Optimized culturing yields high success rates and preserves molecular heterogeneity, enabling personalized screening for high-grade gliomas
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE248544 | GEO | 2025/05/27
REPOSITORIES: GEO
Similar Datasets
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
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 | GSE248543 | GEO
Project description:Optimized culturing yields high success rates and preserves molecular heterogeneity, enabling personalized screening for high-grade gliomas
| PRJNA1044088 | ENA
Project description:Optimized culturing yields high success rates and preserves molecular heterogeneity, enabling personalized screening for high-grade gliomas
| PRJNA1044750 | ENA
Project description:Optimized culturing yields high success rates and preserves molecular heterogeneity, enabling personalized screening for high-grade gliomas [scRNA-seq]
| PRJNA1044752 | ENA
Project description:PurposeGliomas are brain tumors with dismal prognoses. The standard-of-care treatments for gliomas include surgical resection, radiation, and temozolomide administration; however, they have been ineffective in providing significant increases in median survival. Antigen-specific cancer vaccines and immune checkpoint blockade may provide promising immunotherapeutic approaches for gliomas.Experimental designWe have developed immunotherapy delivery vehicles based on synthetic high-density lipoprotein (sHDL) loaded with CpG, a Toll-like receptor-9 agonist, and tumor-specific neoantigens to target gliomas and elicit immune-mediated tumor regression.ResultsWe demonstrate that vaccination with neoantigen peptide-sHDL/CpG cocktail in combination with anti-PD-L1 immune checkpoint blocker elicits robust neoantigen-specific T-cell responses against GL261 cells and eliminated established orthotopic GL261 glioma in 33% of mice. Mice remained tumor free upon tumor cell rechallenge in the contralateral hemisphere, indicating the development of immunologic memory. Moreover, in a genetically engineered murine model of orthotopic mutant IDH1 (mIDH1) glioma, sHDL vaccination with mIDH1 neoantigen eliminated glioma in 30% of animals and significantly extended the animal survival, demonstrating the versatility of our approach in multiple glioma models.ConclusionsOverall, our strategy provides a general roadmap for combination immunotherapy against gliomas and other cancer types.
| S-EPMC7442596 | biostudies-literature
Project description:Methylobacterium extorquens strains are the best-studied methylotrophic model system, and their metabolism of single carbon compounds has been studied for over 50 years. Here we develop a new system for high-throughput batch culture of M. extorquens in microtiter plates by jointly optimizing the properties of the organism, the growth media and the culturing system. After removing cellulose synthase genes in M. extorquens strains AM1 and PA1 to prevent biofilm formation, we found that currently available lab automation equipment, integrated and managed by open source software, makes possible reliable estimates of the exponential growth rate. Using this system, we developed an optimized growth medium for M. extorquens using response surface methodologies. We found that media that used EDTA as a metal chelator inhibited growth and led to inconsistent culture conditions. In contrast, the new medium we developed with a PIPES buffer and metals chelated by citrate allowed for fast and more consistent growth rates. This new Methylobacterium PIPES ('MP') medium was also robust to large deviations in its component ingredients which avoided batch effects from experiments that used media prepared at different times. MP medium allows for faster and more consistent growth than other media used for M. extorquens.
| S-EPMC3639900 | biostudies-literature
Project description:BackgroundThe use of human pluripotent stem cell-derived retinal cells for cell therapy strategies and disease modelling relies on the ability to obtain healthy and organised retinal tissue in sufficient quantities. Generating such tissue is a lengthy process, often taking over 6 months of cell culture, and current approaches do not always generate large quantities of the major retinal cell types required.MethodsWe adapted our previously described differentiation protocol to investigate the use of stirred-tank bioreactors. We used immunohistochemistry, flow cytometry and electron microscopy to characterise retinal organoids grown in standard and bioreactor culture conditions.ResultsOur analysis revealed that the use of bioreactors results in improved laminar stratification as well as an increase in the yield of photoreceptor cells bearing cilia and nascent outer-segment-like structures.ConclusionsBioreactors represent a promising platform for scaling up the manufacture of retinal cells for use in disease modelling, drug screening and cell transplantation studies.
| S-EPMC5998504 | biostudies-literature
Project description:Individualizing patient treatment is a core objective of the medical field. Reaching this objective has been elusive owing to the complex set of factors contributing to both disease and health; many factors, from genes to proteins, remain unknown in their role in human physiology. Accurately diagnosing, monitoring, and treating disorders requires advances in biomarker discovery, the subsequent development of accurate signatures that correspond with dynamic disease states, as well as therapeutic interventions that can be continuously optimized and modulated for dose and drug selection. This work highlights key breakthroughs in the development of enabling technologies that further the goal of personalized and precision medicine, and remaining challenges that, when addressed, may forge unprecedented capabilities in realizing truly individualized patient care.
| S-EPMC7924935 | biostudies-literature
Project description:The pangenomic diversity in Burkholderia pseudomallei is high, with approximately 5.8% of the genome consisting of genomic islands. Genomic islands are known hotspots for recombination driven primarily by site-specific recombination associated with tRNAs. However, recombination rates in other portions of the genome are also high, a feature we expected to disrupt gene order. We analyzed the pangenome of 37 isolates of B. pseudomallei and demonstrate that the pangenome is 'open', with approximately 136 new genes identified with each new genome sequenced, and that the global core genome consists of 4568±16 homologs. Genes associated with metabolism were statistically overrepresented in the core genome, and genes associated with mobile elements, disease, and motility were primarily associated with accessory portions of the pangenome. The frequency distribution of genes present in between 1 and 37 of the genomes analyzed matches well with a model of genome evolution in which 96% of the genome has very low recombination rates but 4% of the genome recombines readily. Using homologous genes among pairs of genomes, we found that gene order was highly conserved among strains, despite the high recombination rates previously observed. High rates of gene transfer and recombination are incompatible with retaining gene order unless these processes are either highly localized to specific sites within the genome, or are characterized by symmetrical gene gain and loss. Our results demonstrate that both processes occur: localized recombination introduces many new genes at relatively few sites, and recombination throughout the genome generates the novel multi-locus sequence types previously observed while preserving gene order.
| S-EPMC4613141 | biostudies-literature