Protocol for Using CRISPR-Cas9 to Generate a Monocyte Cell Line Harboring a Single-Nucleotide Polymorphism

We established a step-by-step approach for generating a single-nucleotide mutation in the promoter region of an immune regulatory gene in human monocyte THP-1 cells by employing a plasmid-based CRISPR-Cas9 system delivered via transfection with a homology-directed repair template DNA (HDR). Key steps include designing a single-guide RNA (sgRNA), cloning it into a CRISPR plasmid encoding the Cas9 protein, transfection of the plasmid constructs along with single-stranded oligonucleotide repair template (ssODNs) into THP-1 cells, followed by selection and validation. This approach provides a precise and relevant model to investigate the role of single polymorphisms in the regulation of inflammatory gene expression in human monocytes. In addition to the rs1024611 single-nucleotide polymorphism (SNP), this CRISPR/Cas9-based strategy is broadly applicable to functional studies of noncoding and coding variants in innate immune genes. Key features • Precise genome editing: CRISPR-Cas9-mediated editing of the rs1024611 SNP in the endogenous CCL2 promoter in THP-1 cells using a single-stranded donor oligonucleotide. • Generate THP-1 monocytic cell lines: Differing only at the rs1024611 locus, allowing precise comparison of allele-specific effects on the same genetic background. • The protocol includes strategies for single-cell cloning, PCR-based genotyping, and Sanger sequencing to confirm precise genome editing. • While this study focuses on the CCL2-2518 SNP, it provides a framework for future investigations of other noncoding variants or regulatory SNPs in immune-related genes.