IRF7-deficient MDCK cell based on CRISPR/Cas9 technology for enhancing influenza virus replication and improving vaccine production

USP1 inhibits influenza A and B virus replication in MDCK cells by mediating RIG-I deubiquitination

The post-translational modification and stability regulation of RIG-I play critical roles in promoting IFN-I production and maintaining immune homeostasis. In this study, we found that ubiquitin-specific peptidase 1 (USP1) promotes RIG-I protein stability through deubiquitination, which in turn enhances antiviral immunity through the production of inflammatory cytokines, and inhibits the replication of influenza virus in MDCK cells. In contrast, USP1 knockdown inhibited the deubiquitination of RIG-I, decreased the RIG-I protein level, and significantly increased the influenza virus titer. Meanwhile, inhibition of USP1 expression did not have a significant effect on the proliferation of MDCK cells, suggesting that USP1 could be used as a target gene to establish a vaccine-producing MDCK cell line. The above results provide a more comprehensive understanding of the function of USP1 and the antiviral response mechanism, and provide a theoretical and methodological basis for the screening of target genes for the artificial establishment of high-yield MDCK cell lines for vaccine production.

Insights into IAV Replication and Lipid Metabolism in Suspension-Adapted MDCK-STAT1-KO Cells

OBJECTIVES

The industrial production of influenza vaccines is facing significant challenges, particularly in improving virus production efficiency. Despite advances in cell culture technologies, our understanding of the production characteristics of high-yield suspension cell lines remains limited, thereby impeding the development of efficient vaccine production platforms. This study aims to investigate the key features of STAT1 knockout suspension-adapted MDCK cells (susMDCK-STAT1-KO) in enhancing influenza A virus (IAV) production.

METHODS

Suspension-adapted susMDCK-STAT1-KO cells were compared to suspension-adapted wild-type MDCK cells (susMDCK) for IAV production. Virus quantification, gene expression analysis, and cholesterol deprivation assays were performed. Metabolite profiles, viral RNA quantification, and lipid and dry weight measurements were also conducted to assess the viral replication and release efficiency.

RESULTS

The susMDCK-STAT1-KO cells exhibited significantly improved virus adsorption (64%) and entry efficiency (75%) for the H1N1 virus, as well as accelerated viral transcription and replication for both the H1N1 and H9N2 viruses. Virus release was identified as a limiting factor, with a 100-fold higher intracellular-to-extracellular viral RNA ratio. However, the STAT1-KO cells showed a 2.39-fold higher release rate (750 virions/cell/h) and 3.26-fold greater RNA release for the H1N1 virus compared to wild-type cells. A gene expression analysis revealed enhanced lipid metabolism, particularly cholesterol synthesis, as a key factor in viral replication and release. Cholesterol deprivation resulted in reduced viral titers, confirming the critical role of intracellular cholesterol in IAV production.

CONCLUSIONS

This study demonstrates the enhanced influenza virus production capacity of susMDCK-STAT1-KO cells, with significant improvements in viral yield, replication, and release efficiency. The findings highlight the importance of STAT1-mediated immune modulation and cholesterol metabolism in optimizing virus production. These insights provide a foundation for the development of more efficient vaccine production platforms, with implications for large-scale industrial applications.

Innovations in cell culture-based influenza vaccine manufacturing - from static cultures to high cell density cultivations

Influenza remains a serious global health concern, causing significant morbidity and mortality each year. Vaccination is crucial to mitigate its impact, but requires rapid and efficient manufacturing strategies to handle timing and supply. Traditionally relying on egg-based production, the field has witnessed a paradigm shift toward cell culture-based methods offering enhanced flexibility, scalability, and process safety. This review provides a concise overview of available cell substrates and technological advancements. We summarize crucial steps toward process intensification - from roller bottle production to dynamic cultures on carriers and from suspension cultures in batch mode to high cell density perfusion using various cell retention devices. Moreover, we compare single-use and conventional systems and address challenges including defective interfering particles. Taken together, we describe the current state-of-the-art in cell culture-based influenza virus production to sustainably meet vaccine demands, guarantee a timely supply, and keep up with the challenges of seasonal epidemics and global pandemics.

IRF7-deficient MDBK cell based on CRISPR/Cas9 technology for enhancing IBRV replication

Infectious bovine rhinotracheitis (IBR), characterized by acute respiratory lesions in cattle, is a major infectious disease caused by bovine alphaherpesvirus-1 (BoAHV-1). Control of this disease is primarily depending on vaccination. Madin-Darby bovine kidney cells (MDBK) being the main host cells and the important production platform for IBR vaccines. However, innate immune genes inhibit viral replication. Accordingly, the aim of this study was developing of IRF7 gene deleted MDBK cells to facilitate the production of high-titer vaccines. The CRISPR/Cas9 technology was used to knock out the IRF7 gene in MDBK cells and the impact on virus replication was examined using virus growth curves, CCK-8 assays, cell scratch assays, and qPCR. The knockout of the IRF7 gene in MDBK cells led to an increased replication capacity of IBRV and a significant reduction in type I interferons expression, specifically IFN-α and IFN-β. This indicates that IRF7 -/-MDBK cell lines can effectively result in production of IBRV with high-titer, which will enhance the development of inactivated or attenuated vaccines.

Developments and current challenges in the process of cell culture-based seasonal influenza vaccine manufacture in Japan

Seasonal influenza is an acute respiratory infection primarily caused by influenza A and B viruses, which circulate annually and cause substantial morbidity and mortality worldwide. Annual influenza vaccination is currently the most effective measure for preventing influenza and greatly reduces the risk of disease severity and the incidence of complications and death. Annual seasonal influenza vaccines are traditionally produced in Japan and many other countries using viruses propagated in embryonated chicken eggs. However, at present, the effectiveness of the seasonal influenza vaccines has some significant limitations, partly because of egg-adaptive mutations in the antigenic sites of the influenza virus haemagglutinin, which are caused by the continued evolution of seasonal influenza viruses. To overcome the limitations of egg-based influenza vaccine production, a mammalian cell culture-based influenza vaccine production system has been developed in Japan in the past decade as an alternative to the current production method. In this review, I have summarised the progress in the development of cell-based seasonal influenza vaccines and discussed the technological challenges encountered in the development of influenza vaccines.

Synthetic Cell Lines for Inducible Packaging of Influenza A Virus

Influenza A virus (IAV) is a negative-sense RNA virus that causes seasonal infections and periodic pandemics, inflicting huge economic and human costs on society. The current production of influenza virus for vaccines is initiated by generating a seed virus through the transfection of multiple plasmids in HEK293 cells followed by the infection of seed viruses into embryonated chicken eggs or cultured mammalian cells. We took a system design and synthetic biology approach to engineer cell lines that can be induced to produce all viral components except hemagglutinin (HA) and neuraminidase (NA), which are the antigens that specify the variants of IAV. Upon the transfection of HA and NA, the cell line can produce infectious IAV particles. RNA-Seq transcriptome analysis revealed inefficient synthesis of viral RNA and upregulated expression of genes involved in host response to viral infection as potential limiting factors and offered possible targets for enhancing the productivity of the synthetic cell line. Overall, we showed for the first time that it was possible to create packaging cell lines for the production of a cytopathic negative-sense RNA virus. The approach allows for the exploitation of altered kinetics of the synthesis of viral components and offers a new method for manufacturing viral vaccines.

Knockout of IRF3 and IRF7 genes by CRISPR/Cas9 technology enhances porcine virus replication in the swine testicular (ST) cell line

Antiviral vaccines for pig diseases are essential to prevent epidemic outbreaks. However, their production is often hindered by inefficient manufacturing processes that yield lower quantities of the vaccine. To accelerate the progress of various areas of bioproduction, we have considered the necessity of enhancing viral replication efficiency by optimizing ST (swine testicular) cell lines that are commonly utilized in virus manufacturing. CRISPR/Cas9 gene-editing technology were utilized to create IRF3 or IRF7 knockout cell lines that facilitate high-titer viral stock production. Compared to the parental cell lines, the ST IRF3/7 KO cell line displayed a compromised antiviral response to a panel of viruses (Porcine epidemic diarrhea virus, Senecavirus A, Parainfluenza virus 5, and Getah virus), as evidenced by decreased expression of interferon and certain antiviral factors. The inhibition of these responses led to heightened viral replication and increased cytopathic effects, ultimately promoting apoptosis. As a result, the development of these cell lines offers a more efficient approach for biopharmaceutical companies to boost their virus production and reduce associated costs.

Ruxolitinib accelerates influenza A virus adaptation in the Madin-Darby canine kidney (MDCK) cell line

AIM

To investigate the effect of ruxolitinib medium supplement, separately and in combination with trypsin, on influenza A virus (IAV) adaptation and propagation in the Madin-Darby canine kidney (MDCK) cell line.

METHODS AND RESULTS

Two consecutive passages of three egg-based IAV strains were performed in the MDCK cell line with medium (a) without additives; (b) with a combination of ruxolitinib and trypsin; (c) with ruxolitinib; and (d) trypsin. Adaptation without a medium additive failed in both passages. After a single passage, the probability of the IAV adaptation was highly significantly influenced by the type of additive (binomial generalized linear model, χ22 = 23.84, P < 0.00001). The highest probability of adaptation was achieved with the combination of ruxolitinib and trypsin, followed by ruxolitinib alone and trypsin. After the two consecutive passages, the influence of the type of medium additive on the probability of virus adaptation was no longer significant. In two of three IAV MDCK-adapted strains, the type of medium additive had no significant influence on virus yields.

CONCLUSION

Ruxolitinib accelerates the adaptation of IAV in the MDCK cell line both individually and together with trypsin.

TRAF3 deficiency in MDCK cells improved sensitivity to the influenza A virus

Tumor necrosis factor receptor-associated factor 3 (TRAF3), an adaptor protein, has significant and varying effects on immunity depending on cell types. The role of TRAF3 in Madin-Darby Canine Kidney Epithelial (MDCK) cell resistance to influenza A virus (IVA) remains elusive. In the present study, CRISPR-Cas9 gene editing technology was used to construct the TRAF3 knockout MDCK cells (MDCK-TRAF3-/-). Hemagglutination assay, plaque assay, transcriptome, and quantitative real-time PCR were performed after IVA infection. The results showed that after IVA infection, HA titers and virus titers were promoted, interferon I-related pathways were significantly blocked, and transcription of several antiviral-related genes was significantly decreased in MDCK-TRAF3-/- cells. Thus, our study suggests that TRAF3 gene knockout reduced MDCK cell's resistance to IVA, thereby resulting in a promising way for IVA isolation and vaccine manufacturing.

RSAD2 Is an Effective Target for High-Yield Vaccine Production in MDCK Cells

Increasingly, attention has focused on improving vaccine production in cells using gene editing technology to specifically modify key virus regulation-related genes to promote virus replication. In this study, we used DIA proteomics analysis technology to compare protein expression differences between two groups of MDCK cells: uninfected and influenza A virus (IAV) H1N1-infected cells 16 h post infection (MOI = 0.01). Initially, 266 differentially expressed proteins were detected after infection, 157 of which were upregulated and 109 were downregulated. We screened these proteins to 23 genes related to antiviral innate immunity regulation based on functional annotation database analysis and verified the mRNA expression of these genes using qPCR. Combining our results with published literature, we focused on the proteins RSAD2, KCNN4, IDO1, and ISG20; we verified their expression using western blot, which was consistent with our proteomics results. Finally, we knocked down RSAD2 using lentiviral shRNA expression vectors and found that RSAD2 inhibition significantly increased IAV NP gene expression, effectively promoting influenza virus replication with no significant effect on cell proliferation. These results indicate that RSAD2 is potentially an effective target for establishing high-yield vaccine MDCK cell lines and will help to fully understand the interaction mechanism between host cells and influenza viruses.