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Optimized culturing yields high success rates and preserves molecular heterogeneity, enabling personalized screening for high-grade gliomas

ABSTRACT: Optimized culturing yields high success rates and preserves molecular heterogeneity, enabling personalized screening for high-grade gliomas

PROVIDER: PRJNA1044750 | ENA |

REPOSITORIES: ENA

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Optimized culturing yields high success rates and preserves molecular heterogeneity, enabling personalized screening for high-grade gliomas

Project description:Optimized culturing yields high success rates and preserves molecular heterogeneity, enabling personalized screening for high-grade gliomas

| PRJNA1044088 | ENA

Optimized culturing yields high success rates and preserves molecular heterogeneity, enabling personalized screening for high-grade gliomas [scRNA-seq]

Project description:Optimized culturing yields high success rates and preserves molecular heterogeneity, enabling personalized screening for high-grade gliomas [scRNA-seq]

| PRJNA1044752 | ENA

Optimized culturing yields high success rates and preserves molecular heterogeneity, enabling personalized screening for high-grade gliomas

Project description:Robust and reliable and in vitro models are essential in the discovery of new treatment options for high-grade glioma (HGG), however, establishing successful patient-derived cell cultures has posed significant challenges. We established glioma stem-like cell (GSC) cultures from 114 consecutive HGG specimens, obtained via traditional surgical resection and/or ultrasonic aspiration, using fully-dissociated single cells (single cell-derived, SCD) and partially dissociated tissue fragments (3D-derived, 3DD). Copy number profiling assessed genetic similarities, while single-cell RNA sequencing evaluated transcriptomic heterogeneity. Proof-of-concept personalized drug screening was performed using a panel of approved anti-cancer agents. Higher success rates in establishing GSC cultures were obtained from ultrasonic aspirates (SCD and 3DD) and 3DD surgical samples compared to SCD cultures from surgical samples. Combining these approaches in parallel yielded a 96% success rate. In rare cases, copy number variations in original tumor tissue were lost in culture, leading to discernible changes in cell morphology. Single-cell sequencing revealed greater heterogeneity of transcriptomic clusters in ultrasonic aspiration-derived cultures compared to resection-derived cultures. Our study's protocol supported the screening of 20 anti-cancer agents within a clinically-relevant timeframe in 16 of 18 consecutive HGG samples. Our optimized protocol therefore provides a reliable tool for generating HGG cell cultures which capture the tumors’ molecular characteristics and supports precision medicine applications.

2025-05-27 | GSE248469 | GEO

Optimized culturing yields high success rates and preserves molecular heterogeneity, enabling personalized screening for high-grade gliomas [scRNA-seq]

2025-05-27 | GSE248543 | GEO

Optimized culturing yields high success rates and preserves molecular heterogeneity, enabling personalized screening for high-grade gliomas

Project description:This SuperSeries is composed of the SubSeries listed below.

2025-05-27 | GSE248544 | GEO

Host cell gene and pathway changes associated with high baculovirus in vitro production yields

Project description:Baculovirus-insect cell culture technology is applied for the production of veterinary and human vaccines‚ gene delivery vectors‚ and biopesticides. The current study investigated systemic cell – virus interactions under different cell culture conditions resulting in differing in virus occlusion bodies (OB)/cell yields for HearNPV infected Hzea cells. 22 microarrays were used. While mRNA levels for most genes decreased, a core set of 14 genes consistently increased in all 11 different infection conditions studied‚ suggesting a conserved up regulation pattern of these genes upon baculovirus infections. KEGG pathway analysis found strongest responses by the genes for the E3 ubiquitin-protein ligase Topors in the ubiquitin proteasome pathway‚ GAPDH in the glycolytic pathway‚ and host DNA ligase and DNA helicase in the replication process. Weighted co expression network analysis determined a module and 5 hub genes that strongly correlated to OB/cell yields. The endoplasmic reticulum functional group was particularly reduced in low producing systems. Total virus mRNA and viral genome levels had positive correlations to OB/cell yields. Virus genes were expressed in a similar temporal pattern regardless of the cell lines‚ media or infection cell densityies used. The virus Chitinase gene and Superoxide dismutase gene may be particularly important for high productivities. Overall this genome-scale expression study of different infection conditions provides insights into host insect cell responses to baculovirus infections and suggests gene expression changes that are likely important for high virus yields.

2014-11-25 | GSE63595 | GEO

High-quality genome and methylomes illustrate features underlying evolutionary success of oaks.

Project description:High-quality genome and methylomes illustrate features underlying evolutionary success of oaks.

| PRJNA731856 | ENA

Therapeutic targeting of ATR yields durable regressions in high replication stress tumors

Project description:Therapeutic targeting of ATR yields durable regressions in high replication stress tumors

| PRJNA691391 | ENA

Therapeutic targeting of ATR yields durable regressions in high replication stress tumors

Project description:Therapeutic targeting of ATR yields durable regressions in high replication stress tumors

| PRJNA691392 | ENA

NAA enhances cell yields by inhibiting apoptosis pathway

Project description:The in vitro cell culturing witnessed its applications in both scientific research and industrial activities, its optimization leads to practical benefits, either through shortening the doubling time, or simplification of engineering requests, or both. Literature searching highlighted a role of a synthetic auxin derivative 1-Naphthaleneacetic acid (NAA) in optimizing plant cell culturing. Here, by measuring cell counts and their activities via CCK8 tests, we observed an up to 2-fold increase in the yield of in vitro cultured human cells. We tested different types of human cell lines and primary natural killer cells, found that NAA was effective in all the cells tested. The PI staining and FACS analysis suggested that NAA did not affect the cell cycling. Apoptosis-specific dye staining analysis implicated that NAA rescued cell death. We further did bulk RNA sequencing and identified the lipid metabolism-engaging and anti-apoptosis gene, ANGPTL4, was enhanced in expression upon NAA treatment. Studies on ANGPTL4 knockout cells indicated that ANGPTL4 is required for NAA-mediated response. Thus, our data identified a beneficial role of NAA in human cell culturing and highlighted its potency in the in vitro cell culturing

2023-10-18 | GSE245281 | GEO

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