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: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:HEK293 Transcriptome during rAAV production (HEK293 cells from Mass Biologics in BalanCD HEK293 Medium)
| PRJNA1254762 | ENA
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:Recombinant Adeno-associated viruses (rAAV) are commonly used in gene therapy for preclinical research and therapeutic applications. Despite its clinical efficacy, the manufacturing of rAAV faces challenges in productivity and quality, leading to limited availability. In this study, we aimed to identify compounds that increase the capacity of cells to produce AAV9 with a high-throughput small-molecule screening strategy. With the Arrayed Targeted Library for AAV Screening platform, we screened a library of 3,300 small molecules and identified several targets, including cell-cycle modulators, G protein-coupled receptor modulators, histone deacetylate inhibitors, Janus kinase inhibitors, and metabolic modulators. Most notably, we identified Polo-like kinase isoform 1 (PLK1) inhibitors as enhancers of AAV production. PLK1 inhibition using HMN-214 increased AAV production, and was largely consistent across HEK293 cell lines, vector payloads and capsid serotypes. Using cell cycle and RNA-sequencing analysis, we show that PLK1 inhibition halts cells in the G2/M phase and blocks their exit from the M to G1 phase. These findings can be used to develop more cost-effective methods to increase AAV yield during production in the manufacturing process.
2025-01-22 | GSE273692 | GEO