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Singh R, Fatima E, Thakur L, Singh S, Ratan C, Kumar N. Advancements in CHO metabolomics: techniques, current state and evolving methodologies. Front Bioeng Biotechnol 2024; 12:1347138. [PMID: 38600943 PMCID: PMC11004234 DOI: 10.3389/fbioe.2024.1347138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/28/2024] [Indexed: 04/12/2024] Open
Abstract
Background: Investigating the metabolic behaviour of different cellular phenotypes, i.e., good/bad grower and/or producer, in production culture is important to identify the key metabolite(s)/pathway(s) that regulate cell growth and/or recombinant protein production to improve the overall yield. Currently, LC-MS, GC-MS and NMR are the most used and advanced technologies for investigating the metabolome. Although contributed significantly in the domain, each technique has its own biasness towards specific metabolites or class of metabolites due to various reasons including variability in the concept of working, sample preparation, metabolite-extraction methods, metabolite identification tools, and databases. As a result, the application of appropriate analytical technique(s) is very critical. Purpose and scope: This review provides a state-of-the-art technological insights and overview of metabolic mechanisms involved in regulation of cell growth and/or recombinant protein production for improving yield from CHO cultures. Summary and conclusion: In this review, the advancements in CHO metabolomics over the last 10 years are traced based on a bibliometric analysis of previous publications and discussed. With the technical advancement in the domain of LC-MS, GC-MS and NMR, metabolites of glycolytic and nucleotide biosynthesis pathway (glucose, fructose, pyruvate and phenylalanine, threonine, tryptophan, arginine, valine, asparagine, and serine, etc.) were observed to be upregulated in exponential-phase thereby potentially associated with cell growth regulation, whereas metabolites/intermediates of TCA, oxidative phosphorylation (aspartate, glutamate, succinate, malate, fumarate and citrate), intracellular NAD+/NADH ratio, and glutathione metabolic pathways were observed to be upregulated in stationary-phase and hence potentially associated with increased cell-specific productivity in CHO bioprocess. Moreover, each of technique has its own bias towards metabolite identification, indicating their complementarity, along with a number of critical gaps in the CHO metabolomics pipeline and hence first time discussed here to identify their potential remedies. This knowledge may help in future study designs to improve the metabolomic coverage facilitating identification of the metabolites/pathways which might get missed otherwise and explore the full potential of metabolomics for improving the CHO bioprocess performances.
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Affiliation(s)
- Rita Singh
- Translational Health Science and Technology Institute, Faridabad, India
- Jawaharlal Nehru University, New Delhi, India
| | - Eram Fatima
- Translational Health Science and Technology Institute, Faridabad, India
- Jawaharlal Nehru University, New Delhi, India
| | - Lovnish Thakur
- Translational Health Science and Technology Institute, Faridabad, India
- Jawaharlal Nehru University, New Delhi, India
| | - Sevaram Singh
- Translational Health Science and Technology Institute, Faridabad, India
- Jawaharlal Nehru University, New Delhi, India
| | - Chandra Ratan
- Translational Health Science and Technology Institute, Faridabad, India
- Jawaharlal Nehru University, New Delhi, India
| | - Niraj Kumar
- Translational Health Science and Technology Institute, Faridabad, India
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Targeting DNA repair pathways with B02 and Nocodazole small molecules to improve CRIS-PITCh mediated cassette integration in CHO-K1 cells. Sci Rep 2023; 13:3116. [PMID: 36813818 PMCID: PMC9947112 DOI: 10.1038/s41598-023-29863-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 02/11/2023] [Indexed: 02/24/2023] Open
Abstract
CRISPR-mediated integration could be used to develop the recombinant CHO (rCHO) cells by knock-in into the hotspot loci. However, low HDR efficiency besides the complex donor design is the main barrier for achieving so. The recently introduced MMEJ-mediated CRISPR system (CRIS-PITCh) uses a donor with short homology arms, being linearized in the cells via two sgRNAs. In this paper, a new approach to improve CRIS-PITCh knock-in efficiency by employing small molecules was investigated. Two small molecules, B02, a Rad51 inhibitor, and Nocodazole, a G2/M cell cycle synchronizer, were used to target the S100A hotspot site using a bxb1 recombinase comprised landing pad in CHO-K1 cells. Following transfection, the CHO-K1 cells were treated with the optimum concentration of one or combination of small molecules, being determined by the cell viability or flow cytometric cell cycle assay. Stable cell lines were generated and the single-cell clones were achieved by the clonal selection procedure. The finding showed that B02 improved the PITCh-mediated integration approximately twofold. In the case of Nocodazole treatment, the improvement was even more significant, up to 2.4-fold. However, the combinatorial effects of both molecules were not substantial. Moreover, according to the copy number and out-out PCR analyses, 5 and 6 of 20 clonal cells exhibited mono-allelic integration in Nocodazole and B02 groups, respectively. The results of the present study as the first attempt to enhance the CHO platform generation by exploiting two small molecules in the CRIS-PITCh system could be used in future researches to establish rCHO clones.
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Ding SL, Liu X, Zhao XY, Wang KT, Xiong W, Gao ZL, Sun CY, Jia MX, Li C, Gu Q, Zhang MZ. Microcarriers in application for cartilage tissue engineering: Recent progress and challenges. Bioact Mater 2022; 17:81-108. [PMID: 35386447 PMCID: PMC8958326 DOI: 10.1016/j.bioactmat.2022.01.033] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 12/11/2022] Open
Abstract
Successful regeneration of cartilage tissue at a clinical scale has been a tremendous challenge in the past decades. Microcarriers (MCs), usually used for cell and drug delivery, have been studied broadly across a wide range of medical fields, especially the cartilage tissue engineering (TE). Notably, microcarrier systems provide an attractive method for regulating cell phenotype and microtissue maturations, they also serve as powerful injectable carriers and are combined with new technologies for cartilage regeneration. In this review, we introduced the typical methods to fabricate various types of microcarriers and discussed the appropriate materials for microcarriers. Furthermore, we highlighted recent progress of applications and general design principle for microcarriers. Finally, we summarized the current challenges and promising prospects of microcarrier-based systems for medical applications. Overall, this review provides comprehensive and systematic guidelines for the rational design and applications of microcarriers in cartilage TE.
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Affiliation(s)
- Sheng-Long Ding
- Center of Foot and Ankle Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China
| | - Xin Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xi-Yuan Zhao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Ke-Tao Wang
- Center of Foot and Ankle Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China
| | - Wei Xiong
- Center of Foot and Ankle Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China
| | - Zi-Li Gao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Cheng-Yi Sun
- Center of Foot and Ankle Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China
| | - Min-Xuan Jia
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Cheng Li
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Engineering Medicine, Beihang University, Beijing, 100083, China
| | - Qi Gu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regeneration, University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Ming-Zhu Zhang
- Center of Foot and Ankle Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China
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Lavado-García J, Pérez-Rubio P, Cervera L, Gòdia F. The cell density effect in animal cell-based bioprocessing: Questions, insights and perspectives. Biotechnol Adv 2022; 60:108017. [PMID: 35809763 DOI: 10.1016/j.biotechadv.2022.108017] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/31/2022] [Accepted: 07/01/2022] [Indexed: 11/28/2022]
Abstract
One of the main challenges in the development of bioprocesses based on cell transient expression is the commonly reported reduction of cell specific productivity at increasing cell densities. This is generally known as the cell density effect (CDE). Many efforts have been devoted to understanding the cell metabolic implications to this phenomenon in an attempt to design operational strategies to overcome it. A comprehensive analysis of the main studies regarding the CDE is provided in this work to better define the elements comprising its cause and impact. Then, examples of methodologies and approaches employed to achieve successful transient expression at high cell densities (HCD) are thoroughly reviewed. A critical assessment of the limitations of the reported studies in the understanding of the CDE is presented, covering the leading hypothesis of the molecular implications. The overall analysis of previous work on CDE may offer useful insights for further research into manufacturing of biologics.
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Affiliation(s)
- Jesús Lavado-García
- Grup d'Enginyeria Cel·lular i Bioprocessos, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Campus de Bellaterra, Cerdanyola del Vallès, 08193 Barcelona, Spain; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark.
| | - Pol Pérez-Rubio
- Grup d'Enginyeria Cel·lular i Bioprocessos, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Campus de Bellaterra, Cerdanyola del Vallès, 08193 Barcelona, Spain
| | - Laura Cervera
- Grup d'Enginyeria Cel·lular i Bioprocessos, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Campus de Bellaterra, Cerdanyola del Vallès, 08193 Barcelona, Spain
| | - Francesc Gòdia
- Grup d'Enginyeria Cel·lular i Bioprocessos, Escola d'Enginyeria, Universitat Autònoma de Barcelona, Campus de Bellaterra, Cerdanyola del Vallès, 08193 Barcelona, Spain
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Shao X, Wang C, Wang C, Han L, Han Y, Nižetić D, Zhang Y, Han L. Mechanical Stress Induces a Transient Suppression of Cytokine Secretion in Astrocytes Assessed at the Single-Cell Level with a High-Throughput Microfluidic Chip. Adv Healthc Mater 2021; 10:e2100698. [PMID: 34549544 DOI: 10.1002/adhm.202100698] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 08/27/2021] [Indexed: 11/11/2022]
Abstract
Brain cells are constantly subjected to mechanical signals. Astrocytes are the most abundant glial cells of the central nervous system (CNS), which display immunoreactivity and have been suggested as an emerging disease focus in the recent years. However, how mechanical signals regulate astrocyte immunoreactivity, and the cytokine release in particular, remains to be fully characterized. Here, human neural stem cells are used to induce astrocytes, from which the release of 15 types of cytokines are screened, and nine of them are detected using a protein microfluidic chip. When a gentle compressive force is applied, altered cell morphology and reinforced cytoskeleton are observed. The force induces a transient suppression of cytokine secretions including IL-6, MCP-1, and IL-8 in the early astrocytes. Further, using a multiplexed single-cell culture and protein detection microfluidic chip, the mechanical effects at a single-cell level are analyzed, which validates a concerted downregulation by force on IL-6 and MCP-1 secretions in the cells releasing both factors. This work demonstrates an original attempt of employing the protein detection microfluidic chips in the assessment of mechanical regulation on the brain cells at a single-cell resolution, offering novel approach and unique insights for the understanding of the CNS immune regulation.
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Affiliation(s)
- Xiaowei Shao
- Institute of Marine Science and Technology Shandong University Qingdao 266237 China
- Suzhou Research Institute Shandong University Suzhou 215123 China
- Lee Kong Chian School of Medicine Nanyang Technological University Singapore 308232
| | - Chunhua Wang
- Institute of Marine Science and Technology Shandong University Qingdao 266237 China
| | - Chao Wang
- Institute of Marine Science and Technology Shandong University Qingdao 266237 China
| | - Lei Han
- Institute of Marine Science and Technology Shandong University Qingdao 266237 China
| | - Yunrui Han
- Institute of Marine Science and Technology Shandong University Qingdao 266237 China
| | - Dean Nižetić
- Lee Kong Chian School of Medicine Nanyang Technological University Singapore 308232
- The Blizard Institute Barts and The London School of Medicine Queen Mary University of London London E1 2AT UK
| | - Yu Zhang
- Institute of Marine Science and Technology Shandong University Qingdao 266237 China
| | - Lin Han
- Institute of Marine Science and Technology Shandong University Qingdao 266237 China
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Purkayastha P, Jaiswal MK, Lele TP. Molecular cancer cell responses to solid compressive stress and interstitial fluid pressure. Cytoskeleton (Hoboken) 2021; 78:312-322. [PMID: 34291887 DOI: 10.1002/cm.21680] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 01/19/2023]
Abstract
Alterations to the mechanical properties of the microenvironment are a hallmark of cancer. Elevated mechanical stresses exist in many solid tumors and elicit responses from cancer cells. Uncontrolled growth in confined environments gives rise to elevated solid compressive stress on cancer cells. Recruitment of leaky blood vessels and an absence of functioning lymphatic vessels causes a rise in the interstitial fluid pressure. Here we review the role of the cancer cell cytoskeleton and the nucleus in mediating both the initial and adaptive cancer cell response to these two types of mechanical stresses. We review how these mechanical stresses alter cancer cell functions such as proliferation, apoptosis, and migration.
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Affiliation(s)
- Purboja Purkayastha
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas, USA
| | - Manish K Jaiswal
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas, USA
| | - Tanmay P Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas, USA.,Department of Biomedical Engineering, Texas A&M University, College Station, Texas, USA.,Department of Translational Medical Sciences, Texas A&M University, Houston, Texas, USA
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