Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1236707 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We performed absolute quantification (AQUA) of viral proteins by targeted quantitative proteomics and conducted tandem mass tag (TMT)-based proteomics on the three rAAV and wtAAV production systems to identify potential factors limiting rAAV productivity in HEK293 cells
2024-07-03 | PXD050484 | Pride
Project description:Recombinant adeno-associated viruses (rAAVs) are a cornerstone of modern gene therapy, offering precise delivery and stable transgene expression with minimal immunogenicity. Despite clinical advancements, large-scale rAAV production faces significant challenges such as low yield, high costs, and variability, hindering its scalability. Recent research suggests that miRNAs and snoRNAs can modulate viral replication, transcriptional regulation, and host defense mechanisms, making them attractive targets for improving rAAV production. This study examines the expression profiles of microRNAs (miRNAs) and small nucleolar RNAs (snoRNAs) during rAAV plasmid transfection and production in HEK293F cells. We used microarrays to detail differential expression during rAAV production versus mock transfection and basal expression and identified significantly up- and down-regulated small non-coding RNAs (ncRNAs).
2025-08-08 | GSE289823 | GEO
Project description:To understand the response of host cells to rAAV vector production via plasmid transfection, samples were collected throughout the course of three 50 L production batches and analyzed by bulk RNA sequencing of polyadenylated transcripts (RNA-seq). Gene ontology analysis determined that upregulated pathways included inflammatory and antiviral responses. Systematic analyses of the cellular transcriptional response to rAAV production indicates that these host cells are not passively supporting vector manufacture, and therefore may illuminate genes and pathways that influence rAAV production, thereby enabling the rational design of next-generation manufacturing platforms to support safe, effective, and affordable AAV-based gene therapies.
2023-02-06 | GSE224405 | GEO
Project description:Human embryonal kidney cells (HEK-293) are the most common host cells used for transient recombinant adeno-associated virus (rAAV) production in pharmaceutical industry. To better cover the expected gene therapy product demands in the future, different traditional strategies such as cell line sub-cloning and/or addition of chemical substances to the fermentation media have been used to maximize titers and improve product quality. A more effective and advanced approach to boost yield can be envisaged by characterizing the transcriptome of different HEK-293 cell line pedigrees with distinct rAAV productivity patterns to subsequently identify potential gene targets for cell engineering. In this work, the mRNA expression profile of three HEK-293 cell lines, resulting in various yields during a fermentation batch process for rAAV production, was investigated to gain basic insight into cell variability and eventually to identify genes that correlate with productivity. Mock runs using only transfection reagents were performed in parallel as a control. We found significant differences in gene regulatory behaviors between the three cell lines at different growth and production stages. The evaluation of these transcriptomics profiles combined with collected in-process control parameters and titers shed some light on potential cell engineering targets to maximize transient production of rAAV in HEK-293 cells Comparison of three HEK-293 suspension cell lines transcriptomics during an AAV production process
2024-05-13 | GSE226054 | GEO
Project description:Production of rAAV by plasmid transfection induces antiviral and inflammatory responses in suspension HEK293
| PRJNA930839 | ENA
Project description:HEK293 Transcriptome during rAAV production (HEK293 cells from Mass Biologics in BalanCD HEK293 Medium)
| PRJNA1254762 | ENA
Project description:In this comparative proteomic analysis, we focused on proteins in the nuclear fraction. As the nucleus is the epicenter of DNA uptake, transcription, capsid assembly and packaging. Three HEK-293 cell samples i) not transfected, ii) MOCK plasmid transfected, and iii) triple-transfected with rAAV2-production plasmids were harvested 24 h and 72 h after transfection. In total 3384 proteins in all samples were identified revealing regulated proteins due to transfection and rAAV production.
2025-07-21 | PXD062079 | Pride
Project description:Recombinant adeno-associated virus (rAAV) is a widely used viral vector for gene therapy. Despite its clinical efficacy, the manufacturing of rAAV faces challenges in productivity and quality, leading to limited availability. To address the growing demand, next-generation process development should be informed by a mechanistic understanding of the cellular response to rAAV. In this study, we performed transcriptomic analysis of 5 cell lines with variable capacities for rAAV production. Using an intersectional approach, we assessed the transcriptional response to rAAV production and compared transcriptional profiles between high and baseline producers to identify possible targets for enhancing production. Modulation of cell cycle and nucleosome components suggested a reduction of proliferative capacity and a shift toward DNA replication to support rAAV production. During rAAV production, we observed upregulation of several core functions including transcription, stress response, and Golgi and endoplasmic reticulum organization. Conversely, inhibitors of DNA-binding proteins and mitochondrial components were consistently downregulated during rAAV production. We next performed a drug connectivity analysis of these results and identified 5 classes of drugs predicted to enhance rAAV production. Validation studies confirmed the efficacy of HDAC and microtubule inhibitors. Our data uncover novel and previously identified pathways that may enhance rAAV productivity, potentially enabling a path to engineer improved processes and cell lines for higher yields and better quality rAAV production.
2024-08-29 | GSE269485 | GEO
Project description:<p>Human embryonic kidney 293 (HEK293) cells have been successfully adapted from adherent to suspension culture and have been widely applied in both scientific research and the pharmaceutical industry. However, the alterations in cells during the adaptation have not been well described, which raise some uncertainties and concerns regarding the underlying changes and cell behavior.</p><p>In this work, we adapted adherent HEK293 to suspension culture with desirable cell growth and high production titers for recombinant adenoviral vectors, and cells at several stages throughout the process were characterized. First, we obtained three strains of suspension cells from adherent parental HEK293 cells by gradually phasing out fetal bovine serum in original Dulbecco’s modified essential medium with a simultaneous medium replacement with four serum-free suspension culture media, and one strain was chosen as the preferred candidate for further studies due to its satisfying cell conditions and adenoviral vector productivity. Slower cell growth rate, lower glucose uptake, increased lactate production, weaker cell-surface adhesion, and prolonged S phase in the cell cycle were observed in suspension cells compared to their adherent counterparts. We further performed transcriptomics, proteomics, and metabolomics analysis to identify key switches in cells. A total of 2476 differential genes were found, including 1218 up-regulated genes and 1258 down-regulated genes in suspension cells. A similar and correlated pattern was observed in the proteomic study: an almost balanced up-down regulation between suspension and adherent cells, and 702 differentially expressed metabolites were identified by untargeted metabolomics. By virtue of enrichment analysis on differentially expressed genes, proteins and metabolites, we summarized that HEK293 adherent cells survived and adapted to suspension culture by structural remodelling, metabolic network reconstruction and inherent stress resistance. Additionally, we identified claudin7 as a key player involved in suspension transformation in both transcriptomic and proteomic aspects. Our results provide a molecular enlightenment for the mechanism of suspension adaptation and new directions for the rational design of genetically engineered HEK293-derived cell lines for viral-vectored vaccine production.</p>
2025-12-16 | MTBLS13517 | MetaboLights