CRISPR has changed the way scientists are able to approach their research. The popularity of CRISPR stems from its simplicity and ease of use. Researchers can theoretically create any gene edit in any cell in just a few days. However, in practice, it isn’t that simple. Obtaining high quality and reproducible editing results you can trust takes experience and optimization.
In the past, most researchers needed to isolate and expand clonal cell lines containing the genome change they wanted, which added several months to the timeline before the engineered cells could be used in experiments. High knockout efficiencies (80-90% KO frequency) can now be quickly and inexpensively generated in a heterogeneous population of cells, referred to as a Knockout Cell Pool, allowing researchers to either directly assay the edited cell pool or generate clonal cell lines as quickly as possible. This breakthrough has made CRISPR much more accessible to scientists, and more researchers are now able to take advantage of genome engineering in their research without needing to learn and optimize CRISPR protocols.
The CRISPR-Cas9 gene editing system consists of two components: a guide RNA (gRNA) and a CRISPR-associated (Cas) endonuclease, which together form a ribonucleoprotein complex (RNP). The guide RNA contains a sequence complementary to the target DNA site, which directs the Cas to where it will cut. Cas9 from Streptococcus pyogenes (SpCas9) is a commonly-used endonuclease for CRISPR editing. Once bound to the target, Cas9 “cuts” the DNA double helix, making a double-strand break (DSB). The cell treats the DSB as DNA damage, which activates the cellular non-homologous end joining (NHEJ) or homology-directed repair (HDR) pathways to attempt to fix the damage.
The DSBs are most commonly fixed by the NHEJ pathway, which generates different repair products and often introduces insertions or deletions (indels). Therefore, cells within a CRISPR-edited culture are a mix of unedited (wild type) cells and edited cells with different indels, some of which induce knockouts of the target gene or sequence. These cultures of heterogeneous cells are called knockout (KO) cell pools. Note that the use of the word “pool” here is different from pooled library screens generated by introducing sgRNAs targeting multiple genes into cell culture.
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Generating CRISPR Knockout Cell Pools
There are three main steps in the workflow to generate CRISPR KO cell pools:
Once these steps are completed, the engineered cells can either be used in assays right away while still in a heterogenous population, or clones can be isolated and expanded.
CRISPR is replacing RNAi as the best option to investigate gene function because it is more specific and results in more complete loss-of-function, making the results easier to interpret with confidence.
Schematic of the process used to generate knockout cell pools. 1. Design and synthesize gRNA. 2. Transfect cells: introduce ribonucleoprotein complexes (gRNA and Cas9 protein) into a cell culture. After CRISPR editing takes place, the culture contains a mix of cells with different indels as well as unedited cells (a KO cell pool). 3. Analyze editing & KO efficiency: assess the indel frequency & KO score of the pool. 4. Conduct assays and/or generate clonal cell lines.
The first step in generating a knockout cell pool is to design and synthesize a guide RNA for the target gene. Each guide RNA is composed of two components, a CRISPR RNA (crRNA) and a trans-activating RNA (tracrRNA). These components may be linked to form a continuous molecule called a single guide RNA (sgRNA) or annealed to form a two-piece guide (cr:tracrRNA). Using cr:tracrRNAs can be less expensive but requires extra lab time and may not be as reliable.
As the specificity of CRISPR is determined by the guide RNA, designing an optimum gRNA sequence is a key factor for performing a successful CRISPR experiment. Several design tools are available to help researchers design highly specific guide RNAs with low off-target effects. EditCo’s free and easy-to-use CRISPR Design Tool enables you to design guides within 5 minutes.
After designing and generating the guide RNA, the next step is to introduce the CRISPR components into cells via one of several possible transfection methods, such as lipofection, electroporation, nucleofection, or microinjection. The choice of the transfection method depends on the cell type and experimental goals. Lipofection, for instance, requires no external equipment, but may not work as effectively as other methods with some cell types. Electroporation and nucleofection (a type of electroporation) are often effective for transfecting challenging cell types, and microinjection is commonly used for injecting the CRISPR machinery into embryos.
Learn more about the different transfection methods in our comprehensive CRISPR transfection guide.
After transfection, the editing efficiency (indicated by indel frequency) should be analyzed by sequencing the genomic DNA. As next-generation sequencing is expensive, researchers often use Sanger sequencing for their analysis. EditCo’s Inference of CRISPR Edits (ICE) software tool efficiently analyzes CRISPR editing data with NGS-level quality. From the results, one can determine the frequency of each type of indel generated in the pool, as well as the proportion of sequences in the CRISPR-edited population that lead to gene knockout (KO Score).
Learn how to use ICE with this step-by-step guide.
It is important to remember that editing efficiency does not equate to knockout efficiency. Each KO cell pool contains a mix of cells with different indels, only some of which cause knockouts. EditCo’s ICE tool calculates a Knockout (KO) Score, the percentage of knockout-inducing sequences in a CRISPR-edited pool.
Pools with high KO frequencies are suitable for direct use in many types of assays, without a requirement for first generating clonal cell lines.
Cell pools with efficient knockouts can be used to identify gene function. One can assess the function of a gene by inducing a genotypic aberration that directly leads to an observable phenotypic effect. For instance, if the gene knocked out encodes for a protein responsible for cell proliferation, then cell abundance can be measured using proliferation assays.
Similar methods can be applied to test any genotype-phenotype relationship including, but not limited to, signaling pathway involvement, differentiation ability, and drug response.
One particularly useful application of KO pools is identifying the contributions of specific genes to disease states. A gene thought to be associated with disease can be knocked out in a cell pool. If the knockout results in a disease phenotype, then further analyses can be conducted to validate the findings. Ultimately, this information may be used to develop a disease model.
High-throughput screens are used to investigate genotype-phenotype relationships on a large scale. For each screen, a gRNA library is applied to cells to systematically knock out hundreds or thousands of genes. The phenotypic effects of each knockout can then be assessed. Loss-of-function screens can be used to identify gene function in entire biological pathways or disease states. They have also been critical to the process of drug discovery. For instance, a knockout that confers resistance or sensitivity to a drug may provide information about the drug’s target.
CRISPR knockout cell pools with high KO frequencies can be used to screen small molecule libraries to identify potential therapeutic compounds. For instance, cell pools with a gene KO that induces a disease can be generated, and a library of compounds can be systematically applied. Resulting phenotypes can be assessed to determine if any of the compounds affected the disease state of the cells.
All immunoassays utilize antibodies that are specific for their target proteins. For each assay, the specificity of an antibody to a particular protein must be validated to avoid non-specific results. To test antibody specificity, a cell pool can be generated with a knockout of the antibody’s protein target. Because less target protein is made in the pool, subsequent immunoblot or immunofluorescence analyses (which use the antibody to detect and visualize the protein) should have a proportionally lower signal. If this is observed, it is a good indication that the protein is indeed the antibody’s target.
As discussed above, knockout cell pools with high knockout efficiencies are an economical and time-efficient option for many types of loss-of-function assays. CRISPR KO cell pools are becoming the method of choice for many researchers investigating gene function, replacing the older RNAi-based approaches.
In most cases, the gene knockout does not impact cell viability, and the total population of edited cells does not change over time. However, because KO cell pools contain a mix of edited and wild type cells, the knockout efficiency may vary over time. For instance, if wild type cells proliferate faster or if the knockout induces cell death, the percentage of KO cells in the pool may gradually decrease (and the protein knockout could be lost).
If a pool has low KO efficiency, this effect is likely to have a more substantial impact on the cell population, making it difficult to assay the cell pools directly. For research in which changes in cell populations may be a concern, including work that requires long time spans and cells with confirmed knockouts, using CRISPR Knockout Cell Clones may be more appropriate.
While concerns about cell viability post-KO are warranted, we find only a very small proportion (~2%) of gene KOs affect population dynamics and therefore are required to be made into clonal cells.
Due to the low editing efficiency attained using other methods and without a dedicated CRISPR editing workflow and experience, generating knockout cells using CRISPR can be challenging and expensive. There is a better way! EditCo’s Knockout Cell Pool product is an affordable option to generate human gene knockout cells with high editing efficiency - that are guaranteed to work!