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Kretzmer C, Narasimhan RL, Lal RD, Balassi V, Ravellette J, Kotekar Manjunath AK, Koshy JJ, Viano M, Torre S, Zanda VM, Kumravat M, Saldanha KMR, Chandranpillai H, Nihad I, Zhong F, Sun Y, Gustin J, Borgschulte T, Liu J, Razafsky D. De novo assembly and annotation of the CHOZN® GS -/- genome supports high-throughput genome-scale screening. Biotechnol Bioeng 2022; 119:3632-3646. [PMID: 36073082 PMCID: PMC9825924 DOI: 10.1002/bit.28226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/20/2022] [Accepted: 08/28/2022] [Indexed: 01/11/2023]
Abstract
Chinese hamster ovary (CHO) cells have been used as the industry standard for the production of therapeutic monoclonal antibodies for several decades. Despite significant improvements in commercial-scale production processes and media, the CHO cell has remained largely unchanged. Due to the cost and complexity of whole-genome sequencing and gene-editing it has been difficult to obtain the tools necessary to improve the CHO cell line. With the advent of next-generation sequencing and the discovery of the CRISPR/Cas9 system it has become more cost effective to sequence and manipulate the CHO genome. Here, we provide a comprehensive de novo assembly and annotation of the CHO-K1 based CHOZN® GS-/- genome. Using this platform, we designed, built, and confirmed the functionality of a whole genome CRISPR guide RNA library that will allow the bioprocessing community to design a more robust CHO cell line leading to the production of life saving medications in a more cost-effective manner.
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Affiliation(s)
- Corey Kretzmer
- Upstream Research and Development, MilliporeSigmaSt. LouisMissouriUSA
| | - Rajagopalan Lakshmi Narasimhan
- Bioinformatics, IT R&D Applications, Merck (Sigma‐Aldrich Chemicals Pvt. Ltd., A subsidiary of Merck KGaA, Darmstadt, Germany)BangaloreIndia
| | - Rahul Deva Lal
- Bioinformatics, IT R&D Applications, Merck (Sigma‐Aldrich Chemicals Pvt. Ltd., A subsidiary of Merck KGaA, Darmstadt, Germany)BangaloreIndia
| | - Vincent Balassi
- Upstream Research and Development, MilliporeSigmaSt. LouisMissouriUSA
| | - James Ravellette
- Upstream Research and Development, MilliporeSigmaSt. LouisMissouriUSA
| | - Ajaya Kumar Kotekar Manjunath
- Bioinformatics, IT R&D Applications, Merck (Sigma‐Aldrich Chemicals Pvt. Ltd., A subsidiary of Merck KGaA, Darmstadt, Germany)BangaloreIndia
| | - Jesvin Joy Koshy
- Bioinformatics, IT R&D Applications, Merck (Sigma‐Aldrich Chemicals Pvt. Ltd., A subsidiary of Merck KGaA, Darmstadt, Germany)BangaloreIndia
| | - Marta Viano
- Istituto di Ricerche Biomediche “A. Marxer” RBM S.p.A.IvreaItaly
| | - Serena Torre
- Istituto di Ricerche Biomediche “A. Marxer” RBM S.p.A.IvreaItaly
| | - Valeria M. Zanda
- Istituto di Ricerche Biomediche “A. Marxer” RBM S.p.A.IvreaItaly
| | - Mausam Kumravat
- Bioinformatics, IT R&D Applications, Merck (Sigma‐Aldrich Chemicals Pvt. Ltd., A subsidiary of Merck KGaA, Darmstadt, Germany)BangaloreIndia
| | - Keith Metelo Raul Saldanha
- Bioinformatics, IT R&D Applications, Merck (Sigma‐Aldrich Chemicals Pvt. Ltd., A subsidiary of Merck KGaA, Darmstadt, Germany)BangaloreIndia
| | - Harikrishnan Chandranpillai
- Bioinformatics, IT R&D Applications, Merck (Sigma‐Aldrich Chemicals Pvt. Ltd., A subsidiary of Merck KGaA, Darmstadt, Germany)BangaloreIndia
| | - Ifra Nihad
- Bioinformatics, IT R&D Applications, Merck (Sigma‐Aldrich Chemicals Pvt. Ltd., A subsidiary of Merck KGaA, Darmstadt, Germany)BangaloreIndia
| | - Fei Zhong
- Life Science Bioinformatics, IT, MilliporeSigmaSt. LouisMissouriUSA
| | - Yi Sun
- Bioinformatics, IT R&D Applications, MilliporeSigmaSt. LouisMissouriUSA
| | - Jason Gustin
- Upstream Research and Development, MilliporeSigmaSt. LouisMissouriUSA
| | | | - Jiajian Liu
- Life Science Bioinformatics, IT, MilliporeSigmaSt. LouisMissouriUSA
| | - David Razafsky
- Upstream Research and Development, MilliporeSigmaSt. LouisMissouriUSA
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Wu D, Poddar A, Ninou E, Hwang E, Cole MA, Liu SJ, Horlbeck MA, Chen J, Replogle JM, Carosso GA, Eng NWL, Chang J, Shen Y, Weissman JS, Lim DA. Dual genome-wide coding and lncRNA screens in neural induction of induced pluripotent stem cells. Cell Genom 2022; 2:100177. [PMID: 36381608 DOI: 10.1016/j.xgen.2022.100177] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Human chromosomes are pervasively transcribed, but systematic understanding of coding and lncRNA genome function in cell differentiation is lacking. Using CRISPR interference (CRISPRi) in human induced pluripotent stem cells, we performed dual genome-wide screens - assessing 18,905 protein-coding and 10,678 lncRNA loci - and identified 419 coding and 201 lncRNA genes that regulate neural induction. Integrative analyses revealed distinct properties of coding and lncRNA genome function, including a 10-fold enrichment of lncRNA genes for roles in differentiation compared to proliferation. Further, we applied Perturb-seq to obtain granular insights into neural induction phenotypes. While most coding hits stalled or aborted differentiation, lncRNA hits were enriched for the genesis of diverse cellular states, including those outside the neural lineage. In addition to providing a rich resource (danlimlab.shinyapps.io/dualgenomewide) for understanding coding and lncRNA gene function in development, these results indicate that the lncRNA genome regulates lineage commitment in a manner fundamentally distinct from coding genes.
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Shifrut E, Carnevale J, Tobin V, Roth TL, Woo JM, Bui CT, Li PJ, Diolaiti ME, Ashworth A, Marson A. Genome-wide CRISPR Screens in Primary Human T Cells Reveal Key Regulators of Immune Function. Cell 2018; 175:1958-1971.e15. [PMID: 30449619 DOI: 10.1016/j.cell.2018.10.024] [Citation(s) in RCA: 299] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 09/08/2018] [Accepted: 10/08/2018] [Indexed: 12/11/2022]
Abstract
Human T cells are central effectors of immunity and cancer immunotherapy. CRISPR-based functional studies in T cells could prioritize novel targets for drug development and improve the design of genetically reprogrammed cell-based therapies. However, large-scale CRISPR screens have been challenging in primary human cells. We developed a new method, single guide RNA (sgRNA) lentiviral infection with Cas9 protein electroporation (SLICE), to identify regulators of stimulation responses in primary human T cells. Genome-wide loss-of-function screens identified essential T cell receptor signaling components and genes that negatively tune proliferation following stimulation. Targeted ablation of individual candidate genes characterized hits and identified perturbations that enhanced cancer cell killing. SLICE coupled with single-cell RNA sequencing (RNA-seq) revealed signature stimulation-response gene programs altered by key genetic perturbations. SLICE genome-wide screening was also adaptable to identify mediators of immunosuppression, revealing genes controlling responses to adenosine signaling. The SLICE platform enables unbiased discovery and characterization of functional gene targets in primary cells.
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Affiliation(s)
- Eric Shifrut
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Julia Carnevale
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Victoria Tobin
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Theodore L Roth
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jonathan M Woo
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Christina T Bui
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - P Jonathan Li
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Morgan E Diolaiti
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Alan Ashworth
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Alexander Marson
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
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