Performance consistency of fed-batch cultures across multiple systems used in upstream process development

Each stage of cell culture process development requires fit for purpose tools. The selection of a fed-batch cultivation system is often based on throughput and cost. However, the process knowledge derived from different systems and scales is not necessarily identical. Hence, a careful evaluation of systems which are already established or newly implemented is essential. We recently introduced a novel high throughput fed-batch screening system (1) and the objective of this study was to provide data on how it compares with other systems used in early and late stage cell culture process development. We describe the performance of 12 different recombinant CHO cell lines expressing the same antibody in fed-batch culture systems ranging from a few hundred microliters to lab scale. The 12 cell lines were selected based on distinct phenotypes covering a range which can be expected in typical industrial process development projects. The cell lines were cultivated using the same expansion and fed-batch protocol (proprietary fed-batch system). The following cultivation systems were evaluated: shaking 96-deepwell plates, 50 mL vented shake tubes, micro-scale bioreactors (ambr15TM system) and lab-scale bioreactors (3L). The results of this study show both the limitations and the potential of each cultivation system and their suitability for process development, process characterization and scale-up. The shaking systems offer unprecedented parallel throughput but are limited with respect to culture control (e. g. lack of pH and pO2 control). Despite their limitations, they are expected to be used in the future as important tools for early process development and for the improvement of fed-batch platform processes. On the other hand, the data obtained from this study show that micro- and lab-scale bioreactors represent ideal tools for the confirmation of process consistency. Both micro- and lab-scale systems will be extensively used in the future to support tech transfers and perform process characterization studies

Generating glycan variants for biological activity testing by means of parallel experimental design and multivariate analysis

For more than 20 years, the industry has mainly invested in productivity enhancements. Recently, the focus of cell-culture process development began to shift. The modulation of quality attributes of recombinant therapeutic protein has gained substantial interest as demonstrated by the plethora of recent publications describing the effect of cell culture media on post-translational modifications of recombinant proteins1. Focusing on glycosylation, our team has developed a toolbox of media design beyond the commonly known media components and a rational high-throughput experimental design method. We identified and tested a large variety of novel cell culture compatible chemical components in industrial relevant Chinese hamster ovary cell lines (CHO) expressing recombinant antibodies and antibody fusion molecules. The compounds were evaluated in five different parallel 96-DWP fed-batch experiments, considering their mode of biological action. Viable cell density, viability and product titer were monitored and purified supernatants underwent N-glycan analysis by 2AB-UPLC and site-specific glycan-peptide analysis. Multivariate analysis identified the best performing glycosylation modulators, which were confirmed in spin tubes. Intracellular nucleotide and nucleotide sugar levels were analyzed by capillary electrophoresis, the gene expression by next-generation sequencing technologies, and the impact of the generated glycan variants on the biological activity was assessed. Non-targeted metabolite profiling was carried out to build a multivariate model linking metabolites with the glycan fingerprint. The screening experiments in 96-DWP produced a large glycosylation distribution diversity2,3. Subsequent D-optimal quadratic design in shake tubes confirmed the outcome of the selection process and provided a solid basis for sequential process development at a larger scale. The glycosylation profile with respect to the glycosylation specifications was greatly improved in shake tube experiments: 75% of the conditions were equally close or closer to the specifications than the best 25% in 96-deepwell plates. Further enhancement enabled us to generate extreme glycosylation variants, including high mannose, afucosylated, galactosylated as well as sialic acid species of both a mAb and an antibody fusion molecule with three N-glycosylation sites. The glycan variants induced significant responses in the respective in vitro biological activity assays. Moreover, metabolites correlating with time-dependent glycan profiling data were pinpointed and the glycan distribution of an external data set predicted. Our data highlight the great potential of cell culture medium optimization to modulate product quality and show the feasibility of the generation of a wide range of glycan variants suitable for biological activity testing. [1] Brühlmann D, Jordan M, Hemberger J, Sauer M, Stettler M and Broly H, Tailoring recombinant protein quality by rational media design, Biotechnology Progress 2015, 31:615–629. [2] Brühlmann D, Muhr A, Parker R, Vuillemin T, Bucsella B, Torre S, La Neve F, Lembo A, Haas T, Sauer M, Souquet J, Broly H, Hemberger J, Jordan M, Cell culture media supplemented with raffinose reproducibly enhances high mannose glycan formation, Journal of Biotechnology 2017, 252:32-42. [3] Brühlmann D, Sokolov M, Butté A, Sauer M, Hemberger J, Souquet J, Broly H, Jordan M, Parallel experimental design and multivariate analysis provides efficient screening of cell culture media supplements to improve Biosimilar product quality, Biotechnology and Bioengineering 2017, 114(7):1363-1631

Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism

Increased risk for autism spectrum disorders (ASD) is attributed to hundreds of genetic loci. The convergence of ASD variants have been investigated using various approaches, including protein interactions extracted from the published literature. However, these datasets are frequently incomplete, carry biases and are limited to interactions of a single splicing isoform, which may not be expressed in the disease-relevant tissue. Here we introduce a new interactome mapping approach by experimentally identifying interactions between brain-expressed alternatively spliced variants of ASD risk factors. The Autism Spliceform Interaction Network reveals that almost half of the detected interactions and about 30% of the newly identified interacting partners represent contribution from splicing variants, emphasizing the importance of isoform networks. Isoform interactions greatly contribute to establishing direct physical connections between proteins from the de novo autism CNVs. Our findings demonstrate the critical role of spliceform networks for translating genetic knowledge into a better understanding of human diseases

Hidden intra-mandibular carcinoma cuniculatum appearing in a patient with metastatic prostate cancer: a case report

Abstract Background Whereas the incidence of cancers increases, overall survival of cancerous patients improves. Preventing the onset of second primary cancer is a new public health challenge and requires a special attention from organ specialists. We report a rare case of carcinoma cuniculatum in a context of metastatic prostate cancer. No case was previously described. Diagnosis delay of carcinoma cuniculatum is frequent and particularly in case of endophytic intra-osseous topography. The aim of this case report is to remind that persistent pain requires medical evaluation to rule out any possibility of second primary cancer. Case presentation A 78-year-old patient followed for a metastatic prostate cancer had been describing neuralgic dental pain in the lower posterior left quadrant for several months. Healing delay of tooth #37 (second left mandibular molar) extraction socket in the painful region led to an intra-alveolar incisional biopsy, which showed a tumor widely invading the mandibular body. Radiologic, histopathologic and clinical elements finally concluded to an intra-osseous carcinoma cuniculatum. Duration of total treatment (oral biopsy to hemimandibulectomy) and follow up were about five months and one year respectively. Patient died before reconstruction. Conclusion This case recalls that any persistent tooth pain affecting cancer patients requires a thorough review to exclude any secondary primary cancers or any metastasis of the oral cavity and more specifically in jawbones

Lactate metabolism shift in CHO cell culture: the role of mitochondrial oxidative activity

Lactate production is monitored in industrial processes as a crucial metabolite for cultured mammalian cells. Typically lactate is strongly produced during the exponential growth phase, while its net consumption is frequently observed when cells enter into the stationary phase. Such a metabolic shift is desirable because it seems to favor optimal process performance. However, this shift is neither generic nor can it be easily controlled, as the mechanisms modulating lactate production/consumption in cell culture are still under investigation. In this study different lactate profiles were observed in a chemically defined medium for the parental CHO-S cells and a non-recombinant subclone. The initial lactate production phase, which is typical for fast growing cells, was similar for both cell lines. After glutamine depletion the situation changed: the parental cell line promptly switched to net lactate consumption, whereas the subclone continued to produce lactate until glucose was depleted as well. We speculated that the extra lactate production would be ascribed to a different mitochondrial oxidative capacity in the subclone. Therefore, the mitochondrial membrane potential and oxygen consumption were measured for both cell lines. Indeed, a correlation between high lactate production and a reduced oxidative metabolism was found. Interestingly, this particular metabolic phenotype was also strongly influenced by the medium composition: both cell lines underwent a switch to lactate consumption when cultivated in a second medium, while a third one promoted continuous lactate production even for the parental CHO cells. Again, the correlation between lactate profile and oxidative metabolism was confirmed, pointing to a central role of mitochondria on lactate metabolism

High expression of the aspartate–glutamate carrier Aralar1 favors lactate consumption in CHO cell culture

Process performance of mammalian cell cultures can be strongly impacted by high lactate accumulation, which can be a clone or media-dependent characteristic. In this study, the expression of specific genes was measured in several Chinese hamster ovary cell lines under culture conditions leading to different lactate profiles. A reduced expression of two genes was observed under conditions of high lactate accumulation: AGC1/Aralar1, a member of the malate–aspartate shuttle (MAS) and Timm8a1. Overexpression of either of these two genes in the lactate-producing cell line diminished lactate accumulation. This was achieved by promoting a metabolic switch to lactate consumption after day 6, while maintaining a glycolytic rate similar to the parental cells. On the other hand, the biochemical inhibition of MAS activity increased lactate accumulation. All together, these results indicate MAS as a key factor to promote a shift to lactate consumption in cultivated Chinese hamster ovary cells

Predictive Clinical and Biological Criteria for Gene Panel Positivity in Suspected Inherited Autoinflammatory Diseases: Insights from a Case–Control Study

In order to assess the clinical and biological criteria that predict gene panel positivity in patients with a suspected inherited genetic autoinflammatory disease, we conducted a case–control study. These new selection criteria could replace the national multidisciplinary staff approval before performing genetic testing that has been required since 2019. The study involved 119 positive gene panels matched by panel sizes to 119 randomly selected negative gene panels. The patients were referred to our laboratory for genetic testing between June 2012, and March 2023. The clinical and biological criteria were extracted from a prospectively filled database. We focused our evaluation on accuracy and the positive predictive value. Neonatal symptom onset and deafness had the highest accuracies among all criteria associated with the positivity panel, with 92.9% (88.6; 96.0) and 92.6% (88.5; 95.6), respectively. However, it is important to note that the associated Positive Predictive Values (PPVs) cannot exceed 50%. Despite finding a statistical association between clinical and biological criteria and panel positivity, the predictive values of these criteria were not sufficient to recommend Next-Generation Sequencing (NGS) gene panel testing without the national multidisciplinary staff evaluation

Applicability and Efficiency of NGS in Routine Diagnosis: In-Depth Performance Analysis of a Complete Workflow for CFTR Mutation Analysis.

BACKGROUND:Actually, about 2000 sequence variations have been documented in the CFTR gene requiring extensive and multi-step genetic testing in the diagnosis of cystic fibrosis and CFTR-related disorders. We present a two phases study, with validation and performance monitoring, of a single experiment methodology based on multiplex PCR and high throughput sequencing that allows detection of all variants, including large rearrangements, affecting the coding regions plus three deep intronic loci. METHODS:A total of 340 samples, including 257 patients and 83 previously characterized control samples, were sequenced in 17 MiSeq runs and analyzed with two bioinformatic pipelines in routine diagnostic conditions. We obtained 100% coverage for all the target regions in every tested sample. RESULTS:We correctly identified all the 87 known variants in the control samples and successfully confirmed the 62 variants identified among the patients without observing false positive results. Large rearrangements were identified in 18/18 control samples. Only 17 patient samples showed false positive signals (6.6%), 12 of which showed a borderline result for a single amplicon. We also demonstrated the ability of the assay to detect allele specific dropout of amplicons when a sequence variation occurs at a primer binding site thus limiting the risk for false negative results. CONCLUSIONS:We described here the first NGS workflow for CFTR routine analysis that demonstrated equivalent diagnostic performances compared to Sanger sequencing and multiplex ligation-dependent probe amplification. This study illustrates the advantages of NGS in term of scalability, workload reduction and cost-effectiveness in combination with an improvement of the overall data quality due to the simultaneous detection of SNVs and large rearrangements

Rapid genetic and phenotypic changes in Pseudomonas aeruginosa clinical strains during ventilator-associated pneumonia

Abstract Treatment with antibiotics leads to the selection of isolates with increased resistance. We investigated if evolution towards resistance was associated with virulence changes, in the context of P. aeruginosa ventilator-associated pneumonia (VAP). Four patients were selected because they had multiple VAP episodes during short periods (12 days to 5 weeks), with emergence of resistance. We performed whole-genome sequencing of 12 P. aeruginosa from bronchoalveolar lavages or blood culture (3 isolates per patient). Production of quorum sensing-dependent virulence factors, serum resistance, cytotoxicity against A549 cells, biofilm production, and twitching motility were studied. Each patient was infected with a unique strain. For all patients, resistance development was explained by genetic events in ampD, mexR or oprD. Additional variations were detected in virulence- and/or fitness-associated genes (algB, gacA, groEL, lasR, mpl, pilE, pilM, rhlR) depending on the strain. We noticed a convergence towards quorum sensing deficiency, correlated with a decrease of pyocyanin and protease production, survival in serum, twitching motility and cytotoxicity. In one patient, changes in pilM and pilE were related to enhanced twitching. We show that the emergence of resistance in P. aeruginosa is associated with virulence modification, even in acute infections. The consequences of this short-term pathoadaptation need to be explored