CRISPR/Cas9: Transcending the Reality of Genome Editing

Abstract

With the expansion of the microbiology field of research, a new genome editing tool arises from the biology of bacteria that holds the promise of achieving precise modifications in the genome with a simplicity and versatility that surpasses previous genome editing methods. This new technique, commonly named CRISPR/Cas9, led to a rapid expansion of the biomedical field; more specifically, cancer characterization and modeling have benefitted greatly from the genome editing capabilities of CRISPR/Cas9. In this paper, we briefly summarize recent improvements in CRISPR/Cas9 design meant to overcome the limitations that have arisen from the nuclease activity of Cas9 and the influence of this technology in cancer research. In addition, we present challenges that might impede the clinical applicability of CRISPR/Cas9 for cancer therapy and highlight future directions for designing CRISPR/Cas9 delivery systems that might prove useful for cancer therapeutics.

Keywords: CRISPR/Cas9; Cas9 regulation; cancer; gene editing; multiplex CRISPR/Cas9; phage-derived vectors.

Figure 1

CRISPR/Cas9 Mechanism of Action The original bacterial CRISPR/Cas9 design has been translated into an engineered instrument for genome editing purposes and is capable of introducing specific modifications in the target cell. In this regard, the vector comprising the crRNA and tracrRNA that together constitute the RNA molecule for Cas9 guidance (gRNA) is introduced in the desired cell, where it passes the cytoplasmic milieu toward the nucleus. After delivery to the nucleus, the Cas9 gene encoded by the experimental vector is transcribed and exported into the cytoplasm for translation of Cas9 nuclease. After synthesis of the active protein, the gRNA, transcribed by its own promoter, interacts with the Cas9 nuclease, resulting in the ribonucleic-protein effector complex that is internalized back into the nucleus. The cleavage of the double-stranded genomic DNA takes place in a guided manner, where the crRNA sequence of gRNA directs Cas9 toward the specific locus, based on sequence complementarity, which is positioned adjacent to the PAM. When cleaved, the continuity of the host DNA can be restored through NHEJ, where the hanging ends join together, creating small indels, or through HDR in the presence of a donor DNA.

Figure 2

Strategies for Regulating Cas9 Nuclease Activity Increased levels of Cas9 can lead to unspecific cleavage, which causes hazardous effects in the target cell, resulting in off-target effects (red 5′ in Figure 1). Different strategies have been implemented to minimize and control the activity of Cas9. (A) Introduction of a Tet-controlled promoter that allows monitoring of Cas9 expression through an on/off system dependent on Tet/Dox. (B) Fusion of Cas9 with an estrogen receptor domain (ERT2) that enables the supervision of Cas9 activity through 4-HT presence/absence. (C) Control of the enzymatic activity via intein and its splicing properties. The N-terminal and C-terminal domains of Cas9, each containing a fused intein domain, are joined together by a splicing event, and, upon expression of gRNA, the intein is auto-excised, and gRNA forms with Cas9 an active complex. (D) Holding of Cas9 activity through fusion with light-responsive elements, which allows Cas9 performance only after stimulation with blue light. (E) A self-restricted CRISPR/Cas9 system that contains, in the engineered vector, a gRNA that targets the Cas9 gene itself, resulting in an auto-regulated loop. CRY2, cryptochrome circadian clock 2; VP64, viral protein 64 transactivation domain; CIBN, N-terminal domain of CIB1; P, promoter.

Figure 3

Generation and Quality Control of sgRNA Libraries for CRISPR/Cas9-Mediated Phenotypic Screening The first step illustrates the synthesis of sgRNA libraries consisting of a heterogeneous population of sequences approximately 100 bases in length with a reduced number of mutations. Quality control is significantly facilitated when a barcode of a known sequence is incorporated into each sgRNA and analyzed at the final stages through next-generation sequencing (NGS). After detachment of oligonucleotides from the solid support, the targeted sequences are amplified through PCR and then cloned in lentiviral vectors that contain a selection marker for antibiotic resistance (e.g., puromycin) and also an enrichment sequence that can be detected with the help of fluorescence-activated cell sorting (FACS) (e.g., GFP). Every sgRNA is under the activity of an U6 promoter that will facilitate its expression. The entire complex is packed in viruses that are further used for the transduction of the target cells. The first selection consists of the capacity of cells to survive in an antibiotic-enriched medium because of their integrated gene for puromycin or any other antibiotic that is used in the experiment. The second selection consists of the enrichment of the transduced cell population through GFP selection by FACS. The remaining cells that contain the viral construct are then collected for DNA extraction and analyzed through NGS, which detects individual sgRNAs because of the inserted barcode.