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Novak N, Baumann M, Friss A, Cairns V, DeMaria C, Borth N. LncRNA analysis of mAb producing CHO clones reveals marker and engineering potential. Metab Eng 2023; 78:26-40. [PMID: 37196898 DOI: 10.1016/j.ymben.2023.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/09/2023] [Accepted: 05/14/2023] [Indexed: 05/19/2023]
Abstract
Long non-coding RNAs (lncRNAs) are a potential new cell line engineering tool for improvement of yield and stability of CHO cells. In this study, we performed RNA sequencing of mAb producer CHO clones to study the lncRNA and protein coding transcriptome in relation to productivity. First, a robust linear model was used to identify genes correlating to productivity. To unravel specific patterns in expression of these genes, we employed weighted gene coexpression analysis (WGCNA) to find coexpressed modules, looking both for lncRNAs and coding genes. There was little overlap in the genes associated with productivity between the two products studied, possibly due to the difference in absolute range of productivity between the two mAbs. Therefore, we focused on the product with higher productivity and stronger candidate lncRNAs. To evaluate their potential as engineering targets, these candidate lncRNAs were transiently overexpressed or deleted by stable CRISPR Cas9 knock out both in a high and a low productivity subclone. We found that the thus achieved expression level of the identified lncRNAs, as confirmed by qPCR, does correlate well to productivity, so that they represent good markers that may be used for early clone selection. Additionally, we found that the deletion of one tested lncRNA region decreased viable cell density (VCD), prolonged culture time and increased cell size, final titer and specific productivity per cell. These results demonstrate the feasibility and usefulness of engineering lncRNA expression in production cell lines.
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Affiliation(s)
- Neža Novak
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria; ACIB, Austrian Centre of Industrial Biotechnology, Graz, Austria
| | - Martina Baumann
- ACIB, Austrian Centre of Industrial Biotechnology, Graz, Austria
| | - Amy Friss
- Sanofi Biopharmaceutics Development, Framingham, MA, USA
| | - Victor Cairns
- Sanofi Biopharmaceutics Development, Framingham, MA, USA
| | | | - Nicole Borth
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria; ACIB, Austrian Centre of Industrial Biotechnology, Graz, Austria.
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Genome sequence comparison between Chinese hamster ovary (CHO) DG44 cells and mouse using end sequences of CHO BAC clones based on BAC-FISH results. Cytotechnology 2018; 70:1399-1407. [PMID: 29987698 DOI: 10.1007/s10616-018-0233-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 06/16/2018] [Indexed: 11/26/2022] Open
Abstract
Chinese hamster ovary (CHO) cells have frequently been used in biotechnology as a mammalian host cell platform for expressing genes of interest. Previously, we constructed a detailed physical chromosomal map of the CHO DG44 cell line by fluorescence in situ hybridization (FISH) imaging using 303 bacterial artificial chromosome (BAC) clones as hybridization probes (BAC-FISH). BAC-FISH results revealed that the two longest chromosomes were completely paired. However, other chromosomes featured partial deletions or rearrangements. In this study, we determined the end sequences of 303 BAC clones (BAC end sequences), which were used for BAC-FISH probes. Among 606 BAC-end sequences (BESs) (forward and reverse ends), 558 could be determined. We performed a comparison between all determined BESs and mouse genome sequences using NCBI BLAST. Among these 558 BESs, 465 showed high homology to mouse chromosomal sequences. We analyzed the locations of these BACs in chromosomes of the CHO DG44 cell line using a physical chromosomal map. From the obtained results, we investigated the regional similarities among CHO chromosomes (A-T) and mouse chromosomes (1-19 and sex) about 217 BESs (46.7% of 465 high homologous BESs). Twenty-three specific narrow regions in 13 chromosomes of the CHO DG44 cell line showed high homology to mouse chromosomes, but most of other regions did not show significant correlations with the mouse genome. These results contribute to accurate alignments of chromosomes of Chinese hamster and its genome sequence, analysis of chromosomal instability in CHO cells, and the development of target locations for gene and/or genome editing techniques.
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Chen C, Le H, Follstad B, Goudar CT. A Comparative Transcriptomics Workflow for Analyzing Microarray Data From CHO Cell Cultures. Biotechnol J 2017; 13:e1700228. [PMID: 29215210 DOI: 10.1002/biot.201700228] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 11/16/2017] [Indexed: 01/15/2023]
Abstract
Microarray-based comparative transcriptomics analysis is a powerful tool to understand therapeutic protein producing mammalian cell lines at the gene expression level. However, an integrated analysis workflow specifically designed for end-to-end analysis of microarray data for CHO cells, the most prevalent host for commercial recombinant protein production, is lacking. To address this gap, an automated data analysis workflow in R that leverages public domain analysis modules is developed to analyze microarray based gene expression data. In addition to testing the global transcriptome differences of CHO cells at different conditions, the workflow identifies differentially expressed genes and pathways with intuitive visualizations as the outputs. The utility of this automated workflow is demonstrated by comparing the transcriptomic profiles of recombinant protein expressing CHO cells with and without a temperature shift. Statistically significant differential expression at the gene, pathway, and global transcriptome levels are identified and visualized. An automated workflow like the one developed in this study will enable rapid translation of CHO culture microarray data into biologically relevant information for mechanism-driven cell line optimization and bioprocess development.
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Affiliation(s)
- Chun Chen
- Drug Substance Technologies, Process Development, Amgen Inc., 1 Amgen Center Drive, Thousand Oaks, CA 91320, USA
| | - Huong Le
- Drug Substance Technologies, Process Development, Amgen Inc., 1 Amgen Center Drive, Thousand Oaks, CA 91320, USA
| | - Brian Follstad
- Drug Substance Technologies, Process Development, Amgen Inc., 1 Amgen Center Drive, Thousand Oaks, CA 91320, USA
| | - Chetan T Goudar
- Drug Substance Technologies, Process Development, Amgen Inc., 1 Amgen Center Drive, Thousand Oaks, CA 91320, USA
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Shridhar S, Klanert G, Auer N, Hernandez-Lopez I, Kańduła MM, Hackl M, Grillari J, Stralis-Pavese N, Kreil DP, Borth N. Transcriptomic changes in CHO cells after adaptation to suspension growth in protein-free medium analysed by a species-specific microarray. J Biotechnol 2017; 257:13-21. [DOI: 10.1016/j.jbiotec.2017.03.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 03/07/2017] [Accepted: 03/11/2017] [Indexed: 11/26/2022]
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Effect of alpha lipoic acid on in vitro development of bovine secondary preantral follicles. Theriogenology 2017; 88:124-130. [DOI: 10.1016/j.theriogenology.2016.09.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Revised: 09/05/2016] [Accepted: 09/06/2016] [Indexed: 12/28/2022]
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6
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Pfizenmaier J, Junghans L, Teleki A, Takors R. Hyperosmotic stimulus study discloses benefits in ATP supply and reveals miRNA/mRNA targets to improve recombinant protein production of CHO cells. Biotechnol J 2016; 11:1037-47. [PMID: 27214792 DOI: 10.1002/biot.201500606] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 03/07/2016] [Accepted: 05/12/2016] [Indexed: 01/02/2023]
Abstract
Biopharmaceuticals are predominantly produced by Chinese hamster ovary (CHO) cells cultivated in fed-batch mode. Hyperosmotic culture conditions (≥ 350 mOsmol kg(∑1) ) resulting from feeding of nutrients may enhance specific product formation rates (qp ). As an improved ATP supply was anticipated to enhance qp this study focused on the identification of suitable miRNA/mRNA targets to increase ATP levels. Therefor next generation sequencing and a compartment specific metabolomics approach were applied to analyze the response of an antibody (mAB) producing CHO cell line upon osmotic shift (280 → 430 mOsmol kg(-1) ). Hyperosmotic culture conditions caused a ∼2.6-fold increase of specific ATP formation rates together with a ∼1.7-fold rise in cytosolic and mitochondrial ATP-pools, thus showing increased ATP supply. mRNA expression analysis identified several genes encoding glycosylated proteins with strictly tissue related function. In addition, hyperosmotic culture conditions induced an upregulation of miR-132-3p, miR-132-5p, miR-182, miR-183, miR-194, miR-215-3p, miR-215-5p which have all been related to cell cycle arrest/proliferation in cancer studies. In relation to a previous independent CHO study miR-183 may be the most promising target to enhance qp by stable overexpression. Furthermore, deletion of genes with presumably dispensable function in suspension growing CHO cells may enhance mAB formation by increased ATP levels.
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Affiliation(s)
- Jennifer Pfizenmaier
- University of Stuttgart, Institute of Biochemical Engineering, Stuttgart, Germany
| | - Lisa Junghans
- University of Stuttgart, Institute of Biochemical Engineering, Stuttgart, Germany
| | - Attila Teleki
- University of Stuttgart, Institute of Biochemical Engineering, Stuttgart, Germany
| | - Ralf Takors
- University of Stuttgart, Institute of Biochemical Engineering, Stuttgart, Germany.
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Vishwanathan N, Le H, Le T, Hu WS. Advancing biopharmaceutical process science through transcriptome analysis. Curr Opin Biotechnol 2014; 30:113-9. [DOI: 10.1016/j.copbio.2014.06.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2014] [Revised: 06/13/2014] [Accepted: 06/13/2014] [Indexed: 01/02/2023]
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8
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Statistical methods for mining Chinese hamster ovary cell ‘omics data: from differential expression to integrated multilevel analysis of the biological system. ACTA ACUST UNITED AC 2014. [DOI: 10.4155/pbp.14.50] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Farrell A, McLoughlin N, Milne JJ, Marison IW, Bones J. Application of Multi-Omics Techniques for Bioprocess Design and Optimization in Chinese Hamster Ovary Cells. J Proteome Res 2014; 13:3144-59. [DOI: 10.1021/pr500219b] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Amy Farrell
- Characterisation
and Comparability Laboratory, NIBRT − The National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co. Dublin, Ireland
| | - Niaobh McLoughlin
- Characterisation
and Comparability Laboratory, NIBRT − The National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co. Dublin, Ireland
| | - John J. Milne
- Characterisation
and Comparability Laboratory, NIBRT − The National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co. Dublin, Ireland
| | - Ian W. Marison
- Laboratory
of Integrated Bioprocessing, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Jonathan Bones
- Characterisation
and Comparability Laboratory, NIBRT − The National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co. Dublin, Ireland
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Transcriptome analyses of CHO cells with the next-generation microarray CHO41K: development and validation by analysing the influence of the growth stimulating substance IGF-1 substitute LongR(3.). J Biotechnol 2014; 178:23-31. [PMID: 24613301 DOI: 10.1016/j.jbiotec.2014.02.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 02/07/2014] [Accepted: 02/25/2014] [Indexed: 11/24/2022]
Abstract
The increasing importance of Chinese hamster ovary (CHO) cells for the production of pharmaceutical proteins has awakened the demand to understand the cellular metabolism of these cells. However, satisfactory gene expression studies have yet been impractical due to insufficient coverage of sequences. In this work, previously determined sequence information of CHO cells and newly derived data from 454 and Illumina sequencing was used to establish the CHO41K microarray which contains 41,304 probes. Self-hybridisation was performed for replica determination and samples were run in triplicates to increase statistical power. For determination of technical variance, confidence intervals at an M-value of ±0.6 for 95% and at ±2.3 for 99% of the probes were calculated. Intra-microarray and slide to slide variance was not detectable. In a first application, this microarray enabled an in-depth look inside the cellular transcriptome of CHO cells cultured in the presence or absence of the growth supporting substance "insulin like growth factor 1" (IGF-1) analogue LongR(3). Its effect on the cells ranged from enhanced growth to delay of cell death as well as cytoskeletal installation. Suggesting that under supplementation, a minimised cellular effort in installation of a large cytoskeleton occurs, possibly in favour of promoting faster cell division.
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Kildegaard HF, Baycin-Hizal D, Lewis NE, Betenbaugh MJ. The emerging CHO systems biology era: harnessing the ‘omics revolution for biotechnology. Curr Opin Biotechnol 2013; 24:1102-7. [DOI: 10.1016/j.copbio.2013.02.007] [Citation(s) in RCA: 139] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 01/17/2013] [Accepted: 02/09/2013] [Indexed: 11/29/2022]
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12
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Advances in Mammalian cell line development technologies for recombinant protein production. Pharmaceuticals (Basel) 2013; 6:579-603. [PMID: 24276168 PMCID: PMC3817724 DOI: 10.3390/ph6050579] [Citation(s) in RCA: 201] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 03/28/2013] [Accepted: 04/10/2013] [Indexed: 01/20/2023] Open
Abstract
From 2006 to 2011, an average of 15 novel recombinant protein therapeutics have been approved by US Food and Drug Administration (FDA) annually. In addition, the expiration of blockbuster biologics has also spurred the emergence of biosimilars. The increasing numbers of innovator biologic products and biosimilars have thus fuelled the demand of production cell lines with high productivity. Currently, mammalian cell line development technologies used by most biopharmaceutical companies are based on either the methotrexate (MTX) amplification technology or the glutamine synthetase (GS) system. With both systems, the cell clones obtained are highly heterogeneous, as a result of random genome integration by the gene of interest and the gene amplification process. Consequently, large numbers of cell clones have to be screened to identify rare stable high producer cell clones. As such, the cell line development process typically requires 6 to 12 months and is a time, capital and labour intensive process. This article reviews established advances in protein expression and clone screening which are the core technologies in mammalian cell line development. Advancements in these component technologies are vital to improve the speed and efficiency of generating robust and highly productive cell line for large scale production of protein therapeutics.
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Datta P, Linhardt RJ, Sharfstein ST. An 'omics approach towards CHO cell engineering. Biotechnol Bioeng 2013; 110:1255-71. [DOI: 10.1002/bit.24841] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 12/19/2012] [Accepted: 01/02/2013] [Indexed: 12/15/2022]
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Doolan P, Barron N, Kinsella P, Clarke C, Meleady P, O'Sullivan F, Melville M, Leonard M, Clynes M. Microarray expression profiling identifies genes regulating sustained cell specific productivity (S-Qp) in CHO K1 production cell lines. Biotechnol J 2012; 7:516-26. [DOI: 10.1002/biot.201100255] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 09/26/2011] [Accepted: 12/01/2011] [Indexed: 11/10/2022]
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15
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Clarke C, Doolan P, Barron N, Meleady P, Madden SF, DiNino D, Leonard M, Clynes M. CGCDB: A web-based resource for the investigation of gene coexpression in CHO cell culture. Biotechnol Bioeng 2012; 109:1368-70. [DOI: 10.1002/bit.24416] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Revised: 12/13/2011] [Accepted: 12/15/2011] [Indexed: 11/08/2022]
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16
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Clarke C, Doolan P, Barron N, Meleady P, O'Sullivan F, Gammell P, Melville M, Leonard M, Clynes M. Large scale microarray profiling and coexpression network analysis of CHO cells identifies transcriptional modules associated with growth and productivity. J Biotechnol 2011; 155:350-9. [DOI: 10.1016/j.jbiotec.2011.07.011] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2011] [Revised: 07/07/2011] [Accepted: 07/08/2011] [Indexed: 12/31/2022]
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