkable changes in expression patterns upon cryopreservation of PBMCs, with a strong loss of signal intensities to background levels for several transcripts.
2011-07-22 | GSE24753 | GEO
Project description:To detect the differentially expressed genes and subsequently identify disease-related signatures and potential biomarkers for patients with ovarian endometriomas in the serum before and 3 months after the ultrasound-guided ethanol sclerotherapy in patients with ovarian endometriomas. we have employed the KangChen Bio-technology Corp. NimbleGen Human Gene Expression Microarray 12x135K. Among these, six genes showed statistical significance including IL6, CD36, JUNB, B4GALT1, HES1, and NR4A1, which were also validated by qPCR analysis. The gene expression in human blood was measured before and 3 months after the ultrasound-guided ethanol sclerotherapy in the same patients with ovarian endometriomas.
2015-05-28 | E-GEOD-69310 | biostudies-arrayexpress