Clair Gallagher

MiR-7 Triggers Cell Cycle Arrest at the G1/S Transition by Targeting Multiple Genes Including Skp2 and Psme3

MiR-7 acts as a tumour suppressor in many cancers and abrogates proliferation of CHO cells in culture. In this study we demonstrate that miR-7 targets key regulators of the G1 to S phase transition, including Skp2 and Psme3, to promote increased levels of p27KIP and temporary growth arrest of CHO cells in the G1 phase. Simultaneously, the down-regulation of DNA repair-specific proteins via miR-7 including Rad54L, and pro-apoptotic regulators such as p53, combined with the up-regulation of anti-apoptotic factors like p-Akt, promoted cell survival while arrested in G1. Thus miR-7 can co-ordinate the levels of multiple genes and proteins to influence G1 to S phase transition and the apoptotic response in order to maintain cellular homeostasis. This work provides further mechanistic insight into the role of miR-7 as a regulator of cell growth in times of cellular stress.

CHO cell culture longevity and recombinant protein yield are enhanced by depletion of miR-7 activity via sponge decoy vectors.

Improving the efficiency of recombinant protein production by CHO cells is highly desirable as more complex proteins (MAbs, fusion proteins, blood/clotting factors, etc.) go into development and come onto the market. Previous reports have shown that microRNA (miRNA)-7 overexpression arrests the growth of CHO cells and that its depletion increases the proliferation of various cell types. In this study we generated stable CHO clones that overexpressed a miR-7-specific decoy transcript (sponge) downstream of a green fluorescent protein reporter gene. The miR-7 sponge efficiently diverted miR-7 away from its endogenous targets as exemplified by the increased expression of CDC7. Although the sponge effectively sequestered miR-7, it also appeared to protect the bound miRNA sequence from degradation in the cell, as exemplified by the apparent increase in mature miR-7 levels without any change in primary transcription. Phenotypically, CHO clones with sequestered miR-7 displayed improved maximum cell density (40%), significantly improved viability and an almost two-fold increase in yield of secreted protein in a fed-batch culture. These findings demonstrate that miRNA sponge transcripts could potentially be used in cell line development projects to generate producer clones that grow to higher densities and last longer in the bioreactor - thereby improving product yield.

Demodex-Associated Bacillus Proteins Induce an Aberrant Wound Healing Response in a Corneal Epithelial Cell Line: Possible Implications for Corneal Ulcer Formation in Ocular Rosacea

PURPOSE The aim of the work presented here was to establish the response of a corneal epithelial cell line (hTCEpi) to protein extracted from a bacterium (Bacillus oleronius) previously isolated from a Demodex mite from a rosacea patient. METHODS The response of the corneal epithelial cell line to Bacillus proteins was measured in terms of alterations in cell migration and invasiveness. Changes in the expression of metalloproteinase genes and proteins were also assessed. RESULTS The results indicated increased cell migration (14.5-fold, P = 0.001) as measured using 8-μm PET inserts (BD Falcon) in a transwell assay and invasiveness (1.7-fold, P = 0.003) as measured using 8-μm Matrigel (BD Biocoat) invasion inserts in a 24-well plate assay format, following exposure to the Bacillus proteins. Cells exposed to the Bacillus protein showed a dose-dependent increase in expression of genes coding for matrix metalloprotease (MMP)-3 (61-fold) and MPP-9 (301-fold). This dose-dependent increase in gene expression was also reflected in elevated levels of MMP-9 protein (1.34-fold, P = 0.033) and increased matrix metalloprotease activity (1.96-fold, P = 0.043) being present in the culture supernatant. Cells also displayed reduced levels of β-integrin (1.25-fold, P = 0.01), indicative of increased motility and elevated levels of vinculin (2.7-fold, P = 0.0009), suggesting altered motility. CONCLUSIONS The results indicate that exposure of corneal epithelial cells to Bacillus proteins results in an aberrant wound healing response as visualized using a scratch wound assay. These results suggest a possible link between the high density of Demodex mites on the eyelashes of ocular rosacea patients and the development of corneal ulcers.

Re-programming CHO cell metabolism using miR-23 tips the balance towards a highly productive phenotype

microRNA engineering of CHO cells has already proved successful in enhancing various industrially relevant phenotypes and producing various recombinant products. A single miRNAs ability to interact with multiple mRNA targets allows their regulatory capacity to extend to processes such as cellular metabolism. Various metabolic states have previously been associated with particular CHO cell phenotypes such as glycolytic or oxidative metabolism accommodating growth and productivity, respectively. miR-23 has previously been demonstrated to play a role in glutamate metabolism resulting in enhanced oxidative phosphorylation through the TCA cycle. Re-programming cellular bioenergetics through miR-23 could tip the balance, forcing mammalian production cells to be more productive by favoring metabolic channelling into oxidative metabolism. CHO clones depleted of miR-23 using a miR-sponge decoy demonstrated an average ∼three-fold enhanced specific productivity with no impact on cell growth. Using a cell respirometer, mitochondrial activity was found to be enhanced by ∼30% at Complex I and II of the electron transport system. Additionally, label-free proteomic analysis uncovered various potential novel targets of miR-23 including LE1 and IDH1, both implicated in oxidative metabolism and mitochondrial activity. These results demonstrate miRNA-based engineering as a route to re-programming cellular metabolism resulting in increased productivity, without affecting growth.

Loss of photoreceptor potential from retinal progenitor cell cultures, despite improvements in survival.

Retinal degeneration (RD) results from photoreceptor apoptosis. Cell transplantation, one potential therapeutic approach, requires expandable stem cells that can form mature photoreceptors when differentiated. Freshly dissociated primary retinal cells from postnatal day 2-6 (PN2-6) mouse retina can give rise, post-transplantation, to photoreceptors in adult recipients. Unfortunately, incorporation rates are low; moreover, photoreceptor potential is lost if the same PN2-6 cells are cultured prior to transplantation. We investigated the identity of the cells forming photoreceptors post-transplantation, using FACS sorted primary postnatal day (PN) 3-5 Rho-eGFP retinal cells. Higher integration rates were achieved for cells that were expressing Rho-eGFP at PN3-5, indicating that post-mitotic photoreceptor precursors already expressing rhodopsin form the majority of integrating rods. We then investigated improvement of cell culture protocols for retinal progenitor cells (RPCs) derived from PN3-5 retinal cells in vitro. We succeeded in improving RPC survival and growth rates 25-fold, by modifying retinal dissociation, replacing N2 supplement with B27 supplement minus retinoic acid (B27-RA) and coating flasks with fibronectin. However, levels of rhodopsin and similar photoreceptor-specific markers still diminished rapidly during growth in vitro, and did not re-appear after in vitro differentiation. Similarly, transplanted RPCs, whether proliferating or differentiated, did not form photoreceptors in vivo. Cultured RPCs upregulate genes such as Sox2 and nestin, markers of more primitive neural stem cells. Use of these cells for RD treatment will require identification of triggers that favour terminal photoreceptor differentiation and survival in vitro prior to transplantation.

Prolonged pre-incubation increases the susceptibility of Galleria mellonella larvae to bacterial and fungal infection

Galleria mellonella larvae are widely used for assessing the virulence of microbial pathogens and for measuring the in vivo activity of antimicrobial agents and produce results comparable to those that can be obtained using mammals. The aim of the work described here was to ascertain the effect of pre-incubation at 15°C for 1, 3, 6 or 10 weeks on the susceptibility of larvae to infection with Candida albicans and Staphylococcus aureus. Larvae infected with C. albicans after 1 week pre-incubation at 15°C showed 73.3 ± 3.3% survival at 24 hours post-infection while those infected after 10 weeks pre-incubation showed 30 ± 3.3% survival (P < 0.01). Larvae infected with S. aureus after 1 week pre-incubation showed 65.5 ± 3.3% survival after 24 hours while those infected after 10 weeks pre-incubation showed 13.3 ± 3.3% (P < 0.001). Analysis of the haemocyte density in larvae pre-incubated for 3–10 weeks showed a reduction in haemocytes over time but a proportionate increase in the density of granular haemocytes in the population as determined by FACS analysis. Proteomic analysis revealed decreased abundance of proteins associated with metabolic pathways (e.g. malate dehydrogenase, fructose-1,6-bisphosphatase, glyceraldehyde-3-phosphate dehydrogenase) and prophenoloxidase. G. mellonella larvae are a useful in vivo model system but the duration of the pre-incubation stage significantly affects their susceptibility to microbial pathogens possibly as a result of altered metabolism.

Towards next generation CHO cell biology: Bioinformatics methods for RNA-Seq-based expression profiling

High throughput, cost effective next generation sequencing (NGS) has enabled the publication of genome sequences for Cricetulus griseus and several Chinese hamster ovary (CHO) cell lines. RNA‐Seq, the utilization of NGS technology to study the transcriptome, is expanding our understanding of the CHO cell biological system in areas ranging from the analysis of transcription start sites to the discovery of small noncoding RNAs. The analysis of RNA‐Seq data, often comprised of several million short reads, presents a considerable challenge. If the CHO cell biology field is to fully exploit the potential of RNA‐Seq, the development of robust data analysis pipelines is critical. In this manuscript, we outline bioinformatics approaches for the stages of a typical RNA‐Seq expression profiling experiment including quality control, pre‐processing, alignment and de novo transcriptome assembly. Algorithms for the analysis of mRNA and microRNA (miRNA) expression as well as methods for the detection of alternative splicing from RNA‐Seq data are also presented. At this relatively early stage of Cricetulus griseus genome assembly and annotation, it is likely that a combination of isoform deconvolution and raw count based methods will provide the most complete picture of transcript expression patterns in CHO cell RNA‐Seq experiments.

Exposure of a corneal epithelial cell line (hTCEpi) to Demodex-associated Bacillus proteins results in an inflammatory response.

PURPOSE A role for a bacterium, Bacillus oleronius, originally isolated from a Demodex mite, in the induction of ocular rosacea has been proposed. The aim of this work was to characterize the response of a corneal epithelial cell line to Bacillus proteins, as this might give an insight into how such proteins contribute to the symptoms of ocular rosacea in vivo. METHODS The effect of exposing Bacillus protein preparation on human telomerase-immortalized corneal epithelial cells (hTCEpi) was measured by monitoring changes in cell proliferation and the expression of a number of genes associated with inflammation. The production of inflammatory cytokines was measured and the expression and activity of MMP-9 was quantified. RESULTS Exposure of hTCEpi cells to 2 or 6 μg/mL Bacillus protein resulted in a dose-dependent reduction in cell proliferation. Exposure of cells to 6 μg/mL Bacillus protein did not induce apoptosis, but there was an increase in the expression of genes coding for IL-6 (13.8-fold), IL-1β (4.0-fold), IL-8 (11.1-fold), and TNF-α (4.1-fold). Increased expression of genes coding for the defensins, CCL20 (4.5-fold) and S100A7 (6.8-fold) also was observed. Elevated production of IL-6 and IL-8 was evident from cells exposed to 2 and 6 μg/mL Bacillus protein. The hTCEpi cells demonstrated increased MMP-9 expression (3.2-fold, P = 0.003) and activity (2.2-fold, P = 0.0186) after 48 hours of exposure to 6 μg/mL Bacillus protein preparation. CONCLUSIONS The results suggest that interaction of Demodex-associated Bacillus proteins with the corneal surface could lead to tissue degradation and inflammation, possibly leading to corneal scarring.

Engineering CHO cell growth by stable manipulation of miRNA expression

Background MiRNAs are small non-coding RNAs involved in many biological functions such as cell proliferation and apoptosis (1), cell cycle (2), homeostasis (3) and cell metabolism (4). They are highly conserved between species. They are capable of regulating hundreds of genes in a post-transcriptional manner by translation repression and/or mRNA degradation (5). These characteristics make miRNAs attractive tools for CHO cell engineering as multiple genes may be targeted simultaneously and possibly entire biological pathways can be manipulated. After temperature-shifting CHO cell culture from 37°C to 31°C, several miRNAs were found differentially regulated of which miR-7 was found to be down-regulated. Our laboratory has previously demonstrated that transient overexpression of miR-7 using mimics of mature endogenous miR-7, leads to a significant decrease in cell growth (6). On the other hand, transient inhibition using inhibitors of mature endogenous miR-7 provoked increased cell growth, though to a lesser extent. As this antisense technology is transient, another strategy was chosen to study the impact of stable miR-7 inhibition on CHO phenotypes. “Sponge” technology is an effective tool to stably sequester endogenous miRNAs (7) by introducing a decoy target reporter gene. This approach can be used to understand post-transcriptional regulation in CHO cells and to identify cellular pathways related to cell growth, cell viability and cell productivity key phenotypes for cell bioprocess improvement.

Proteomics in biomanufacturing control: Protein dynamics of CHO‐K1 cells and conditioned media during apoptosis and necrosis

Cell viability has a critical impact on product quantity and quality during the biomanufacturing of therapeutic proteins. An advanced understanding of changes in the cellular and conditioned media proteomes upon cell stress and death is therefore needed for improved bioprocess control. Here, a high pH/low pH reversed phase data independent 2D‐LC‐MSE discovery proteomics platform was applied to study the cellular and conditioned media proteomes of CHO‐K1 apoptosis and necrosis models where cell death was induced by staurosporine exposure or aeration shear in a benchtop bioreactor, respectively. Functional classification of gene ontology terms related to molecular functions, biological processes, and cellular components revealed both cell death independent and specific features. In addition, label free quantitation using the Hi3 approach resulted in a comprehensive shortlist of 23 potential cell viability marker proteins with highest abundance and a significant increase in the conditioned media upon induction of cell death, including proteins related to cellular stress response, signal mediation, cytoskeletal organization, cell differentiation, cell interaction as well as metabolic and proteolytic enzymes which are interesting candidates for translating into targeted analysis platforms for monitoring bioprocessing response and increasing process control.