CRISPR Screen Sequencing, An Innovative Sequencing Technology that Can Facilitate COVID-19 Research

Clustered regularly interspaced short palindromic repeats, or CRISPR, is one of the most phenomenal discoveries that paved the way for modern genome screening and editing technologies. CRISPR is a family of DNA found in the genome of prokaryotes, specifically bacteria and archaea. These sequences contain DNA fragments from known bacteriophages that infect the particular prokaryote. Studies have revealed the reason behind these organisms having such sequences is that when a bacteriophage infects the bacteria, they keep a fragment of the infecting DNA and use it to destroy similar bacteriophages that would again infect the organism. This discovery has provided an insight into the antiviral defense system of prokaryotes and its potential application in molecular studies. CRISPR has been applied to different technologies such as genome editing using CRISPR-Cas9 and CRISPR screening (genome-wide and loss-of-function screening). During the recent COVID-19 pandemic, CRISPR screening has helped tremendously in understanding host responses to viral infection.

CRISPR screening is used to detect genes that elicit a particular function in the cell such as genes for pathogenicity or for drug resistance. The basic principle of this technology is to knock out one gene per cell and different genes per cell population, in the attempt to detect significant genes that affect the growth and development, and possibly the pathogenicity of a particular organism. After knocking out the genes and successfully growing the cells, whole-genome sequencing is performed to determine whether the particular sequences have been removed from the genome of the organism.

COVID-19, caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2 virus), is currently infecting and affecting major populations in the world. Recent approaches to the study of this virus have been focused on the viral characteristics, hoping to understand the infection and pathogenicity. However, this has been replaced by a new approach, understanding host genes that are essential for effective viral infection so that potent vaccines can be developed to stop the spread of the disease. Identifying the host genes that respond to COVID-19 infection could help in understanding the pathogenicity of the virus, host susceptibility, and reveal novel therapeutic targets.

CRISPR screening technology has been helpful in determining the mechanism of infection of SARS-CoV-2 and the host response to the disease. Using CRISPR screening, scientists from the New York Genome Center has been able to compare genes from the different members of the coronavirus in an attempt to find similar targets that can be treated with established drugs and vaccines. A particular study using genome-scale and loss-of-function CRISPR screening revealed that using a similar pathway as cholesterol biosynthesis, viral genes find its way into host genes. This finding helped the scientists identify the drug that targets cholesterol production to prevent viral infection. The screens revealed several genes that either confer resistance or sensitization to the virus that can be controlled by established medicines and potential host-directed therapeutic targets with genes that inhibit viral replication and viral-induced cell death. These results greatly aid in the development of most needed patient-specific therapeutics.

References:

1. Barrangou, R. The roles of CRISPR-Cas systems in adaptive immunity and beyond. Current Opinion in Immunology. 2015, 32: 36-41.
2. Wei, J., Alfajaro, M.M., DeWeirdt, P.C., et al. Genome-wide CRISPR Screens Reveal Host Factors Critical for SARS-CoV-2 Infection. Cell, 2020, 184, 1-16.