Mugdha Gadgil

Manganese increases high mannose glycoform on monoclonal antibody expressed in CHO when glucose is absent or limiting: Implications for use of alternate sugars

Alternate sugars such as galactose and fructose are metabolized at a slower rate than glucose and result in lower accumulation of lactate. While low lactate accumulation is desirable, we report that complete substitution of glucose with these sugars results in an increase in M5 high mannose glycans. Surprisingly, this increase is much higher when the culture is supplemented with manganese: for example, when cells are cultured with galactose, M5 high mannose glycan content increased from 5% at 1 nM Mn2+ in the basal medium to 32% with 16 µM Mn2+ supplementation. When galactose is supplemented with glucose maintained at low concentrations, a small reduction in high mannose glycans is seen. In control cultures with glucose, the high mannose content was however <2% in this range of Mn2+ concentration. By varying Mn2+ and glucose supplementation levels, with or without galactose, we systematically demonstrate that Mn2+ concentration and glucose availability, together, significantly affect the high mannose glycan content. To our knowledge, this is the first report that shows that the effect of Mn2+ on high mannose glycan content depends on glucose availability. At each Mn2+ supplementation level evaluated, galactosylation percentages were highest for cultures where galactose was supplemented with glucose at non‐limiting concentration.

Controlled release of nutrients to mammalian cells cultured in shake flasks

Though cell culture‐based protein production processes are rarely carried out under batch mode of operation, cell line and initial process development operations are usually carried out in batch mode due to simplicity of operation in widely used scale down platforms like shake flasks. Nutrient feeding, if performed, is achieved by bolus addition of concentrated feed solution at different intervals, which leads to large transient increases in nutrient concentrations. One negative consequence is increased waste metabolite production. We have developed a hydrogel‐based nutrient delivery system for continuous feeding of nutrients in scale down models like shake flasks without the need for manual feed additions or any additional infrastructure. Continuous delivery also enables maintaining nutrient concentrations at low levels, if desired. The authors demonstrate the use of these systems for continuous feeding of glucose and protein hydrolysate to a suspension Chinese Hamster Ovary (CHO) culture in a shake flask. Glucose feeding achieved using the glucose‐loaded hydrogel resulted in a 23% higher integral viable cell density and an 89% lower lactate concentration at the end of the culture when compared with a bolus‐feed of glucose.

Comparison of feature selection and classification combinations for cancer classification using microarray data

High throughput gene expression data can be used to identify biomarker profiles for classification. The accuracy of microarray based sample classification depends on the algorithm employed for selecting the features (genes) used for classification, and the classification algorithm. We have evaluated the performance of over 2000 combinations of feature selection and classification algorithms in classifying cancer datasets. One of these combinations (SVM for ranking genes + SMO) shows excellent classification accuracy using a small number of genes across three cancer datasets tested. Notably, classification using 15 selected genes yields 96% accuracy for a dataset obtained on an independent microarray platform.

In situ pH maintenance for mammalian cell cultures in shake flasks and tissue culture flasks

pH in animal cell cultures decreases due to production of metabolites like lactate. pH control via measurement and base addition is not easily possible in small‐scale culture formats like tissue‐culture flasks and shake flasks. A hydrogel‐based system is reported for in situ pH maintenance without pH measurement in such formats, and is demonstrated to maintain pH between 6.8 and 7.2 for a suspension CHO cell line in CD CHO medium and between 7.3 and 7.5 for adherent A549 cells in DMEM:F12 containing 10% FBS. This system for pH maintenance, along with our previous report of hydrogels for controlled nutrient delivery in shake flasks can allow shake flasks to better mimic bioreactor‐based fed batch operation for initial screening during cell line and process development for recombinant protein production in mammalian cells.

Cell line development for biomanufacturing processes: recent advances and an outlook

At the core of a biomanufacturing process for recombinant proteins is the production cell line. It influences the productivity and product quality. Its characteristics also dictate process development, as the process is optimized to complement the producing cell to achieve the target productivity and quality. Advances in the past decade, from vector design to cell line screening, have greatly expanded our capability to attain producing cell lines with certain desired traits. Increasing availability of genomic and transcriptomic resources for industrially important cell lines coupled with advances in genome editing technology have opened new avenues for cell line development. These developments are poised to help biosimilar manufacturing, which requires targeting pre-defined product quality attributes, e.g., glycoform, to match the innovator’s range. This review summarizes recent advances and discusses future possibilities in this area.

Effect of addition of 'carrier' DNA during transient protein expression in suspension CHO culture.

Transient protein expression using polyethyleneimine as a transfection agent is useful for the rapid production of small amounts of recombinant proteins. It is known that an increase in extracellular DNA concentration during transfection can lead to a nonlinear increase in intracellular DNA concentration. We present an approach that hypothesizes that this nonlinearity can be used to decrease the amount of plasmid required for productive transfections. Through addition of non coding ‘carrier’ DNA to increase total DNA concentration during transfection, we report a statistically significant increase in protein (IgG) expression per unit plasmid used for transfection. This approach could be useful to increase protein yields for large scale transfections under conditions where plasmid availability is limited.

Meta analysis of gene expression changes upon treatment of A549 cells with anti-cancer drugs to identify universal responses

A meta-analysis of publicly available gene expression changes in A549 cells upon treatment with anti-cancer drugs is reported. To reduce false positives, both fold-change and significance level cutoffs were used. Simulated datasets and permutation analysis were used to guide choice of ratio cutoff. Of the genes identified, FDXR is the only gene differentially expressed in six of the seven drug treatments. Though FDXR has been reported to be differentially expressed upon treatment with 5-fluorouracil and its expression correlated to long term disease survival, to our knowledge this is a first study implicating a wide effect of anti-cancer drug treatment on FDXR expression. The other genes identified which are differentially expressed in four out of the seven drug treatments are CDKN1A and PARVB which are upregulated and MYC, HBP1, LDLR, SIM2, ALX1 and GPHN which are downregulated.

CHO cells adapted to inorganic phosphate limitation show higher growth and higher pyruvate carboxylase flux in phosphate replete conditions

Inorganic phosphate (Pi) is an essential ion involved in diverse cellular processes including metabolism. Changes in cellular metabolism upon long term adaptation to Pi limitation have been reported in E. coli. Given the essential role of Pi, adaptation to Pi limitation may also result in metabolic changes in animal cells. In this study, we have adapted CHO cells producing recombinant IgG to limiting Pi conditions for 75 days. Not surprisingly, adapted cells showed better survival under Pi limitation. Here, we report the finding that such cells also showed better growth characteristics compared to control in batch culture replete with Pi (higher peak density and integral viable cell density), accompanied by a lower specific oxygen uptake rate and cytochrome oxidase activity towards the end of exponential phase. Surprisingly, the adapted cells grew to a lower peak density under glucose limitation. This suggests long term Pi limitation may lead to selection for an altered metabolism with higher dependence on glucose availability for biomass assimilation compared to control. Steady state U‐13C glucose labeling experiments suggest that adapted cells have a higher pyruvate carboxylase flux. Consistent with this observation, supplementation with aspartate abolished the peak density difference whereas supplementation with serine did not abolish the difference. This supports the hypothesis that cell growth in the adapted culture might be higher due to a higher pyruvate carboxylase flux. Decreased fitness under carbon limitation and mutations in the sucABCD operon has been previously reported in E. coli upon long term adaptation to Pi limitation, suggestive of a similarity in cellular response among such diverse species.

Comparison of methods for identifying periodically varying genes

Several methods have been reported for identifying periodically varying genes from gene expression datasets. We compare the performance of five existing methods and a combination of G-statistic and autocovariance (called GVAR) using simulated sine-function-based and cell-cycle-based datasets. Based on this analysis we recommend appropriate methods for different experimental situations (length of the time series, sampling interval and noise level). No single method performs the best under all tested conditions. None of the evaluated methods perform well at high noise levels for short time series data. At lower noise levels, GVAR performed the best.

Shear stress increases cytotoxicity and reduces transfection efficiency of liposomal gene delivery to CHO-S cells

Animal cells in suspension experience shear stress in different situations such as in vivo due to hemodynamics, or in vitro due to agitation in large-scale bioreactors. Shear stress is known to affect cell physiology, including binding and uptake of extracellular cargo. In adherent cells the effects of exposure to shear stress on particle binding kinetics and uptake have been studied. There are however no reports on the effect of shear stress on extracellular cargo delivery to suspension cells. In this study, we have evaluated the effect of shear stress on transfection of CHO-S cells using Lipofectamine 2000 in a simple flow apparatus. Our results show decreased cell growth and transfection efficiency upon lipoplex assisted transfection of CHO-S while being subjected to shear stress. This effect is not seen to the same extent when cells are exposed to shear stress in absence of the lipoplex complex and subsequently transfected, or if the lipoplex is subjected to shear stress and subsequently used to transfect the cells. It is also not seen to the same extent when cells are exposed to shear stress in presence of liposome alone, suggesting that the observed effect is dependent on interaction of the lipoplex with cells in the presence of shear stress. These results suggest that studies involving liposomal DNA delivery in presence of shear stress such as large scale transient protein expression should account for the effect of shear during lipoplex assisted DNA delivery.