1
|
Jerabek T, Weiß L, Fahrion H, Zeh N, Raab N, Lindner B, Fischer S, Otte K. In pursuit of a minimal CHO genome: Establishment of large-scale genome deletions. N Biotechnol 2024; 79:100-110. [PMID: 38154614 DOI: 10.1016/j.nbt.2023.12.007] [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: 10/20/2023] [Revised: 11/27/2023] [Accepted: 12/24/2023] [Indexed: 12/30/2023]
Abstract
Chinese hamster ovary (CHO) cells are the most commonly used mammalian cell line for the production of complex therapeutic glycoproteins. As CHO cells have evolved as part of a multicellular organism, they harbor many cellular functions irrelevant for their application as production hosts in industrial bioprocesses. Consequently, CHO cells have been the target for numerous genetic engineering efforts in the past, but a tailored host cell chassis holistically optimized for its specific task in a bioreactor is still missing. While the concept of genome reduction has already been successfully applied to bacterial production cells, attempts to create higher eukaryotic production hosts exhibiting reduced genomes have not been reported yet. Here, we present the establishment and application of a large-scale genome deletion strategy for targeted excision of large genomic regions in CHO cells. We demonstrate the feasibility of genome reduction in CHO cells using optimized CRISPR/Cas9 based experimental protocols targeting large non-essential genomic regions with high efficiency. Achieved genome deletions of non-essential genetic regions did not introduce negative effects on bioprocess relevant parameters, although we conducted the largest reported genomic excision of 864 kilobase pairs in CHO cells so far. The concept presented serves as a directive to accelerate the development of a significantly genome-reduced CHO host cell chassis paving the way for a next generation of CHO cell factories.
Collapse
Affiliation(s)
- Tobias Jerabek
- University of Applied Sciences Biberach, Institute of Applied Biotechnology, Biberach, Germany.
| | - Linus Weiß
- University of Applied Sciences Biberach, Institute of Applied Biotechnology, Biberach, Germany
| | - Hannah Fahrion
- University of Applied Sciences Biberach, Institute of Applied Biotechnology, Biberach, Germany
| | - Nikolas Zeh
- University of Applied Sciences Biberach, Institute of Applied Biotechnology, Biberach, Germany; Boehringer Ingelheim Pharma GmbH & Co KG, Bioprocess Development Biologicals, Cell Line Development, Biberach, Germany
| | - Nadja Raab
- University of Applied Sciences Biberach, Institute of Applied Biotechnology, Biberach, Germany
| | - Benjamin Lindner
- Boehringer Ingelheim Pharma GmbH & Co KG, Bioprocess Development Biologicals, Cell Line Development, Biberach, Germany
| | - Simon Fischer
- Boehringer Ingelheim Pharma GmbH & Co KG, Bioprocess Development Biologicals, Cell Line Development, Biberach, Germany
| | - Kerstin Otte
- University of Applied Sciences Biberach, Institute of Applied Biotechnology, Biberach, Germany
| |
Collapse
|
2
|
Leitner K, Motheramgari K, Borth N, Marx N. Nanopore Cas9-targeted sequencing enables accurate and simultaneous identification of transgene integration sites, their structure and epigenetic status in recombinant Chinese hamster ovary cells. Biotechnol Bioeng 2023; 120:2403-2418. [PMID: 36938677 DOI: 10.1002/bit.28382] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/27/2023] [Accepted: 03/12/2023] [Indexed: 03/21/2023]
Abstract
The integration of a transgene expression construct into the host genome is the initial step for the generation of recombinant cell lines used for biopharmaceutical production. The stability and level of recombinant gene expression in Chinese hamster ovary (CHO) can be correlated to the copy number, its integration site as well as the epigenetic context of the transgene vector. Also, undesired integration events, such as concatemers, truncated, and inverted vector repeats, are impacting the stability of recombinant cell lines. Thus, to characterize cell clones and to isolate the most promising candidates, it is crucial to obtain information on the site of integration, the structure of integrated sequence and the epigenetic status. Current sequencing techniques allow to gather this information separately but do not offer a comprehensive and simultaneous resolution. In this study, we present a fast and robust nanopore Cas9-targeted sequencing (nCats) pipeline to identify integration sites, the composition of the integrated sequence as well as its DNA methylation status in CHO cells that can be obtained simultaneously from the same sequencing run. A Cas9-enrichment step during library preparation enables targeted and directional nanopore sequencing with up to 724× median on-target coverage and up to 153 kb long reads. The data generated by nCats provides sensitive, detailed, and correct information on the transgene integration sites and the expression vector structure, which could only be partly produced by traditional Targeted Locus Amplification-seq data. Moreover, with nCats the DNA methylation status can be analyzed from the same raw data without prior DNA amplification.
Collapse
Affiliation(s)
- Klaus Leitner
- Austrian Center of Industrial Biotechnology GmbH, Vienna, Austria
| | | | - Nicole Borth
- Austrian Center of Industrial Biotechnology GmbH, Vienna, Austria
- Department of Biotechnology, Institute of Animal Cell Technology and Systems Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Nicolas Marx
- Department of Biotechnology, Institute of Animal Cell Technology and Systems Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| |
Collapse
|
3
|
Srila W, Baumann M, Riedl M, Rangnoi K, Borth N, Yamabhai M. Glutamine synthetase (GS) knockout (KO) using CRISPR/Cpf1 diversely enhances selection efficiency of CHO cells expressing therapeutic antibodies. Sci Rep 2023; 13:10473. [PMID: 37380701 DOI: 10.1038/s41598-023-37288-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 06/19/2023] [Indexed: 06/30/2023] Open
Abstract
The glutamine synthetase (GS)-based Chinese hamster ovary (CHO) selection system is an attractive approach to efficiently identify suitable clones in the cell line generation process for biologics manufacture, for which GS-knockout (GS-KO) CHO cell lines are commonly used. Since genome analysis indicated that there are two GS genes in CHO cells, deleting only 1 GS gene could potentially result in the activation of other GS genes, consequently reducing the selection efficiency. Therefore, in this study, both GS genes identified on chromosome 5 (GS5) and 1 (GS1) of CHO-S and CHO-K1, were deleted using CRISPR/Cpf1. Both single and double GS-KO CHO-S and K1 showed robust glutamine-dependent growth. Next, the engineered CHO cells were tested for their efficiency of selection of stable producers of two therapeutic antibodies. Analysis of pool cultures and subclones after a single round of 25 µM methionine sulfoxinime (MSX) selection indicated that for CHO-K1 the double GS5,1-KO was more efficient as in the case of a single GS5-KO the GS1 gene was upregulated. In CHO-S, on the other hand, with an autologously lower level of expression of both variants of GS, a single GS5-KO was more robust and already enabled selection of high producers. In conclusion, CRISPR/Cpf1 can be efficiently used to knock out GS genes from CHO cells. The study also indicates that for the generation of host cell lines for efficient selection, the initial characterisation of expression levels of the target gene as well as the identification of potential escape mechanisms is important.
Collapse
Affiliation(s)
- Witsanu Srila
- Molecular Biotechnology Laboratory, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Martina Baumann
- Austrian Centre of Industrial Biotechnology (ACIB), Vienna, Austria
| | - Markus Riedl
- Austrian Centre of Industrial Biotechnology (ACIB), Vienna, Austria
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Kuntalee Rangnoi
- Molecular Biotechnology Laboratory, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Nicole Borth
- Austrian Centre of Industrial Biotechnology (ACIB), Vienna, Austria.
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria.
| | - Montarop Yamabhai
- Molecular Biotechnology Laboratory, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, Thailand.
| |
Collapse
|
4
|
Glinšek K, Bozovičar K, Bratkovič T. CRISPR Technologies in Chinese Hamster Ovary Cell Line Engineering. Int J Mol Sci 2023; 24:ijms24098144. [PMID: 37175850 PMCID: PMC10179654 DOI: 10.3390/ijms24098144] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 04/26/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
The Chinese hamster ovary (CHO) cell line is a well-established platform for the production of biopharmaceuticals due to its ability to express complex therapeutic proteins with human-like glycopatterns in high amounts. The advent of CRISPR technology has opened up new avenues for the engineering of CHO cell lines for improved protein production and enhanced product quality. This review summarizes recent advances in the application of CRISPR technology for CHO cell line engineering with a particular focus on glycosylation modulation, productivity enhancement, tackling adventitious agents, elimination of problematic host cell proteins, development of antibiotic-free selection systems, site-specific transgene integration, and CRISPR-mediated gene activation and repression. The review highlights the potential of CRISPR technology in CHO cell line genome editing and epigenetic engineering for the more efficient and cost-effective development of biopharmaceuticals while ensuring the safety and quality of the final product.
Collapse
Affiliation(s)
- Katja Glinšek
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Krištof Bozovičar
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Tomaž Bratkovič
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia
| |
Collapse
|
5
|
Kalkan AK, Palaz F, Sofija S, Elmousa N, Ledezma Y, Cachat E, Rios-Solis L. Improving recombinant protein production in CHO cells using the CRISPR-Cas system. Biotechnol Adv 2023; 64:108115. [PMID: 36758652 DOI: 10.1016/j.biotechadv.2023.108115] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 12/28/2022] [Accepted: 02/03/2023] [Indexed: 02/10/2023]
Abstract
Chinese hamster ovary (CHO) cells are among the most widely used mammalian cell lines in the biopharmaceutical industry. Therefore, it is not surprising that significant efforts have been made around the engineering of CHO cells using genetic engineering methods such as the CRISPR-Cas system. In this review, we summarize key recent studies that have used different CRISPR-Cas systems such as Cas9, Cas13 or dCas9 fused with effector domains to improve recombinant protein (r-protein) production in CHO cells. Here, every relevant stage of production was considered, underscoring the advantages and limitations of these systems, as well as discussing their bottlenecks and probable solutions. A special emphasis was given on how these systems could disrupt and/or regulate genes related to glycan composition, which has relevant effects over r-protein properties and in vivo activity. Furthermore, the related promising future applications of CRISPR to achieve a tunable, reversible, or highly stable editing of CHO cells are discussed. Overall, the studies covered in this review show that despite the complexity of mammalian cells, the synthetic biology community has developed many mature strategies to improve r-protein production using CHO cells. In this regard, CRISPR-Cas technology clearly provides efficient and flexible genetic manipulation and allows for the generation of more productive CHO cell lines, leading to more cost-efficient production of biopharmaceuticals, however, there is still a need for many emerging techniques in CRISPR to be reported in CHO cells; therefore, more research in these cells is needed to realize the full potential of this technology.
Collapse
Affiliation(s)
- Ali Kerem Kalkan
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, UK; Environmental Engineering Department, Gebze Technical University, Turkey
| | - Fahreddin Palaz
- Faculty of Medicine, Hacettepe University, Ankara 06100, Turkey
| | - Semeniuk Sofija
- Centre for Engineering Biology, University of Edinburgh, Edinburgh EH9 3BF, UK; Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Nada Elmousa
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH9 3DW, UK
| | - Yuri Ledezma
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH9 3DW, UK; Biology Department, Faculty of Pure and Natural Sciences, Universidad Mayor de San Andrés, Bolivia
| | - Elise Cachat
- Centre for Engineering Biology, University of Edinburgh, Edinburgh EH9 3BF, UK; Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences University of Edinburgh, Edinburgh EH9 3BF, UK; UK Centre for Mammalian Synthetic Biology, University of Edinburgh, Edinburgh EH8 9YL, UK
| | - Leonardo Rios-Solis
- Centre for Engineering Biology, University of Edinburgh, Edinburgh EH9 3BF, UK; Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh EH9 3DW, UK; School of Natural and Environmental Sciences, Molecular Biology and Biotechnology Division, Newcastle University, Newcastle Upon Tyne, NE1 7RU, UK.
| |
Collapse
|
6
|
Amiri S, Adibzadeh S, Ghanbari S, Rahmani B, Kheirandish MH, Farokhi-Fard A, Dastjerdeh MS, Davami F. CRISPR-interceded CHO cell line development approaches. Biotechnol Bioeng 2023; 120:865-902. [PMID: 36597180 DOI: 10.1002/bit.28329] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 11/28/2022] [Accepted: 01/02/2023] [Indexed: 01/05/2023]
Abstract
For industrial production of recombinant protein biopharmaceuticals, Chinese hamster ovary (CHO) cells represent the most widely adopted host cell system, owing to their capacity to produce high-quality biologics with human-like posttranslational modifications. As opposed to random integration, targeted genome editing in genomic safe harbor sites has offered CHO cell line engineering a new perspective, ensuring production consistency in long-term culture and high biotherapeutic expression levels. Corresponding the remarkable advancements in knowledge of CRISPR-Cas systems, the use of CRISPR-Cas technology along with the donor design strategies has been pushed into increasing novel scenarios in cell line engineering, allowing scientists to modify mammalian genomes such as CHO cell line quickly, readily, and efficiently. Depending on the strategies and production requirements, the gene of interest can also be incorporated at single or multiple loci. This review will give a gist of all the most fundamental recent advancements in CHO cell line development, such as different cell line engineering approaches along with donor design strategies for targeted integration of the desired construct into genomic hot spots, which could ultimately lead to the fast-track product development process with consistent, improved product yield and quality.
Collapse
Affiliation(s)
- Shahin Amiri
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Setare Adibzadeh
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Samaneh Ghanbari
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Behnaz Rahmani
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad H Kheirandish
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
- Department of Medical Biotechnology, School of Advanced Technologies, Tehran University of Medical Sciences, Tehran, Iran
| | - Aref Farokhi-Fard
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Mansoureh S Dastjerdeh
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Fatemeh Davami
- Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| |
Collapse
|
7
|
Zhang Z, Wang W, Ali S, Luo X, Xie L. CRISPR/Cas9-Mediated Multiple Knockouts in Abscisic Acid Receptor Genes Reduced the Sensitivity to ABA during Soybean Seed Germination. Int J Mol Sci 2022; 23:ijms232416173. [PMID: 36555815 PMCID: PMC9784318 DOI: 10.3390/ijms232416173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 12/04/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
Abscisic acid (ABA) is an important plant hormone that regulates numerous functions in plant growth, development, and stress responses. Several proteins regulate the ABA signal transduction mechanism in response to environmental stress. Among them, the PYR1/PYL/RCAR family act as ABA receptors. This study used the CRISPR/Cas9 gene-editing system with a single gRNA to knock out three soybean PYL genes: GmPYL17, GmPYL18, and GmPYL19. The gRNA may efficiently cause varying degrees of deletion of GmPYL17, GmPYL18, and GmPYL19 gene target sequences, according to the genotyping results of T0 plants. A subset of induced alleles was successfully transferred to progeny. In the T2 generation, we obtained double and triple mutant genotypes. At the seed germination stage, CRISPR/Cas9-created GmPYL gene knockout mutants, particularly gmpyl17/19 double mutants, are less susceptible to ABA than the wild type. RNA-Seq was used to investigate the differentially expressed genes related to the ABA response from germinated seedlings under diverse treatments using three biological replicates. The gmpyl17/19-1 double mutant was less susceptible to ABA during seed germination, and mutant plant height and branch number were higher than the wild type. Under ABA stress, the GO enrichment analysis showed that certain positive germination regulators were activated, which reduced ABA sensitivity and enhanced seed germination. This research gives a theoretical basis for a better understanding of the ABA signaling pathway and the participation of the key component at their molecular level, which helps enhance soybean abiotic stress tolerance. Furthermore, this research will aid breeders in regulating and improving soybean production and quality under various stress conditions.
Collapse
Affiliation(s)
- Zhaohan Zhang
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
- Peking University Institute of Advanced Agricultural Sciences, Weifang 261325, China
| | - Wanpeng Wang
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Shahid Ali
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Xiao Luo
- Peking University Institute of Advanced Agricultural Sciences, Weifang 261325, China
- Correspondence: (X.L.); (L.X.)
| | - Linan Xie
- Key Laboratory of Saline-Alkali Vegetative Ecology Restoration, Ministry of Education, College of Life Science, Northeast Forestry University, Harbin 150040, China
- Correspondence: (X.L.); (L.X.)
| |
Collapse
|
8
|
Glinšek K, Kramer L, Krajnc A, Kranjc E, Pirher N, Marušič J, Hellmann L, Podobnik B, Štrukelj B, Ausländer D, Gaber R. Coupling CRISPR interference with FACS enrichment: New approach in glycoengineering of CHO cell lines for therapeutic glycoprotein production. Biotechnol J 2022; 17:e2100499. [PMID: 35481906 DOI: 10.1002/biot.202100499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/10/2022] [Accepted: 04/23/2022] [Indexed: 11/05/2022]
Abstract
Difficulties in obtaining and maintaining the desired level of the critical quality attributes (CQAs) of therapeutic proteins as well as the pace of the development are major challenges of current biopharmaceutical development. Therapeutic proteins, both innovative and biosimilars, are mostly glycosylated. Glycans directly influence the stability, potency, plasma half-life, immunogenicity, and effector functions of the therapeutic. Hence, glycosylation is widely recognized as a process-dependent CQA of therapeutic glycoproteins. Due to the typically high heterogeneity of glycoforms attached to the proteins, control of glycosylation represents one of the most challenging aspects of biopharmaceutical development. Here, we explored a new glycoengineering approach in therapeutic glycoproteins development, which enabled us to achieve the targeted glycoprofile of the Fc-fusion protein in a fast manner. Coupling CRISPRi technology with lectin-FACS sorting enabled downregulation of the endogenous gene involved in fucosylation and further enrichment of CHO cells producing Fc-fusion proteins with reduced fucosylation levels. Enrichment of cells with targeted glycoprofile can lead to time-optimized clone screening and speed up cell line development. Moreover, the presented approach allows isolation of clones with varying levels of fucosylation, which makes it applicable to a broad range of glycoproteins differing in target fucosylation level. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Katja Glinšek
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, Ljubljana, SI-1000, Slovenia
| | - Lovro Kramer
- Novartis Technical Research & Development, Biologics Technical Development, Lek Pharmaceuticals d.d., Kolodvorska 27, Mengeš, SI-1234, Slovenia
| | - Aleksander Krajnc
- Novartis Technical Research & Development, Biologics Technical Development, Lek Pharmaceuticals d.d., Kolodvorska 27, Mengeš, SI-1234, Slovenia
| | - Eva Kranjc
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, Ljubljana, SI-1000, Slovenia
| | - Nina Pirher
- Novartis Technical Research & Development, Biologics Technical Development, Lek Pharmaceuticals d.d., Kolodvorska 27, Mengeš, SI-1234, Slovenia
| | - Jaka Marušič
- Novartis Technical Research & Development, Biologics Technical Development, Lek Pharmaceuticals d.d., Kolodvorska 27, Mengeš, SI-1234, Slovenia
| | - Leon Hellmann
- Novartis Institutes for Biomedical Research, Klybeckstrasse 141, Basel, CH-4057, Switzerland
| | - Barbara Podobnik
- Novartis Technical Research & Development, Biologics Technical Development, Lek Pharmaceuticals d.d., Kolodvorska 27, Mengeš, SI-1234, Slovenia
| | - Borut Štrukelj
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, Ljubljana, SI-1000, Slovenia
| | - David Ausländer
- Novartis Institutes for Biomedical Research, Klybeckstrasse 141, Basel, CH-4057, Switzerland
| | - Rok Gaber
- Novartis Technical Research & Development, Biologics Technical Development, Lek Pharmaceuticals d.d., Kolodvorska 27, Mengeš, SI-1234, Slovenia
| |
Collapse
|
9
|
Marx N, Eisenhut P, Weinguny M, Klanert G, Borth N. How to train your cell - Towards controlling phenotypes by harnessing the epigenome of Chinese hamster ovary production cell lines. Biotechnol Adv 2022; 56:107924. [PMID: 35149147 DOI: 10.1016/j.biotechadv.2022.107924] [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: 12/28/2021] [Revised: 02/03/2022] [Accepted: 02/04/2022] [Indexed: 11/24/2022]
Abstract
Recent advances in omics technologies and the broad availability of big datasets have revolutionized our understanding of Chinese hamster ovary cells in their role as the most prevalent host for production of complex biopharmaceuticals. In consequence, our perception of this "workhorse of the biopharmaceutical industry" has successively shifted from that of a nicely working, but unknown recombinant protein producing black box to a biological system governed by multiple complex regulatory layers that might possibly be harnessed and manipulated at will. Despite the tremendous progress that has been made to characterize CHO cells on various omics levels, our understanding is still far from complete. The well-known inherent genetic plasticity of any immortalized and rapidly dividing cell line also characterizes CHO cells and can lead to problematic instability of recombinant protein production. While the high mutational frequency has been a focus of CHO cell research for decades, the impact of epigenetics and its role in differential gene expression has only recently been addressed. In this review we provide an overview about the current understanding of epigenetic regulation in CHO cells and discuss its significance for shaping the cell's phenotype. We also look into current state-of-the-art technology that can be applied to harness and manipulate the epigenetic network so as to nudge CHO cells towards a specific phenotype. Here, we revise current strategies on site-directed integration and random as well as targeted epigenome modifications. Finally, we address open questions that need to be investigated to exploit the full repertoire of fine-tuned control of multiplexed gene expression using epigenetic and systems biology tools.
Collapse
Affiliation(s)
- Nicolas Marx
- University of Natural Resources and Life Sciences, Vienna, Austria
| | - Peter Eisenhut
- Austrian Centre for Industrial Biotechnology GmbH, Vienna, Austria
| | - Marcus Weinguny
- University of Natural Resources and Life Sciences, Vienna, Austria; Austrian Centre for Industrial Biotechnology GmbH, Vienna, Austria
| | - Gerald Klanert
- Austrian Centre for Industrial Biotechnology GmbH, Vienna, Austria
| | - Nicole Borth
- University of Natural Resources and Life Sciences, Vienna, Austria; Austrian Centre for Industrial Biotechnology GmbH, Vienna, Austria.
| |
Collapse
|
10
|
Peng H, Zheng Y, Zhao Z, Li J. Multigene editing: current approaches and beyond. Brief Bioinform 2021; 22:bbaa396. [PMID: 33428725 DOI: 10.1093/bib/bbaa396] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/15/2020] [Accepted: 12/03/2020] [Indexed: 11/14/2022] Open
Abstract
CRISPR/Cas9 multigene editing is an active and widely studied topic in the fields of biomedicine and biology. It involves a simultaneous participation of multiple single-guide RNAs (sgRNAs) to edit multiple target genes in a way that each gene is edited by one of these sgRNAs. There are possibly numerous sgRNA candidates capable of on-target editing on each of these genes with various efficiencies. Meanwhile, each of these sgRNA candidates may cause unwanted off-target editing at many other genes. Therefore, selection optimization of these multiple sgRNAs is demanded so as to minimize the number of sgRNAs and thus reduce the collective negative effects caused by the off-target editing. This survey reviews wet-laboratory approaches to the implementation of multigene editing and their needs of computational tools for better design. We found that though off-target editing is unavoidable during the gene editing, those disfavored cuttings by some target genes' sgRNAs can potentially become on-target editing sites for some other genes of interests. This off-to-on role conversion is beneficial to optimize the sgRNA selection in multigene editing. We present a preference cutting score to assess those beneficial off-target cutting sites, which have a few mismatches with their host genes' on-target editing sites. These potential sgRNAs can be prioritized for recommendation via ranking their on-target average cutting efficiency, the total off-target site number and their average preference cutting score. We also present case studies on cancer-associated genes to demonstrate tremendous usefulness of the new method.
Collapse
Affiliation(s)
- Hui Peng
- Data Science Institute, University of Technology Sydney, PO Box 123, Ultimo, NSW 2007, Australia
- School of Computing, National University of Singapore, 13 Computing Drive, 117417, Singapore
| | - Yi Zheng
- Data Science Institute, University of Technology Sydney, PO Box 123, Ultimo, NSW 2007, Australia
| | - Zhixun Zhao
- Data Science Institute, University of Technology Sydney, PO Box 123, Ultimo, NSW 2007, Australia
| | - Jinyan Li
- Data Science Institute, University of Technology Sydney, PO Box 123, Ultimo, NSW 2007, Australia
| |
Collapse
|
11
|
Arnesen JA, Hoof JB, Kildegaard HF, Borodina I. Genome Editing of Eukarya. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
12
|
Schmieder V, Novak N, Dhiman H, Nguyen LN, Serafimova E, Klanert G, Baumann M, Kildegaard HF, Borth N. A pooled CRISPR/AsCpf1 screen using paired gRNAs to induce genomic deletions in Chinese hamster ovary cells. ACTA ACUST UNITED AC 2021; 31:e00649. [PMID: 34277363 PMCID: PMC8261548 DOI: 10.1016/j.btre.2021.e00649] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 06/06/2021] [Accepted: 06/16/2021] [Indexed: 12/13/2022]
Abstract
• Development of a small-scale CRISPR/AsCpf1 screen in CHO. • Usage of paired gRNAs enables full deletion of coding or noncoding genomic regions. • Growth perturbing paired gRNAs identified. • Key points for considerations in future screens identified.
Chinese hamster ovary (CHO) cells are the most widely used host for the expression of therapeutic proteins. Recently, significant progress has been made due to advances in genome sequence and annotation quality to unravel the black box CHO. Nevertheless, in many cases the link between genotype and phenotype in the context of suspension cultivated production cell lines is still not fully understood. While frameshift approaches targeting coding genes are frequently used, the non-coding regions of the genome have received less attention with respect to such functional annotation. Importantly, for non-coding regions frameshift knock-out strategies are not feasible. In this study, we developed a CRISPR-mediated screening approach that performs full deletions of genomic regions to enable the functional study of both the translated and untranslated genome. An in silico pipeline for the computational high-throughput design of paired guide RNAs (pgRNAs) directing CRISPR/AsCpf1 was established and used to generate a library tackling process-related genes and long non-coding RNAs. Next generation sequencing analysis of the plasmid library revealed a sufficient, but highly variable pgRNA composition. Recombinase-mediated cassette exchange was applied for pgRNA library integration rather than viral transduction to ensure single copy representation of pgRNAs per cell. After transient AsCpf1 expression, cells were cultivated over two sequential batches to identify pgRNAs which massively affected growth and survival. By comparing pgRNA abundance, depleted candidates were identified and individually validated to verify their effect.
Collapse
Key Words
- AsCpf1, Cpf1 from Acidaminococcus sp BV3L6
- CHO, Chinese hamster ovary
- CPM, counts per million reads mapped
- CRISPR, Clustered Regularly Interspaced Short Palindromic Repeats
- CRISPR/AsCpf1
- Cas9, CRISPR-associated protein 9
- Chinese hamster ovary cells
- Cpf1, CRISPR-associated protein in Prevotella and Francisella
- DE, differentially expressed
- DOWN-TTS, downstream transcription termination site
- DR, differentially represented
- EV, empty vector
- EpoFc, Erythropoietin Fc fusion protein
- FACS, fluorescence activated cell sorting
- FC, fold change
- FDR, false discovery rate
- GS, glutamine synthetase
- Genetic screen
- NGS, next generation sequencing
- NTC, no template control
- PAM, protospacer adjacent motif
- PCA, principal component analysis
- Qp, specific productivity
- RMCE, recombinase-mediated cassette exchange
- TMM, trimmed mean of M values
- UP-TSS, upstream transcription start site
- VCD, viable cell density
- dCas9, deactivated Cas9
- gRNA, guide RNA
- genomic deletion
- lncRNA, long non-coding RNA
- ncGene, non-coding gene
- oligo, oligonucleotide
- paired gRNAs
- pgRNA, paired gRNA
- sgRNA, single guide RNA
- µ, growth rate
Collapse
Affiliation(s)
- Valerie Schmieder
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, Austria.,acib GmbH, Austrian Centre of Industrial Biotechnology, Muthgasse 11, Vienna, Austria
| | - Neža Novak
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, Austria.,acib GmbH, Austrian Centre of Industrial Biotechnology, Muthgasse 11, Vienna, Austria
| | - Heena Dhiman
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, Austria.,acib GmbH, Austrian Centre of Industrial Biotechnology, Muthgasse 11, Vienna, Austria
| | - Ly Ngoc Nguyen
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, Austria.,acib GmbH, Austrian Centre of Industrial Biotechnology, Muthgasse 11, Vienna, Austria
| | - Evgenija Serafimova
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, Austria.,acib GmbH, Austrian Centre of Industrial Biotechnology, Muthgasse 11, Vienna, Austria
| | - Gerald Klanert
- acib GmbH, Austrian Centre of Industrial Biotechnology, Muthgasse 11, Vienna, Austria
| | - Martina Baumann
- acib GmbH, Austrian Centre of Industrial Biotechnology, Muthgasse 11, Vienna, Austria
| | - Helene Faustrup Kildegaard
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, Kgs. Lyngby, Denmark
| | - Nicole Borth
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Muthgasse 18, Vienna, Austria.,acib GmbH, Austrian Centre of Industrial Biotechnology, Muthgasse 11, Vienna, Austria
| |
Collapse
|
13
|
Marx N, Dhiman H, Schmieder V, Freire CM, Nguyen LN, Klanert G, Borth N. Enhanced targeted DNA methylation of the CMV and endogenous promoters with dCas9-DNMT3A3L entails distinct subsequent histone modification changes in CHO cells. Metab Eng 2021; 66:268-282. [PMID: 33965614 DOI: 10.1016/j.ymben.2021.04.014] [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: 02/02/2021] [Revised: 04/02/2021] [Accepted: 04/22/2021] [Indexed: 01/08/2023]
Abstract
With the emergence of new CRISPR/dCas9 tools that enable site specific modulation of DNA methylation and histone modifications, more detailed investigations of the contribution of epigenetic regulation to the precise phenotype of cells in culture, including recombinant production subclones, is now possible. These also allow a wide range of applications in metabolic engineering once the impact of such epigenetic modifications on the chromatin state is available. In this study, enhanced DNA methylation tools were targeted to a recombinant viral promoter (CMV), an endogenous promoter that is silenced in its native state in CHO cells, but had been reactivated previously (β-galactoside α-2,6-sialyltransferase 1) and an active endogenous promoter (α-1,6-fucosyltransferase), respectively. Comparative ChIP-analysis of histone modifications revealed a general loss of active promoter histone marks and the acquisition of distinct repressive heterochromatin marks after targeted methylation. On the other hand, targeted demethylation resulted in autologous acquisition of active promoter histone marks and loss of repressive heterochromatin marks. These data suggest that DNA methylation directs the removal or deposition of specific histone marks associated with either active, poised or silenced chromatin. Moreover, we show that de novo methylation of the CMV promoter results in reduced transgene expression in CHO cells. Although targeted DNA methylation is not efficient, the transgene is repressed, thus offering an explanation for seemingly conflicting reports about the source of CMV promoter instability in CHO cells. Importantly, modulation of epigenetic marks enables to nudge the cell into a specific gene expression pattern or phenotype, which is stabilized in the cell by autologous addition of further epigenetic marks. Such engineering strategies have the added advantage of being reversible and potentially tunable to not only turn on or off a targeted gene, but also to achieve the setting of a desirable expression level.
Collapse
Affiliation(s)
- Nicolas Marx
- BOKU University of Natural Resources and Life Sciences, Vienna, Austria; Austrian Center for Industrial Biotechnology GmbH, Vienna, Austria
| | - Heena Dhiman
- BOKU University of Natural Resources and Life Sciences, Vienna, Austria; Austrian Center for Industrial Biotechnology GmbH, Vienna, Austria
| | - Valerie Schmieder
- BOKU University of Natural Resources and Life Sciences, Vienna, Austria; Austrian Center for Industrial Biotechnology GmbH, Vienna, Austria
| | | | - Ly Ngoc Nguyen
- BOKU University of Natural Resources and Life Sciences, Vienna, Austria; Austrian Center for Industrial Biotechnology GmbH, Vienna, Austria
| | - Gerald Klanert
- Austrian Center for Industrial Biotechnology GmbH, Vienna, Austria
| | - Nicole Borth
- BOKU University of Natural Resources and Life Sciences, Vienna, Austria; Austrian Center for Industrial Biotechnology GmbH, Vienna, Austria.
| |
Collapse
|
14
|
Donini R, Haslam SM, Kontoravdi C. Glycoengineering Chinese hamster ovary cells: a short history. Biochem Soc Trans 2021; 49:915-931. [PMID: 33704400 PMCID: PMC8106501 DOI: 10.1042/bst20200840] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/26/2021] [Accepted: 02/08/2021] [Indexed: 12/25/2022]
Abstract
Biotherapeutic glycoproteins have revolutionised the field of pharmaceuticals, with new discoveries and continuous improvements underpinning the rapid growth of this industry. N-glycosylation is a critical quality attribute of biotherapeutic glycoproteins that influences the efficacy, half-life and immunogenicity of these drugs. This review will focus on the advances and future directions of remodelling N-glycosylation in Chinese hamster ovary (CHO) cells, which are the workhorse of recombinant biotherapeutic production, with particular emphasis on antibody products, using strategies such as cell line and protein backbone engineering.
Collapse
Affiliation(s)
- Roberto Donini
- Department of Life Sciences, Imperial College London, London SW7 2AZ, U.K
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, U.K
| | - Stuart M. Haslam
- Department of Life Sciences, Imperial College London, London SW7 2AZ, U.K
| | - Cleo Kontoravdi
- Department of Chemical Engineering, Imperial College London, London SW7 2AZ, U.K
| |
Collapse
|
15
|
Development of CRISPR-Cas9 genome editing system in Talaromyces marneffei. Microb Pathog 2021; 154:104822. [PMID: 33727171 DOI: 10.1016/j.micpath.2021.104822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 11/21/2022]
Abstract
Talaromyces marneffei is an important pathogenic thermally dimorphic fungus causing systemic talaromycosis mainly prevalent in Southeast Asia. The dimorphic transition between mycelium and yeast is considered crucial for the pathogenicity of T. marneffei. However, the lack of genetic toolbox has been a major impediment for understanding its pathogenicity. Here a CRISPR-Cas9 system was developed to facilitate genetic manipulations in this organism. In this study, the CRISPR-Cas9 gene editing system uses a native U6 snRNA promoter from T. marneffei to drive the expression of sgRNA. Employing this system and PEG-mediated protoplast transformation, the sakA gene was mutated. Sanger sequencing confirmed nearly 40% site-directed mutation rate. The phenotype analysis confirmed the sakA gene function in T. marneffei dimorphic transition. Our study provided a powerful genome-manipulating tool, which could accelerate studies on T. marneffei for further revealing the mechanisms of its pathogenicity.
Collapse
|
16
|
Wu Q, Shou J. Toward precise CRISPR DNA fragment editing and predictable 3D genome engineering. J Mol Cell Biol 2021; 12:828-856. [PMID: 33125070 PMCID: PMC7883824 DOI: 10.1093/jmcb/mjaa060] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/23/2020] [Accepted: 09/23/2020] [Indexed: 02/06/2023] Open
Abstract
Ever since gene targeting or specific modification of genome sequences in mice was achieved in the early 1980s, the reverse genetic approach of precise editing of any genomic locus has greatly accelerated biomedical research and biotechnology development. In particular, the recent development of the CRISPR/Cas9 system has greatly expedited genetic dissection of 3D genomes. CRISPR gene-editing outcomes result from targeted genome cleavage by ectopic bacterial Cas9 nuclease followed by presumed random ligations via the host double-strand break repair machineries. Recent studies revealed, however, that the CRISPR genome-editing system is precise and predictable because of cohesive Cas9 cleavage of targeting DNA. Here, we synthesize the current understanding of CRISPR DNA fragment-editing mechanisms and recent progress in predictable outcomes from precise genetic engineering of 3D genomes. Specifically, we first briefly describe historical genetic studies leading to CRISPR and 3D genome engineering. We then summarize different types of chromosomal rearrangements by DNA fragment editing. Finally, we review significant progress from precise 1D gene editing toward predictable 3D genome engineering and synthetic biology. The exciting and rapid advances in this emerging field provide new opportunities and challenges to understand or digest 3D genomes.
Collapse
Affiliation(s)
- Qiang Wu
- Center for Comparative Biomedicine, MOE Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Institute of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jia Shou
- Center for Comparative Biomedicine, MOE Key Lab of Systems Biomedicine, State Key Laboratory of Oncogenes and Related Genes, Institute of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| |
Collapse
|
17
|
Schweickert PG, Wang N, Sandefur SL, Lloyd ME, Konieczny SF, Frye CC, Cheng Z. CRISPR/Cas12a-mediated CHO genome engineering can be effectively integrated at multiple stages of the cell line generation process for bioproduction. Biotechnol J 2021; 16:e2000308. [PMID: 33369118 DOI: 10.1002/biot.202000308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 12/03/2020] [Accepted: 12/09/2020] [Indexed: 11/10/2022]
Abstract
Most biopharmaceuticals produced today are generated using Chinese hamster ovary (CHO) cells, therefore significant attention is focused on methods to improve CHO cell productivity and product quality. The discovery of gene-editing tools, such as CRISPR/Cas9, offers new opportunities to improve CHO cell bioproduction through cell line engineering. Recently an additional CRISPR-associated protein, Cas12a (Cpf1), was shown to be effective for gene editing in eukaryotic cells, including CHO. In this study, we demonstrate the successful application of CRISPR/Cas12a for the generation of clonally derived CHO knockout (KO) cell lines with improved product quality attributes. While we found Cas12a efficiency to be highly dependent on the targeting RNA used, we were able to generate CHO KO cell lines using small screens of only 96-320 clonally derived cell lines. Additionally, we present a novel bulk culture analysis approach that can be used to quickly assess CRISPR RNA efficiency and determine ideal screen sizes for generating genetic KO cell lines. Most critically, we find that Cas12a can be directly integrated into the cell line generation process through cotransfection with no negative impact on titer or screen size. Overall, our results show CRISPR/Cas12a to be an efficient and effective CHO genome editing tool.
Collapse
Affiliation(s)
- Patrick G Schweickert
- Department of Biological Sciences and the Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | - Ning Wang
- Bioprocess Research and Development, Eli Lilly and Company, Indianapolis, Indiana, USA
| | - Stephanie L Sandefur
- Bioprocess Research and Development, Eli Lilly and Company, Indianapolis, Indiana, USA
| | - Michael E Lloyd
- Bioprocess Research and Development, Eli Lilly and Company, Indianapolis, Indiana, USA
| | - Stephen F Konieczny
- Department of Biological Sciences and the Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | - Christopher C Frye
- Bioprocess Research and Development, Eli Lilly and Company, Indianapolis, Indiana, USA
| | - Zhuo Cheng
- Bioprocess Research and Development, Eli Lilly and Company, Indianapolis, Indiana, USA
| |
Collapse
|
18
|
Kiesslich S, Kamen AA. Vero cell upstream bioprocess development for the production of viral vectors and vaccines. Biotechnol Adv 2020; 44:107608. [PMID: 32768520 PMCID: PMC7405825 DOI: 10.1016/j.biotechadv.2020.107608] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/28/2020] [Accepted: 07/30/2020] [Indexed: 12/13/2022]
Abstract
The Vero cell line is considered the most used continuous cell line for the production of viral vectors and vaccines. Historically, it is the first cell line that was approved by the WHO for the production of human vaccines. Comprehensive experimental data on the production of many viruses using the Vero cell line can be found in the literature. However, the vast majority of these processes is relying on the microcarrier technology. While this system is established for the large-scale manufacturing of viral vaccine, it is still quite complex and labor intensive. Moreover, scale-up remains difficult and is limited by the surface area given by the carriers. To overcome these and other drawbacks and to establish more efficient manufacturing processes, it is a priority to further develop the Vero cell platform by applying novel bioprocess technologies. Especially in times like the current COVID-19 pandemic, advanced and scalable platform technologies could provide more efficient and cost-effective solutions to meet the global vaccine demand. Herein, we review the prevailing literature on Vero cell bioprocess development for the production of viral vectors and vaccines with the aim to assess the recent advances in bioprocess development. We critically underline the need for further research activities and describe bottlenecks to improve the Vero cell platform by taking advantage of recent developments in the cell culture engineering field.
Collapse
Affiliation(s)
- Sascha Kiesslich
- Department of Bioengineering, McGill University, 817 Sherbrooke Street West, Montreal, Quebec H3A 0C3, Canada
| | - Amine A Kamen
- Department of Bioengineering, McGill University, 817 Sherbrooke Street West, Montreal, Quebec H3A 0C3, Canada.
| |
Collapse
|
19
|
CRISPR-Cas9 Genome Editing Tool for the Production of Industrial Biopharmaceuticals. Mol Biotechnol 2020; 62:401-411. [PMID: 32749657 DOI: 10.1007/s12033-020-00265-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/30/2020] [Indexed: 10/23/2022]
Abstract
A broad range of cell lines with characteristic features are used as bio-factories to produce recombinant proteins for basic research and therapeutic purposes. Genetic engineering strategies have been used to manipulate the genome of mammalian cells, insects, and yeasts for heterologous expression. One reason is that the glycosylation pattern of the expression hosts differs somehow from mammalian cells, which may cause immunogenic reactions upon administration in humans. CRISPR-Cas9 is a simple, efficient, and versatile genome engineering tool that can be programmed to precisely make double-stranded breaks at the desired loci. Compared to the classical genome editing methods, a CRISPR-Cas9 system is an ideal tool, providing the opportunity to integrate or delete genes from the target organisms. Besides broadened applications, limited studies have used CRISPR-Cas9 for editing the endogenous pathways in expression systems for biopharmaceutical applications. In the present review, we discuss the use of CRISPR-Cas9 in expression systems to improve host cell lines, increase product yield, and humanize glycosylation pathways by targeting intrinsic genes.
Collapse
|
20
|
Bydlinski N, Coats MT, Maresch D, Strasser R, Borth N. Transfection of glycoprotein encoding mRNA for swift evaluation of N-glycan engineering strategies. Biotechnol Prog 2020; 36:e2990. [PMID: 32134190 PMCID: PMC7507192 DOI: 10.1002/btpr.2990] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 02/18/2020] [Accepted: 03/04/2020] [Indexed: 11/07/2022]
Abstract
N‐glycosylation is defined as a key quality attribute for the majority of complex biological therapeutics. Despite many N‐glycan engineering efforts, the demand to generate desired N‐glycan profiles that may vary for different proteins in a reproducible manner is still difficult to fulfill in many cases. Stable production of homogenous structures with a more demanding level of processing, for instance high degrees of branching and terminal sialylation, is particularly challenging. Among many other influential factors, the level of productivity can steer N‐glycosylation towards less mature N‐glycan structures. Recently, we introduced an mRNA transfection system capable of elucidating bottlenecks in the secretory pathway by stepwise increase of intracellular model protein mRNA load. Here, this system was applied to evaluate engineering strategies for enhanced N‐glycan processing. The tool proves to indeed be valuable for a quick assessment of engineering approaches on the cellular N‐glycosylation capacity at high productivity. The gene editing approaches tested include overexpression of key Golgi‐resident glycosyltransferases, partially coupled with multiple gene deletions. Changes in galactosylation, sialylation, and branching potential as well as N‐acetyllactosamine formation were evaluated.
Collapse
Affiliation(s)
- Nina Bydlinski
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Michael T Coats
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Daniel Maresch
- Department of Chemistry, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Richard Strasser
- Department of Applied Genetics and Cell Biology, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Nicole Borth
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Vienna, Austria.,Austrian Centre of Industrial Biotechnology GmbH, Graz, Austria
| |
Collapse
|
21
|
Schweickert PG, Cheng Z. Application of Genetic Engineering in Biotherapeutics Development. J Pharm Innov 2019. [DOI: 10.1007/s12247-019-09411-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
22
|
Amann T, Schmieder V, Faustrup Kildegaard H, Borth N, Andersen MR. Genetic engineering approaches to improve posttranslational modification of biopharmaceuticals in different production platforms. Biotechnol Bioeng 2019; 116:2778-2796. [PMID: 31237682 DOI: 10.1002/bit.27101] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 03/27/2019] [Accepted: 06/18/2019] [Indexed: 12/18/2022]
Abstract
The number of approved biopharmaceuticals, where product quality attributes remain of major importance, is increasing steadily. Within the available variety of expression hosts, the production of biopharmaceuticals faces diverse limitations with respect to posttranslational modifications (PTM), while different biopharmaceuticals demand different forms and specifications of PTMs for proper functionality. With the growing toolbox of genetic engineering technologies, it is now possible to address general as well as host- or biopharmaceutical-specific product quality obstacles. In this review, we present diverse expression systems derived from mammalians, bacteria, yeast, plants, and insects as well as available genetic engineering tools. We focus on genes for knockout/knockdown and overexpression for meaningful approaches to improve biopharmaceutical PTMs and discuss their applicability as well as future trends in the field.
Collapse
Affiliation(s)
- Thomas Amann
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Valerie Schmieder
- acib GmbH-Austrian Centre of Industrial Biotechnology, Graz, Austria.,Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Helene Faustrup Kildegaard
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Nicole Borth
- Department of Biotechnology, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Mikael Rørdam Andersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| |
Collapse
|
23
|
Klanert G, Fernandez DJ, Weinguny M, Eisenhut P, Bühler E, Melcher M, Titus SA, Diendorfer AB, Gludovacz E, Jadhav V, Xiao S, Stern B, Lal M, Shiloach J, Borth N. A cross-species whole genome siRNA screen in suspension-cultured Chinese hamster ovary cells identifies novel engineering targets. Sci Rep 2019; 9:8689. [PMID: 31213643 PMCID: PMC6582146 DOI: 10.1038/s41598-019-45159-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 05/29/2019] [Indexed: 12/16/2022] Open
Abstract
High-throughput siRNA screens were only recently applied to cell factories to identify novel engineering targets which are able to boost cells towards desired phenotypes. While siRNA libraries exist for model organisms such as mice, no CHO-specific library is publicly available, hindering the application of this technique to CHO cells. The optimization of these cells is of special interest, as they are the main host for the production of therapeutic proteins. Here, we performed a cross-species approach by applying a mouse whole-genome siRNA library to CHO cells, optimized the protocol for suspension cultured cells, as this is the industrial practice for CHO cells, and developed an in silico method to identify functioning siRNAs, which also revealed the limitations of using cross-species libraries. With this method, we were able to identify several genes that, upon knockdown, enhanced the total productivity in the primary screen. A second screen validated two of these genes, Rad21 and Chd4, whose knockdown was tested in additional CHO cell lines, confirming the induced high productivity phenotype, but also demonstrating the cell line/clone specificity of engineering effects.
Collapse
Affiliation(s)
- Gerald Klanert
- Austrian Centre of Industrial Biotechnology, Graz, Austria
- University of Natural Resources and Life Sciences, Vienna, Austria
| | | | - Marcus Weinguny
- Austrian Centre of Industrial Biotechnology, Graz, Austria
- University of Natural Resources and Life Sciences, Vienna, Austria
| | - Peter Eisenhut
- Austrian Centre of Industrial Biotechnology, Graz, Austria
- University of Natural Resources and Life Sciences, Vienna, Austria
| | - Eugen Bühler
- Division of Preclinical Innovation, NCATS, NIH, Rockville, MD, USA
| | - Michael Melcher
- Austrian Centre of Industrial Biotechnology, Graz, Austria
- University of Natural Resources and Life Sciences, Vienna, Austria
| | - Steven A Titus
- Division of Preclinical Innovation, NCATS, NIH, Rockville, MD, USA
| | | | - Elisabeth Gludovacz
- University of Natural Resources and Life Sciences, Vienna, Austria
- Medical University of Vienna, Vienna, Austria
| | - Vaibhav Jadhav
- Austrian Centre of Industrial Biotechnology, Graz, Austria
| | - Su Xiao
- Biotechnology Core Laboratory, NIDDK, NIH, Bethesda, MD, USA
| | - Beate Stern
- Department of Biomedicine, University of Bergen, Bergen, Norway
- UniTargetingResearch AS, Bergen, Norway
| | - Madhu Lal
- Division of Preclinical Innovation, NCATS, NIH, Rockville, MD, USA.
| | - Joseph Shiloach
- Biotechnology Core Laboratory, NIDDK, NIH, Bethesda, MD, USA.
| | - Nicole Borth
- Austrian Centre of Industrial Biotechnology, Graz, Austria.
- University of Natural Resources and Life Sciences, Vienna, Austria.
| |
Collapse
|
24
|
Raab N, Mathias S, Alt K, Handrick R, Fischer S, Schmieder V, Jadhav V, Borth N, Otte K. CRISPR/Cas9-Mediated Knockout of MicroRNA-744 Improves Antibody Titer of CHO Production Cell Lines. Biotechnol J 2019; 14:e1800477. [PMID: 30802343 DOI: 10.1002/biot.201800477] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 01/25/2019] [Accepted: 01/28/2019] [Indexed: 12/18/2022]
Abstract
MicroRNAs (miRNAs) are noncoding RNAs that serve as versatile molecular engineering tools to improve production cells by overexpression or knockdown of miRNAs showing beneficial or adverse effects on cell-culture performance. The genomic knockout (KO) of noncoding RNAs in Chinese hamster ovary (CHO) production cells has not been reported. However, given the significant number of miRNAs showing negative effects on CHO-bioprocess performance and the development of clustered regularly interspaced short palindromic repeats/CRISPR-associated proteins (CRISPR/Cas9), genome editing tools facilitate precise optimization of CHO cells via modulation of noncoding RNAs. In a previous high-content miRNA screen, miR-744 was identified as a potential target associated with reduced productivity. Hence, the genomic miR-744 precursor sequence is deleted by two single guide RNA (sgRNA)-Cas9-mediated DNA double-strand breaks (DSB) flanking the miR-744 locus. After fluorescence-activated cell sorting (FACS), clonal miR-744 KO cell lines are recovered and three of them are confirmed as miR-744 KOs. Impacts of CRISPR/Cas9 editing are characterized at the genetic, transcript, and phenotypic levels. During batch cultivation, antibody titers of miR-744 KOs are significantly increased to 190-311 mg L-1 compared to a nontargeting (NT) sgRNA transfected clonal control with 156 mg L-1 , pointing towards the potential of miRNA KO for cell line engineering.
Collapse
Affiliation(s)
- Nadja Raab
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Hubertus-Liebrecht-Str. 35, Biberach, 88400, Germany
| | - Sven Mathias
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Hubertus-Liebrecht-Str. 35, Biberach, 88400, Germany
| | - Kerstin Alt
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Hubertus-Liebrecht-Str. 35, Biberach, 88400, Germany
- Genetikum, Wegenerstraße 15, Neu-Ulm, 89231, Germany
| | - René Handrick
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Hubertus-Liebrecht-Str. 35, Biberach, 88400, Germany
| | - Simon Fischer
- Boehringer Ingelheim Pharma GmbH & Co KG, Cell Line Development CMB, Birkendorfer Str. 65, Biberach, 88397, Germany
| | - Valerie Schmieder
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria
| | - Vaibhav Jadhav
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria
| | - Nicole Borth
- Austrian Center of Industrial Biotechnology, Muthgasse 11, Vienna, 1190, Austria
- BOKU Vienna, Institute of Biotechnology, Gregor-Mendel-Straße 33, Vienna, 1180, Austria
| | - Kerstin Otte
- Institute of Applied Biotechnology, University of Applied Sciences Biberach, Hubertus-Liebrecht-Str. 35, Biberach, 88400, Germany
| |
Collapse
|
25
|
MacDonald ML, Hamaker NK, Lee KH. Bioinformatic analysis of Chinese hamster ovary host cell protein lipases. AIChE J 2018; 64:4247-4254. [PMID: 30911190 DOI: 10.1002/aic.16378] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Complete, accurate genome assemblies are necessary to design targets for genetic engineering strategies. Successful gene knockdowns and knockouts in Chinese hamster ovary (CHO) cells may prevent the expression of difficult-to-remove host cell proteins (HCPs). HCPs, if not removed, can cause problems in stability, safety, and efficacy of the biotherapeutic. A significantly improved Chinese hamster (CH) reference genome was used to identify new knockout targets with similar predicted functions and characteristics as the difficult-to-remove host cell lipases, LPL, PLBL2, and LPLA2. The CHO-K1 gene and protein sequences of several of these lipases were corrected using the updated CH genome. Sequence alignments were then used to identify conserved regions that may serve as possible targets for multiple simultaneous gene knockouts. Finally, comparison of the CHO-K1 lipase protein sequences to their human orthologs provided insight into which lipases, if persistent in the drug product, could possibly cause immunogenic responses in patients.
Collapse
Affiliation(s)
- Madolyn L. MacDonald
- Delaware Biotechnology Institute University of Delaware Newark DE, 19711
- Center for Bioinformatics and Computational Biology University of Delaware Newark DE, 19711
- Dept. of Computer and Information Sciences University of Delaware Newark DE, 19716
| | - Nathaniel K. Hamaker
- Delaware Biotechnology Institute University of Delaware Newark DE, 19711
- Dept. of Chemical and Biomolecular Engineering University of Delaware Newark DE, 19716
| | - Kelvin H. Lee
- Delaware Biotechnology Institute University of Delaware Newark DE, 19711
- Dept. of Chemical and Biomolecular Engineering University of Delaware Newark DE, 19716
| |
Collapse
|
26
|
Kelly PS, Alarcon Miguez A, Alves C, Barron N. From media to mitochondria–rewiring cellular energy metabolism of Chinese hamster ovary cells for the enhanced production of biopharmaceuticals. Curr Opin Chem Eng 2018. [DOI: 10.1016/j.coche.2018.08.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
27
|
Li T, Zhu L, Xiao B, Gong Z, Liao Q, Guo J. CRISPR-Cpf1-mediated genome editing and gene regulation in human cells. Biotechnol Adv 2018; 37:21-27. [PMID: 30399413 DOI: 10.1016/j.biotechadv.2018.10.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 10/28/2018] [Accepted: 10/30/2018] [Indexed: 12/26/2022]
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR) system is being championed as a robust and flexible tool for genome editing. Compared with CRISPR associated protein 9 (Cas9), the CRISPR from Prevotella and Francisella 1 (Cpf1) protein has some distinct characteristics, including RNase activity, T-rich protospacer adjacent motif (PAM) preference and generation of sticky cutting ends. The extremely low propensity of off-target effects and relatively high editing efficiency represent prominent advantages of Cpf1 over Cas9. CRISPR-Cpf1, alone or fused with function domains, has broadly expanded the applications such as multiplex gene knockout, transcriptional repression or activation and epigenome editing in a drug controlled way. Meanwhile, the modification of CRISPR RNAs (crRNAs) with aptamer RNA achieves great promotion on genome editing. Moreover, disease-associated gene manipulation in mice, tumor mutation detection in patients with cancers, and more yet to come, represent growing demands of CRISPR-Cpf1 in clinical genome therapy. In this review, we summarized the unique properties of Cpf1 and the molecular mechanisms underlying CRISPR-Cpf1 on gene editing and regulation in human cells.
Collapse
Affiliation(s)
- Tianwen Li
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo 315211, China
| | - Linwen Zhu
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo 315211, China
| | - Bingxiu Xiao
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo 315211, China
| | - Zhaohui Gong
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo 315211, China
| | - Qi Liao
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo 315211, China
| | - Junming Guo
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo 315211, China.
| |
Collapse
|
28
|
Amann T, Hansen AH, Kol S, Lee GM, Andersen MR, Kildegaard HF. CRISPR/Cas9-Multiplexed Editing of Chinese Hamster Ovary B4Gal-T1, 2, 3, and 4 Tailors N-Glycan Profiles of Therapeutics and Secreted Host Cell Proteins. Biotechnol J 2018; 13:e1800111. [PMID: 29862652 DOI: 10.1002/biot.201800111] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 05/04/2018] [Indexed: 12/16/2022]
Abstract
In production of recombinant proteins for biopharmaceuticals, N-glycosylation is often important for protein efficacy and patient safety. IgG with agalactosylated (G0)-N-glycans can improve the activation of the lectin-binding complement system and be advantageous in the therapy of lupus and virus diseases. In this study, the authors aimed to engineer CHO-S cells for the production of proteins with G0-N-glycans by targeting B4Gal-T isoform genes with CRISPR/Cas9. Indel mutations in genes encoding B4Gal-T1, -T2, and -T3 with and without a disrupted B4Gal-T4 sequence resulted in only ≈1% galactosylated N-glycans on total secreted proteins of 3-4 clones per genotype. The authors revealed that B4Gal-T4 is not active in N-glycan galactosylation in CHO-S cells. In the triple-KO clones, transiently expressed erythropoietin (EPO) and rituximab harbored only ≈6% and ≈3% galactosylated N-glycans, respectively. However, simultaneous disruption of B4Gal-T1 and -T3 may decrease cell growth. Altogether, the authors present the advantage of analyzing total secreted protein N-glycans after disrupting galactosyltransferases, followed by expressing recombinant proteins in selected clones with desired N-glycan profiles at a later stage. Furthermore, the authors provide a cell platform that prevalently glycosylates proteins with G0-N-glycans to further study the impact of agalactosylation on different in vitro and in vivo functions of recombinant proteins.
Collapse
Affiliation(s)
- Thomas Amann
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Anders Holmgaard Hansen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Stefan Kol
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Gyun Min Lee
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark.,Department of Biological Sciences, KAIST, Daejeon, Republic of Korea
| | - Mikael Rørdam Andersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Helene Faustrup Kildegaard
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
| |
Collapse
|
29
|
Feng X, Zhao D, Zhang X, Ding X, Bi C. CRISPR/Cas9 Assisted Multiplex Genome Editing Technique in Escherichia coli. Biotechnol J 2018; 13:e1700604. [PMID: 29790644 DOI: 10.1002/biot.201700604] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 05/08/2018] [Indexed: 12/23/2022]
Abstract
Genome editing for site-specific chromosome modification is one of the most significant techniques in biological research. While conventional techniques usually deal with one genomic locus at a time, multiple genomic targets are often required to be modified to develop microbial cell factories. Thus, it is necessary to develop techniques for simultaneous editing of multiple loci. In this work, the authors develop a CRISPR/Cas9 assisted multiplex genome editing (CMGE) technique in Escherichia coli. With this editing method, all functional parts are assembled into replicable plasmids, and stringent inducible expression systems are used to control Cas9 gene expression, which is to decouple transformation from editing process to increase editing efficiency. A modular assembly strategy is designed to enable construction of the complex multi-gRNA plasmid. With this technique, two and three loci are able to be modified with 100% and 88.3% efficiencies, while four loci can be edited with more than 30%, which are the best results reported. Although developed in model organism, the strategy of CMGE can be adapted to other prokaryotic cells. This is a well designed and illustrated technique with no special requirement, can be used by any biological lab easily.
Collapse
Affiliation(s)
- Xu Feng
- School of life sciences, China West Normal University, Nanchong 637002, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Dongdong Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xiang Ding
- School of life sciences, China West Normal University, Nanchong 637002, China
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| |
Collapse
|
30
|
Rupp O, MacDonald ML, Li S, Dhiman H, Polson S, Griep S, Heffner K, Hernandez I, Brinkrolf K, Jadhav V, Samoudi M, Hao H, Kingham B, Goesmann A, Betenbaugh MJ, Lewis NE, Borth N, Lee KH. A reference genome of the Chinese hamster based on a hybrid assembly strategy. Biotechnol Bioeng 2018; 115:2087-2100. [PMID: 29704459 PMCID: PMC6045439 DOI: 10.1002/bit.26722] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 03/13/2018] [Accepted: 04/25/2018] [Indexed: 12/20/2022]
Abstract
Accurate and complete genome sequences are essential in biotechnology to facilitate genome‐based cell engineering efforts. The current genome assemblies for Cricetulus griseus, the Chinese hamster, are fragmented and replete with gap sequences and misassemblies, consistent with most short‐read‐based assemblies. Here, we completely resequenced C. griseus using single molecule real time sequencing and merged this with Illumina‐based assemblies. This generated a more contiguous and complete genome assembly than either technology alone, reducing the number of scaffolds by >28‐fold, with 90% of the sequence in the 122 longest scaffolds. Most genes are now found in single scaffolds, including up‐ and downstream regulatory elements, enabling improved study of noncoding regions. With >95% of the gap sequence filled, important Chinese hamster ovary cell mutations have been detected in draft assembly gaps. This new assembly will be an invaluable resource for continued basic and pharmaceutical research.
Collapse
Affiliation(s)
- Oliver Rupp
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Madolyn L MacDonald
- Department of Computer and Information Sciences, University of Delaware, Newark, Delaware.,Delaware Biotechnology Institute, Newark, Delaware
| | - Shangzhong Li
- Department of Bioengineering, University of California, San Diego, California.,Novo Nordisk Foundation Center for Biosustainability, University of California, San Diego, California
| | - Heena Dhiman
- Austrian Center of Industrial Biotechnology, Vienna, Austria.,Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Shawn Polson
- Department of Computer and Information Sciences, University of Delaware, Newark, Delaware.,Delaware Biotechnology Institute, Newark, Delaware
| | - Sven Griep
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Kelley Heffner
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Inmaculada Hernandez
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Karina Brinkrolf
- Department of Biorescources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
| | - Vaibhav Jadhav
- Austrian Center of Industrial Biotechnology, Vienna, Austria
| | - Mojtaba Samoudi
- Novo Nordisk Foundation Center for Biosustainability, University of California, San Diego, California.,Department of Pediatrics, University of California, San Diego, California
| | - Haiping Hao
- Johns Hopkins University Deep Sequencing and Microarray Core, Johns Hopkins University, Baltimore, Maryland
| | | | - Alexander Goesmann
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Michael J Betenbaugh
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Nathan E Lewis
- Department of Bioengineering, University of California, San Diego, California.,Novo Nordisk Foundation Center for Biosustainability, University of California, San Diego, California.,Department of Pediatrics, University of California, San Diego, California
| | - Nicole Borth
- Austrian Center of Industrial Biotechnology, Vienna, Austria.,Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Kelvin H Lee
- Delaware Biotechnology Institute, Newark, Delaware.,Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware
| |
Collapse
|
31
|
Affiliation(s)
- Nicole Borth
- Department of Biotechnology, Universität für Bodenkultur, Austria
| | - Wei-Shou Hu
- Department of Chemical Engineering and Materials Science, University of Minnesota, USA
| |
Collapse
|