Proteomic Profiling of IgG1 Producing CHO Cells Using LC/LC-SPS-MS3: The Effects of Bioprocessing Conditions on Productivity and Product Quality.

The biopharmaceutical market is dominated by monoclonal antibodies, the majority of which are produced in Chinese hamster ovary (CHO) cell lines. Intense cell engineering, in combination with optimization of various process parameters results in increasing product titers. To enable further improvements in manufacturing processes, detailed information about how certain parameters affect cellular mechanisms in the production cells, and thereby also the expressed drug substance, is required. Therefore, in this study the effects of commonly applied changes in bioprocessing parameters on an anti-IL8 IgG1 producing CHO DP-12 cell line were investigated on the level of host cell proteome expression combined with product quality assessment of the expressed IgG1 monoclonal antibody. Applying shifts in temperature, pH and dissolved oxygen concentration, respectively, resulted in altered productivity and product quality. Furthermore, analysis of the cells using two-dimensional liquid chromatography-mass spectrometry employing tandem mass tag based isotopic quantitation and synchronous precursor selection-MS3 detection revealed substantial changes in the protein expression profiles of CHO cells. Pathway analysis indicated that applied bioprocessing conditions resulted in differential activation of oxidative phosphorylation. Additionally, activation of ERK5 and TNFR1 signaling suggested an affected cell cycle. Moreover, in-depth product characterization by means of charge variant analysis, peptide mapping, as well as structural and functional analysis, revealed posttranslational and structural changes in the expressed drug substance. Taken together, the present study allows the conclusion that, in anti-IL8 IgG1 producing CHO DP-12 cells, an improved energy metabolism achieved by lowering the cell culture pH is favorable when aiming towards high antibody production rates while maintaining product quality.

Expanding Proteome Coverage with CHarge Ordered Parallel Ion aNalysis (CHOPIN) Combined with Broad Specificity Proteolysis.

The "deep" proteome has been accessible by mass spectrometry for some time. However, the number of proteins identified in cells of the same type has plateaued at ∼8000-10 000 without ID transfer from reference proteomes/data. Moreover, limited sequence coverage hampers the discrimination of protein isoforms when using trypsin as standard protease. Multienzyme approaches appear to improve sequence coverage and subsequent isoform discrimination. Here we expanded proteome and protein sequence coverage in MCF-7 breast cancer cells to an as yet unmatched depth by employing a workflow that addresses current limitations in deep proteome analysis in multiple stages: We used (i) gel-aided sample preparation (GASP) and combined trypsin/elastase digests to increase peptide orthogonality, (ii) concatenated high-pH prefractionation, and (iii) CHarge Ordered Parallel Ion aNalysis (CHOPIN), available on an Orbitrap Fusion (Lumos) mass spectrometer, to achieve 57% median protein sequence coverage in 13 728 protein groups (8949 Unigene IDs) in a single cell line. CHOPIN allows the use of both detectors in the Orbitrap on predefined precursor types that optimizes parallel ion processing, leading to the identification of a total of 179 549 unique peptides covering the deep proteome in unprecedented detail.

2-D DIGE analysis of the budding yeast pH 6-11 proteome in meiosis.

Meiosis is the cell division that generates haploid gametes from diploid precursors. To provide insight into the functional proteome of budding yeast during meiosis, a 2-D DIGE kinetic approach was used to study proteins in the pH 6-11 range. Nearly 600 protein spots were visualised and 79 spots exhibited statistically significant changes in abundance as cells progressed through meiosis. Expression changes of up to 41-fold were detected and protein sequence information was obtained for 48 spots. Single protein identifications were obtained for 21 spots including different gel mobility forms of 5 proteins. A large number of post-translational events are suggested for these proteins, including processing, modification and import. The data are incorporated into an online 2-DE map of meiotic proteins in budding yeast, which extends our initial DIGE investigation of proteins in the pH 4-7 range. Together, the analyses provide peptide sequence data for 84 protein spots, including 50 single-protein identifications and gel mobility isoforms of 8 proteins. The largest classes of identified proteins include carbon metabolism, protein catabolism, protein folding, protein synthesis and the oxidative stress response. A number of the corresponding genes are required for yeast meiosis and recent studies have identified similar classes of proteins expressed during mammalian meiosis. This proteomic investigation and the resulting protein reference map make an important contribution towards a more detailed molecular view of yeast meiosis.

Dose-dependent cellular and humoral responses in Galleria mellonella larvae following beta-glucan inoculation.

Galleria mellonella larvae were inoculated with different doses of beta-glucan by injection into the haemocoel. Those larvae that had received high doses of beta-glucan (15, 30 or 60microg/larva) demonstrated increased survival following infection with the yeast Candida albicans. High concentrations of glucan induced an increase in haemocyte density and a reduction in yeast proliferation within the haemocoel. Proteomic analysis of glucan-treated larvae revealed increased expression of a variety of peptides some of which may possess antimicrobial properties. Analysis of expression profiles revealed that low doses of beta-glucan (3.75microg/larva) triggered the increased expression of certain peptides (e.g. hemolin) while high dose inoculation was required before the increased expression of others (e.g. archaemetzincin) was evident. These results indicate that low doses of beta-glucan induce a limited immune response while high doses induce an immune response that has the potential to curtail the threat within the haemocoel but also withstand a subsequent infection. Immune priming gives insects the ability to withstand a potentially lethal infection if exposed to a low level of the pathogen 24-48h previously. Immune priming has resource implications and this work indicates that a graded immune response is initiated depending upon the amount of the immune priming agent encountered.

Physical stress primes the immune response of Galleria mellonella larvae to infection by Candida albicans.

Larvae of the greater wax moth (Galleria mellonella) that had been subjected to physical stress by shaking in cupped hands for 2 min showed reduced susceptibility to infection by Candida albicans when infected 24 h after the stress event. Physically stressed larvae demonstrated an increase in haemocyte density and elevated mRNA levels of galiomicin and an inducible metalloproteinase inhibitor (IMPI) but not transferrin or gallerimycin. In contrast, previous work has demonstrated that microbial priming of larvae resulted in the induction of all four genes. Examination of the expression of proteins in the insect haemolymph using 2D electrophoresis and MALDI TOF analysis revealed an increase in the intensity of a number of peptides showing some similarities with proteins associated with the insect immune response to infection. This study demonstrates that non-lethal physical stress primes the immune response of G. mellonella and this is mediated by elevated haemocyte numbers, increased mRNA levels of genes coding for two antimicrobial peptides and the appearance of novel peptides in the haemolymph. This work demonstrates that physical priming increases the insect immune response but the mechanism of this priming is different to that induced by low level exposure to microbial pathogens.

Effect of pre-incubation temperature on susceptibility of Galleria mellonella larvae to infection by Candida albicans.

The use of insects for evaluating the virulence of microbial pathogens and for determining the efficacy of antimicrobial drugs is increasing. When larvae of the greater wax moth Galleria mellonella were incubated at 4 or 37 degrees C for 24 h. prior to infection, they manifested increased resistance to infection by the yeast Candida albicans compared to larvae that had been pre-incubated for 24 h at 30 degrees C. Incubation at 4 or 37 degrees C led to an increase in haemocyte density and the expression of genes coding for gallerimycin, transferrin, an inducible metalloproteinase inhibitor (IMPI) and galiomicin. Peak expression of these genes was recorded at approximately 24 h after the commencement of the 4 or 37 degrees C incubation. These results indicate that exposure of larvae to mild thermal shock conditions induces a protective cellular and humoral immune response mediated by increased numbers of haemocytes and elevated expression of antimicrobial peptides.