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      High-throughput functional screening for next-generation cancer immunotherapy using droplet-based microfluidics

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          Abstract

          Microfluidics system enables high-throughput functional screening of antibodies for cancer immunotherapy.

          Abstract

          Currently, high-throughput approaches are lacking in the isolation of antibodies with functional readouts beyond simple binding. This situation has impeded the next generation of cancer immunotherapeutics, such as bispecific T cell engager (BiTE) antibodies or agonist antibodies against costimulatory receptors, from reaching their full potential. Here, we developed a highly efficient droplet-based microfluidic platform combining a lentivirus transduction system that enables functional screening of millions of antibodies to identify potential hits with desired functionalities. To showcase the capacity of this system, functional antibodies for CD40 agonism with low frequency (<0.02%) were identified with two rounds of screening. Furthermore, the versatility of the system was demonstrated by combining an anti-Her2 × anti-CD3 BiTE antibody library with functional screening, which enabled efficient identification of active anti-Her2 × anti-CD3 BiTE antibodies. The platform could revolutionize next-generation cancer immunotherapy drug development and advance medical research.

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          Most cited references44

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          Multiplex genome engineering using CRISPR/Cas systems.

          Functional elucidation of causal genetic variants and elements requires precise genome editing technologies. The type II prokaryotic CRISPR (clustered regularly interspaced short palindromic repeats)/Cas adaptive immune system has been shown to facilitate RNA-guided site-specific DNA cleavage. We engineered two different type II CRISPR/Cas systems and demonstrate that Cas9 nucleases can be directed by short RNAs to induce precise cleavage at endogenous genomic loci in human and mouse cells. Cas9 can also be converted into a nicking enzyme to facilitate homology-directed repair with minimal mutagenic activity. Lastly, multiple guide sequences can be encoded into a single CRISPR array to enable simultaneous editing of several sites within the mammalian genome, demonstrating easy programmability and wide applicability of the RNA-guided nuclease technology.
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            RNA-guided human genome engineering via Cas9.

            Bacteria and archaea have evolved adaptive immune defenses, termed clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems, that use short RNA to direct degradation of foreign nucleic acids. Here, we engineer the type II bacterial CRISPR system to function with custom guide RNA (gRNA) in human cells. For the endogenous AAVS1 locus, we obtained targeting rates of 10 to 25% in 293T cells, 13 to 8% in K562 cells, and 2 to 4% in induced pluripotent stem cells. We show that this process relies on CRISPR components; is sequence-specific; and, upon simultaneous introduction of multiple gRNAs, can effect multiplex editing of target loci. We also compute a genome-wide resource of ~190 K unique gRNAs targeting ~40.5% of human exons. Our results establish an RNA-guided editing tool for facile, robust, and multiplexable human genome engineering.
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              Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression.

              Targeted gene regulation on a genome-wide scale is a powerful strategy for interrogating, perturbing, and engineering cellular systems. Here, we develop a method for controlling gene expression based on Cas9, an RNA-guided DNA endonuclease from a type II CRISPR system. We show that a catalytically dead Cas9 lacking endonuclease activity, when coexpressed with a guide RNA, generates a DNA recognition complex that can specifically interfere with transcriptional elongation, RNA polymerase binding, or transcription factor binding. This system, which we call CRISPR interference (CRISPRi), can efficiently repress expression of targeted genes in Escherichia coli, with no detectable off-target effects. CRISPRi can be used to repress multiple target genes simultaneously, and its effects are reversible. We also show evidence that the system can be adapted for gene repression in mammalian cells. This RNA-guided DNA recognition platform provides a simple approach for selectively perturbing gene expression on a genome-wide scale. Copyright © 2013 Elsevier Inc. All rights reserved.
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                Author and article information

                Journal
                Sci Adv
                Sci Adv
                SciAdv
                advances
                Science Advances
                American Association for the Advancement of Science
                2375-2548
                June 2021
                11 June 2021
                : 7
                : 24
                : eabe3839
                Affiliations
                [1 ]State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin, China.
                [2 ]HiFiBiO (Shanghai) Co. Ltd., Shanghai, China.
                [3 ]Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China.
                [4 ]Shanghai Institute of Immunology, Faculty of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
                [5 ]Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
                Author notes
                [* ]Corresponding author. Email: hongkai@ 123456nankai.edu.cn
                [†]

                These authors contributed equally to this work.

                Author information
                http://orcid.org/0000-0002-2382-8770
                http://orcid.org/0000-0003-3059-456X
                http://orcid.org/0000-0002-4207-4898
                http://orcid.org/0000-0001-7429-1136
                http://orcid.org/0000-0002-7936-6157
                http://orcid.org/0000-0002-8335-8205
                http://orcid.org/0000-0001-7170-2403
                http://orcid.org/0000-0002-3569-4765
                http://orcid.org/0000-0003-4385-9942
                http://orcid.org/0000-0003-2323-6684
                http://orcid.org/0000-0001-9436-4101
                http://orcid.org/0000-0002-1744-4324
                http://orcid.org/0000-0001-6794-1663
                http://orcid.org/0000-0003-1518-2241
                http://orcid.org/0000-0002-4466-8833
                http://orcid.org/0000-0003-2077-1999
                http://orcid.org/0000-0001-6268-3378
                http://orcid.org/0000-0002-0903-4077
                http://orcid.org/0000-0003-2186-5508
                Article
                abe3839
                10.1126/sciadv.abe3839
                8195480
                34117053
                de72acde-ae6a-445b-b54e-8e31ec988871
                Copyright © 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).

                This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license, which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.

                History
                : 19 August 2020
                : 23 April 2021
                Funding
                Funded by: doi http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;
                Award ID: 81872787
                Funded by: doi http://dx.doi.org/10.13039/501100002858, China Postdoctoral Science Foundation;
                Award ID: 2020M670625
                Funded by: doi http://dx.doi.org/10.13039/501100006606, Natural Science Foundation of Tianjin City;
                Award ID: 19JCZDJC32900
                Funded by: doi http://dx.doi.org/10.13039/501100012226, Fundamental Research Funds for the Central Universities;
                Award ID: ZB19100123
                Funded by: doi http://dx.doi.org/10.13039/501100012226, Fundamental Research Funds for the Central Universities;
                Award ID: 63191212
                Funded by: National Key Research and Development Plan of China;
                Award ID: 2018YFE0200401
                Funded by: National Key Research and Development Plan of China;
                Award ID: 2017YFA0504801
                Funded by: Shanghai Municipal Science and Technology Commission;
                Award ID: 19431902900
                Funded by: the Innovative Research Team of High-level Local Universities in Shanghai;
                Award ID: SSMU-2DCX20180100
                Categories
                Research Article
                Research Articles
                SciAdv r-articles
                Immunology
                Research Methods
                Immunology
                Custom metadata
                Anne Suarez

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