Impacts of cryopreservation on cell type composition and gene expression in bone marrow biopsy from multiple myeloma patients
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PROVIDER: PRJNA679253 | ENA |
REPOSITORIES: ENA
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Project description:As the development of the single cell sequencing technology, the workflow of preserving and processing cells needs to be more flexible and manageable to fit the longitudinal or complex single cell study. Consequently, considering the upstream cell cryopreservation protocol instead of using fresh cells become more common in single cell sequencing experiment. There have been several studies reported that cryopreservation protocol could largely preserve the transcriptomic profiles but it brought slight perturbations to the cells. In this case, the effect of cryopreservation on transcriptomic changes needs to be studied to understand whether there will be any bias in the downstream analysis. In this paper, we compared fresh and cryopreserved CD138+ and CD138- cells from multiple myeloma patients’ bone marrow aspirates to evaluate the impact of cryopreservation on cell population frequency and transcriptome. We found the cryopreservation protocol maintained highly consistent gene expression profiles for myeloma cells (R ≥ 0.96) and their microenvironment (R ≥ 0.9), while it slightly impacted the proportion of certain immune cell subtypes in the CD138- samples. In general, our cryopreservation protocol could well preserve bone marrow aspirate samples from multiple patients.
2020-11-19 | GSE161722 | GEO
Project description:Cryopreservation of mature oocytes is a critical means for female fertility preservation. Despite clinical advances using vitrification preservation method, the high concentrations of toxic penetrating cryoprotectant agents (CPA, up to 4.3 M) and low throughput (only one every experiment) put forward a challenge. Here, we report a synergetic ice inhibition platform via PVA/Fe3O4/GO nanoparticles (PFG NPs), that achieves sharp ice morphology, ice recrystallization, and devitrification inhibition, thus reducing cryodamage both in cooling and warming stages. Oocyte cryopreservation experiment demonstrates the survival rate can attain 98.6% using 2.5 M penetrating CPA while ensuring the scalability (ten oocytes each cryopreservation procedure). In contrast, recovered oocytes via PFG platform show 85 gene variation compared with fresh oocytes, whereas tradition CPA (TCPA) formulation induces 1396 gene changes. Meanwhile, the PFG-cryopreservation oocytes maintain normal ability of fertilization, development, and birth of offspring.
2025-04-30 | GSE244977 | GEO
Project description:Single-cell RNA sequencing reveals gene expression differences between individual cells and also identifies different cell populations that are present in the bulk starting material. To obtain an accurate assessment of patient samples, single-cell suspensions need to be generated as soon as possible once the tissue or sample has been collected. However, this requirement poses logistical challenges for experimental designs involving multiple samples from the same subject since these samples would ideally be processed at the same time to minimize technical variation in data analysis. Although cryopreservation has been shown to largely preserve the transcriptome, it is unclear whether the freeze-thaw process might alter gene expression profiles in a cell-type specific manner or whether changes in cell-type proportions might also occur. To address these questions in the context of multiple myeloma clinical studies, we performed single-cell RNA sequencing (scRNA-seq) to compare fresh and frozen cells isolated from bone marrow aspirates of six multiple myeloma patients, analyzing both myeloma cells (CD138+) and cells constituting the microenvironment (CD138-). We found that cryopreservation using 90% fetal calf serum and 10% dimethyl sulfoxide resulted in highly consistent gene expression profiles when comparing fresh and frozen samples from the same patient for both CD138+ myeloma cells (R ≥ 0.96) and for CD138- cells (R ≥ 0.9). We also demonstrate that CD138- cell-type proportions showed minimal alterations, which were mainly related to small differences in immune cell subtype sensitivity to the freeze-thaw procedures. Therefore, when processing fresh multiple myeloma samples is not feasible, cryopreservation is a useful option in single-cell profiling studies.
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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:Ovarian tissue cryopreservation is an important technique for preserving fertility potential, albeit the associated tissue damage may severely impact post-thaw tissue viability. We collected human ovarian tissues from multiple samples and performed Stereo-Seq high-resolution spatial transcriptomics to comprehensively profile and compare the molecular impacts of two cryopreservation methods - slow freezing and vitrification. We identified 8 major spatial clusters and revealed their functional heterogeneity by subclustering. We then detailed cryopreservation response at both the global and subcluster levels to illustrate overall and niche specific effects. Compared to fresh samples, we observed a decrease in major metabolic pathways in frozen samples with both techniques, whereas vitrified samples have severer decrease than slow-frozen samples. The affected metabolic pathways included those related to proteins, such as ribosomal processes and proteasomal degradation; lipids, specifically sterol and cholesterol metabolism; and overall energy production, which encompassed cellular respiration and mitochondrial processes. On the other hand, slow freezing elicited a strong but balanced inflammatory and tissue remodeling state compared to vitrification. We also reported upregulated cell-cell signaling related to angiogenesis, cellular adhesion and extracellular matrix remodeling in slow-frozen tissue. These pathways were responsible for enhancing tissue repair by coordinating with certain stromal and endothelial subclusters. In summary, our study offered insights on ovarian cell response to cryopreservation, which may guide optimization of ovarian tissue cryopreservation protocols for clinical applications.
2024-05-18 | GSE267323 | GEO
Project description:cryopreservation human testicular tissue
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Project description:Cryopreservation is a key method for long-term storage of biological specimens. The development of optimal cryopreservation condition will reduce the damage from the storage as least as possible. The effect of the cryopreservation condition we used on peripheral blood mononuclear cells (PBMCs) has been previously evaluated with microarray analysis. The emerging single-cell RNA sequencing (scRNA-seq) technology enable deeper exploring cellular heterogeneity and function. In the current study, we further optimized the cryopreservation procedure using FACS analysis, and the method were further evaluated by ScRNA-Seq for two different length of storage time: six months and 12 months in comparison to fresh cells. We identified major immune cell types from both fresh and recovered cryopreserved PBMCs, including monocytes, dendritic cells (DCs), natural Killer (NK) cells, CD4+ T cells, CD8+ T cells, and B cells. The cell viability of all identified immune cell types was relatively stable during the initial 6-month of cryopreservation, while showed10 ~ 40 % decline after cryopreserved for 12 months for different cell types. Furthermore, transcriptome profile of cryopreserved samples did not show obvious perturbation during whole 12 months testing time, although a few key genes involved in stress response or apoptosis, exhibited significant change, especially in monocytes, DC and NK cells. Our results validate that the optimized cryopreservation is a reliable procedure for maintaining these major immune cell types in PBMCs, also highlight the importance of careful assessment of individual sample as variation could be introduced by cryopreservation.
2025-08-07 | GSE304704 | GEO
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: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