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Immunology and Infection

Gene Knock-in by CRISPR/Cas9 and Cell Sorting in Macrophage and T Cell Lines

Published: November 13th, 2021



1The Laboratory of Genetic Regulators in the Immune System, School of Laboratory Medicine, Xinxiang Medical University, 2Centre d’Immunologie de Marseille-Luminy, Aix Marseille Université

This protocol uses fluorescent reporters and cell sorting to simplify knock-in experiments in macrophage and T cell lines. Two plasmids are used for these simplified knock-in experiments, namely a CRISPR/Cas9- and DsRed2-expressing plasmid and a homologous recombination donor plasmid expressing EBFP2, which is permanently integrated at the Rosa26 locus in immune cells.

Functional genomics studies of the immune system require genetic manipulations that involve both deletion of target genes and addition of elements to proteins of interest. Identification of gene functions in cell line models is important for gene discovery and exploration of cell-intrinsic mechanisms. However, genetic manipulations of immune cells such as T cells and macrophage cell lines using CRISPR/Cas9-mediated knock-in are difficult because of the low transfection efficiency of these cells, especially in a quiescent state. To modify genes in immune cells, drug-resistance selection and viral vectors are typically used to enrich for cells expressing the CRIPSR/Cas9 system, which inevitably results in undesirable intervention of the cells. In a previous study, we designed dual fluorescent reporters coupled to CRISPR/Cas9 that were transiently expressed after electroporation. This technical solution leads to rapid gene deletion in immune cells; however, gene knock-in in immune cells such as T cells and macrophages without the use of drug-resistance selection or viral vectors is even more challenging. In this article, we show that by using cell sorting to aid selection of cells transiently expressing CRISPR/Cas9 constructs targeting the Rosa26 locus in combination with a donor plasmid, gene knock-in can be achieved in both T cells and macrophages without drug-resistance enrichment. As an example, we show how to express human ACE2, a receptor of SARS-Cov-2, which is responsible for the current Covid-19 pandemic, in RAW264.7 macrophages by performing knock-in experiments. Such gene knock-in cells can be widely used for mechanistic studies.

Immune cells are critical for defense against pathogens. Both innate and adaptive immunity are required for clearance of infectants and maintenance of tissue homeostasis1,2. Cell line models are essential tools for understanding the molecular fundamentals of the mammalian immune system; they are used in in vitro functional assays, such as those modeling human T cell activation, and in determining the function of genetic factors in activating or dampening immune responses3,4. It is important to note that the mammalian immune system is enormousl....

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1. Design and Plasmid Construction of sgRNAs Targeting Rosa26 Locus

  1. Design guide RNAs around the desired insertion site
    1. Ensure that the insertion site for mouse Rosa26 (hereafter designated as mRosa26) knock-in experiments is located in the first intron of mRosa26; this site has been used in previous studies28,29. For knock-in experiments in human cells, ensure that the .......

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Following the protocol described above to perform knock-in experiments at the mRosa26 locus using murine RAW264.7 macrophages, we designed a targeting vector to express human ACE2, a receptor for the SARS-Cov-2 virus (Figure 2A). Using a similar design, we generated human Jurkat T cells with knock-in of the OST-tagged RASGRP1 fusion protein (Figure 2C). After transfection of three plasmids, two of which were used for expression of CRISPR/Cas9 (DsRed2; p.......

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In our experiments, we demonstrated how to perform knock-in editing in immune cells from construct design to knock-in cell screening and validation using human Jurkat T cells and murine RAW264.7 macrophages as examples. Both T cell and macrophage cell lines are resistant to transfection36,37; however, the problem of low efficiency of CRISPR/Cas9 delivery can be overcome with the aid of fluorescent reporters coupled with cell sorting. This protocol is suitable for.......

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We thank the flow cytometry core facility of Xinxiang Medical University. Development of such technology has been supported by NSFC grants 81601360 to LZ, 81471595 and 32070898 to YL. The work is also supported by Foundation of Henan Educational Committee No. 21IRTSTHN030.


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Name Company Catalog Number Comments
Amersham Imager 600 Ge Healthcare imaging of chemiluminescence
Ampicillin, sodium salt MP Biomedicals 194526
Anti-rabbit IgG, HRP-linked Antibody Cell Signaling Technology 7074 at 1/5000 dilution
Anti-RasGRP1 antibody, clone 10.1 Merck MABS146 1.0 μg/mL of working concentration
AscI New England BioLabs R0558S
β-Actin (D6A8) Rabbit mAb Cell Signaling Technology 8457 at 1/1000 dilution
BamHI-HF New England BioLabs R3136S
BbsI-HF New England BioLabs R3539S
Cellometer Mini Automated Cell Counter Nexcelom Bioscience
E.coli DH5α Competent Cells Takara 9057
DMSO (Dimethyl Sulfoxide) MP Biomedicals 196055
DNeasy Blood & Tissue Kits Qiagen 69506 cell culture reagent
DPBS (10X), no calcium, no magnesium ThermoFisher Scientific 14200075
Dulbecco's Modified Eagle Medium (DMEM) with high glucose HyClone SH30022.01
EcoRI-HF New England BioLabs R3101S
FACSAria™ Fusion BD Biosciences equipped with biosafety cabinet
FACS Canto flow cytometer BD Biosciences
Falcon 5 ml polystyrene round bottom test tube BD Biosciences 352003
Fetal bovine serum (FBS) ThermoFisher Scientific 10099141
FlowJo version 10.7 BD Biosciences
GAPDH (D16H11) XP Rabbit mAb Cell Signaling Technology 5174 at 1/1000 dilution
Goat anti-Mouse IgG (H+L) Secondary Antibody, HRP ThermoFisher Scientific 31430 at 1/5000 dilution
Immobilon ECL Ultra Western HRP Substrate Millipore WBKLS0500
Immobilon-PSQ PVDF Membrane Millipore ISEQ00010
Jurkat ATCC TIB-152
Kanamycin sulfate MP Biomedicals 194531
LB agar powder ThermoFisher Scientific 22700041
Multi-channel Pipette (30-300 μL) Eppendorf, or similar
Neon Transfection System ThermoFisher Scientific MPK5000
Neon Transfection System, 10 μL kit ThermoFisher Scientific MPK1096
Nunc 15 mL Conical Sterile Centrifuge Tubes ThermoFisher Scientific 339651
OneTaq® Hot Start Quick-Load® 2X Master Mix New England BioLabs (M0489) for high GC% template
PageRuler Prestained Protein Ladder, 10 to 180 kDa ThermoFisher Scientific 26616
Pipette tip 0.1-20µl Eppendorf, or similar 0030 075.005
Pipette tip 2-200µl Eppendorf, or similar 0030 075.021
Pipette tip 50-1000µl Eppendorf, or similar 0030 075.064
Plasmid Maxi Kit Qiagen 12163
pX458-DsRed2 Addgene 112219
QIAquick PCR Purification Kit Qiagen 28104 purify plasmid from restriction digestion
Q5 Hot Start High-Fidelity 2X Master Mix New England BioLabs M0494S
RAW264.7 ATCC TIB-71
Recombinant Anti-ACE2 antibody [EPR4435(2)] Abcam ab108252 at 1/1000 dilution
RPMI 1640 Medium HyClone SH30027.01
Strep-Tactin Sepharose beads IBA Lifesciences 2-1201-010
Penicillin-Streptomycin ThermoFisher Scientific 15140122
SYTOX™ Red Dead Cell Stain, for 633 or 635 nm excitation ThermoFisher Scientific S34859
T4 DNA ligase New England BioLabs M0202S
T4 Polynucleotide Kinase New England BioLabs M0201S
Trypan Blue Solution, 0.4% ThermoFisher Scientific 15250061
Trypsin-EDTA solution (0.25%), with phenol red ThermoFisher Scientific 25200056
ZOE Fluorescent Cell Imager Bio-Rad
1.5 mL microtubes, PCR-clean Eppendorf, or similar 0030 125.215
24-well Clear TC-treated Multiple Well Plates Corning 3524
96-well Clear Flat Bottom Polystyrene TC-treated Microplates Corning 3599
96-well Clear Round Bottom TC-treated Microplate Corning 3799

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