Review
Biotechnology & Applied Microbiology
Tobias Jerabek, Christoph Keysberg, Kerstin Otte
Summary: This review highlights recent advances in cellular sub-transcriptomes, sub-proteomes, and secretome analyses for cell line development.
BIOTECHNOLOGY ADVANCES
(2022)
Review
Biotechnology & Applied Microbiology
Tobias Jerabek, Christoph Keysberg, Kerstin Otte
Summary: This review provides an overview of recent advances in the characterization of CHO cells (Chinese hamster ovary cells) using sub-omics approaches and their application in cell line development.
BIOTECHNOLOGY ADVANCES
(2022)
Review
Biotechnology & Applied Microbiology
Nicolas Marx, Peter Eisenhut, Marcus Weinguny, Gerald Klanert, Nicole Borth
Summary: Recent advances have greatly improved our understanding of Chinese hamster ovary (CHO) cells as hosts for producing biopharmaceuticals. Despite progress in characterizing CHO cells on different omics levels, our understanding of its epigenetic regulation is still incomplete. This review provides an overview of epigenetic regulation in CHO cells and discusses its significance in shaping cell phenotype. The review also presents current state-of-the-art technologies for manipulating epigenetic networks and controlling gene expression.
BIOTECHNOLOGY ADVANCES
(2022)
Review
Biotechnology & Applied Microbiology
Hui-Ning Liu, Wei-Hua Dong, Yan Lin, Zhao-Hui Zhang, Tian-Yun Wang
Summary: This review discusses the effect and mechanism of miRNAs on the expression level and quality of recombinant proteins in CHO cells, indicating that miRNAs can enhance protein expression in CHO cells while also affecting the quality of RTPs.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Biochemical Research Methods
Lauren T. Cordova, Hussain Dahodwala, Rebecca Cooley, Kelvin H. Lee
Summary: In this study, researchers evaluated the expression of five DNA repair genes in over 40 CHO cell lines and found a correlation between two genes and cell line stability. Additionally, they found a negative correlation between the expression levels of DNA repair genes and cell age.
BIOTECHNOLOGY JOURNAL
(2023)
Review
Biotechnology & Applied Microbiology
Michelle Combe, Stanislav Sokolenko
Summary: This review documented and quantitatively estimated the impact of media optimization studies on cell culture performance in recombinant protein production using Chinese hamster ovary cells over the last twenty years. While trace elements were found to have a positive impact on cell density and nucleotides showed potential for increasing titer, the impact of specific additives was found to be more variable than perceived. Additives only accounted for a small percentage of variation in cell density and titer, emphasizing the need for studies to consider multiple factors to ensure generalized and further developed observations.
BIOTECHNOLOGY ADVANCES
(2021)
Article
Materials Science, Multidisciplinary
Zhenzhen Chen, Liang Shen, Xiong Zhao, Hongqiang Chen, Yaxuan Xiao, Yonghai Zhang, Xiaoping Yang, Jinhua Zhang, Jinjia Wei, Nanjing Hao
Summary: Microfluidics, especially acoustofluidics, offers new opportunities in chemical and biomedical engineering by manipulating fluids at the micrometer or submicrometer scale. This review discusses the utility of acoustofluidic technology, summarizes different types of acoustic micromixers, highlights their applications in various fields, and identifies the practical challenges that need to be addressed. Overall, this review provides valuable insights for both academic research and industrial applications.
APPLIED MATERIALS TODAY
(2022)
Article
Biochemical Research Methods
Leran Mao, James W. Schneider, Anne S. Robinson
Summary: This study observes that the addition of rosmarinic acid (RA) can increase antibody production and promote cell health through mTOR pathway activation. However, RA also induces cellular stress and DNA damage.
BIOTECHNOLOGY JOURNAL
(2023)
Article
Biotechnology & Applied Microbiology
Nadiya Romanova, Louise Schelletter, Raimund Hoffrogge, Thomas Noll
Summary: Chinese hamster ovary (CHO) cells are commonly used for therapeutic protein production. Exposure to high osmolality can affect cell physiology and protein expression. This study compared the proteome of CHO cells exposed to hyperosmolality with control cells, revealing differentially expressed proteins involved in mitochondrial activation, oxidative stress response, and cell cycle progression. The study also found that protein regulation can affect cell membrane stiffness and permeability.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Review
Biotechnology & Applied Microbiology
Zhengshan Luo, Yifan Yan, Shanshan Du, Yifan Zhu, Fei Pan, Rui Wang, Zheng Xu, Xiaoqi Xu, Sha Li, Hong Xu
Summary: Bacillus amyloliquefaciens, a Gram-positive bacterium, has unique characteristics that make it suitable for industrial applications. Through systems biology and synthetic biology techniques, its productivity characteristics have been optimized. Researchers discuss the potential advantages and recent advancements of B. amyloliquefaciens as a platform for metabolic engineering and industrial applications.
CRITICAL REVIEWS IN BIOTECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Florian Klingler, Lukas Naumann, Patrick Schlossbauer, Leonard Dreyer, Madina Burkhart, Rene Handrick, Hans -Dieter Junker, Friedemann Hesse, Christian Neusuess, Kerstin Otte
Summary: N-linked glycosylation is an important post-translational modification of biopharmaceuticals, and miRNAs have the potential to be used as tools for engineering glycosylation pathways. Novel miRNAs were found to alter N-linked glycosylation patterns on mAbs expressed in CHO cells. A high throughput screening of a complete miRNA mimic library revealed miRNA sequences affecting various glycan features, and a synthetic biology approach enhanced the potential of miRNAs as tools for engineering glycosylation pathways.
METABOLIC ENGINEERING
(2023)
Article
Chemistry, Physical
Sergi Roda, Laura Fernandez-Lopez, Ruben Canadas, Gerard Santiago, Manuel Ferrer, Victor Guallar
Summary: Through studying enzymes with narrow substrate spectra, it was demonstrated that active site parameters can be manipulated to alter substrate specificity and design new enzyme variants with broader substrate promiscuity.
Article
Biotechnology & Applied Microbiology
Swetha Kumar, Venkata Gayatri Dhara, Linda D. Orzolek, Haiping Hao, Abbie J. More, Eduardo Catchon Lau, Michael J. Betenbaugh
Summary: The study found that plant-based hydrolysates, such as cottonseed hydrolysate, can positively impact CHO cell growth and productivity by upregulating transcription and translation, and affecting pathways related to the cell cycle and metabolism.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
Menglin Shang, Taehong Kwon, Jean-Francois P. Hamel, Chwee Teck Lim, Bee Luan Khoo, Jongyoon Han
Summary: The study found that applying hydrostatic pressure in CHO cell culture can increase cell concentration and antibody production, but has no significant effect on non-disulphide-linked antibody aggregates and cell clumping formation.
SCIENTIFIC REPORTS
(2021)
Review
Biotechnology & Applied Microbiology
Tingting Xu, Jihong Zhang, Tianyun Wang, Xiaoyin Wang
Summary: This review focuses on the aggregation of recombinant therapeutic antibodies (RTAs), discussing factors causing aggregation during RTA production and strategies for overcoming RTA aggregation.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Review
Biochemical Research Methods
Esteban Marcellin, Largus T. Angenent, Lars K. Nielsen, Bastian Molitor
Summary: This review explores the potential of gas fermentation and synthetic biology to transform food production and achieve sustainability.
CURRENT OPINION IN BIOTECHNOLOGY
(2022)
Article
Medicine, Research & Experimental
Michael A. MacDonald, Matthias Nobel, Veronica S. Martinez, Kym Baker, Evan Shave, Peter P. Gray, Stephen Mahler, Trent Munro, Lars K. Nielsen, Esteban Marcellin
Summary: The development of death-resistant cell lines using CRISPR technology has proven to be beneficial for monoclonal antibody production. These cell lines showed advantages in fed-batch and perfusion bioreactors, with higher cell densities or longer culture durations in fed-batch, and the ability to culture without bleed in perfusion. This study highlights the potential of rationally engineered cell lines for improving mAb manufacturing processes.
Article
Biochemical Research Methods
Veronica S. Martinez, Pedro A. Saa, Jason Jooste, Kanupriya Tiwari, Lake-Ee Quek, Lars K. Nielsen
Summary: The topology of metabolic networks is modular, with weak connections between modules. This study defines metabolic modules using network topology and validates them using genome-scale metabolic models. The study also explores the role of reversible reactions in metabolic flexibility.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Microbiology
Lorena Azevedo de Lima, Kristina Reinmets, Lars Keld Nielsen, Esteban Marcellin, Audrey Harris, Michael Kopke, Kaspar Valgepea
Summary: RNA sequencing (RNA-seq) is a widely used technique for transcriptome analysis, but the choice of library preparation kits can significantly impact the results. Different commercial products show significant differences in rRNA removal, strand specificity, and transcript abundance distribution. Selecting appropriate sample processing workflows and products is crucial for RNA-seq studies.
MICROBIOLOGY SPECTRUM
(2022)
Article
Engineering, Chemical
Sarang S. Nath, Lars K. Nielsen, John Villadsen
Summary: A novel methodology is developed to convert chemical reactions into electrical circuits, allowing for the study of complex cyclic bionetworks. The approach is demonstrated using a pyramidal reaction network catalyzed by an important enzyme in cancer therapy. The analysis identifies the key mechanisms contributing to the overall reaction rate.
CHEMICAL ENGINEERING SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Tae Kwang Ha, Andreu Odena, Karen Julie la Cour Karottki, Che Lin Kim, Hooman Hefzi, Gyun Min Lee, Helene Faustrup Kildegaard, Lars K. Nielsen, Lise Marie Grav, Nathan E. Lewis
Summary: The use of a dual selection method can greatly improve the efficiency of Chinese hamster ovary (CHO) cell lines in producing biotherapeutic proteins, although it may lead to reduced growth rate and viability. By knocking out the Gs/Aspg genes, a novel dual selectable system was successfully constructed, which showed significantly improved productivity and titer compared to the standard Gs system under the same selection conditions. With further optimization of culture medium and selection conditions, this approach is expected to be an effective addition to industrial workflows for producing recombinant biotherapeutics.
BIOTECHNOLOGY AND BIOENGINEERING
(2023)
Article
Biotechnology & Applied Microbiology
Maja Papez, Victor Jimenez Lancho, Peter Eisenhut, Krishna Motheramgari, Nicole Borth
Summary: This study investigates the stress response of mammalian cells during recombinant protein production and identifies the genetic factors involved. By simulating nutrient stress, the cells induce the ISR signaling pathway to cope with amino acid limitation, leading to inhibition of lipid synthesis and the mTOR pathway. The study also demonstrates the effectiveness of SLAM-seq in detecting short-lived transcription factors and suggests its potential use in dynamic transcriptome profiling in CHO cells.
BIOTECHNOLOGY AND BIOENGINEERING
(2023)
Article
Biochemistry & Molecular Biology
Hanne H. Henriksen, Igor Marin de Mas, Lars K. Nielsen, Joseph Krocker, Jakob Stensballe, Sigurour T. Karvelsson, Niels H. Secher, Ottar Rolfsson, Charles E. Wade, Par I. Johansson
Summary: In trauma patients, shock-induced endotheliopathy (SHINE) is associated with poor prognosis. This study identified four metabolic phenotypes in trauma patients and analyzed their intracellular metabolic profiles using a computational network analysis. One of the phenotypes, characterized by an inability to maintain redox balance, was associated with increased mortality. This research highlights the importance of understanding metabolic patterns in trauma patients for prognosis and potential therapeutic interventions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Giulia Borsi, Krishna Motheramgari, Heena Dhiman, Martina Baumann, Elly Sinkala, Max Sauerland, Julian Riba, Nicole Borth
Summary: This study investigated the variability and diversity of individual cell transcriptomes in CHO and HEK293 cells under different culture conditions using full-length coverage single-cell RNA sequencing. The results showed a batch effect in CHO cells and highlighted the impact of the cell cycle on transcriptome variation.
JOURNAL OF BIOTECHNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Klaus Leitner, Krishna Motheramgari, Nicole Borth, Nicolas Marx
Summary: In this study, a fast and robust nanopore Cas9-targeted sequencing (nCats) pipeline was developed to simultaneously obtain information on integration sites, the composition of the integrated sequence, and its DNA methylation status in CHO cells from the same sequencing run. The data generated by nCats provides sensitive, detailed, and correct information on transgene integration sites and expression vector structure, which can only be partially obtained by traditional Targeted Locus Amplification-seq data. Moreover, nCats allows for the analysis of DNA methylation status from the same raw data without prior DNA amplification.
BIOTECHNOLOGY AND BIOENGINEERING
(2023)
Article
Biochemistry & Molecular Biology
Carmen Bedia, Nuria Dalmau, Lars K. Nielsen, Roma Tauler, Igor Marin de Mas
Summary: Although the dose-effect relationship between Endocrine disruptors (EDs) and tumor malignancy is supported by numerous studies, the impact of chronic exposure to non-lethal concentrations of EDs in cancer remains unknown. This study investigates the molecular processes underlying malignancy in prostate cancer using two complementary computational approaches. Experimental validation confirms predictions, revealing a disruption in metabolic and regulatory pathways.
Article
Biotechnology & Applied Microbiology
Igor Marin de Mas, Helena Herand, Jorge Carrasco, Lars K. Nielsen, Par I. Johansson
Summary: Genome-scale metabolic models (GEMs) are valuable tools for understanding human metabolism and have applications in studying diseases and designing metabolic engineering. This paper presents a novel algorithm-aided protocol that allows for the continuous updating of highly curated GEMs, overcoming the limitations of existing methods.
BIOENGINEERING-BASEL
(2023)
Article
Biotechnology & Applied Microbiology
Neza Novak, Martina Baumann, Amy Friss, Victor Cairns, Christine DeMaria, Nicole Borth
Summary: Long non-coding RNAs (lncRNAs) were found to be correlated with productivity in mAb producer CHO clones. Overexpression or deletion of candidate lncRNAs showed that their expression levels were closely related to productivity. Deletion of one lncRNA region affected cell growth and productivity. These findings demonstrate the feasibility and usefulness of engineering lncRNA expression in production cell lines.
METABOLIC ENGINEERING
(2023)
Article
Biotechnology & Applied Microbiology
Marina de Leeuw, Marta R. A. Matos, Lars Keld Nielsen
Summary: Kinetic models are important for understanding metabolic systems. This paper presents a detailed kinetic model for the central carbon metabolism of Escherichia coli, which has been validated and can be used for studying cellular metabolism and metabolic pathway design.
METABOLIC ENGINEERING
(2023)
Article
Engineering, Environmental
James K. Heffernan, Chun-Yu Lai, R. Axayacatl Gonzalez-Garcia, Lars Keld Nielsen, Jianhua Guo, Esteban Marcellin
Summary: Biogas production from anaerobic digestion is important for energy generation, nutrient recovery, and waste resource valorisation. Removing or altering carbon dioxide content facilitates biogas use as biomethane and can contribute to transitioning into a low carbon and circular economy. Gas fermentation utilising acetogens and renewable H2 offers an alternative for biogas upgrading, enriching the biogas and transforming CO2 into valuable fuels and chemicals in a one-step process.
CHEMICAL ENGINEERING JOURNAL
(2023)
